Starting phenix.real_space_refine on Wed Feb 4 15:17:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j9g_61271/02_2026/9j9g_61271.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j9g_61271/02_2026/9j9g_61271.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j9g_61271/02_2026/9j9g_61271.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j9g_61271/02_2026/9j9g_61271.map" model { file = "/net/cci-nas-00/data/ceres_data/9j9g_61271/02_2026/9j9g_61271.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j9g_61271/02_2026/9j9g_61271.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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 59 5.16 5 C 7211 2.51 5 N 1850 2.21 5 O 2008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11128 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 11100 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1406, 11089 Classifications: {'peptide': 1406} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 50, 'TRANS': 1355} Chain breaks: 2 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 43 Conformer: "B" Number of residues, atoms: 1406, 11089 Classifications: {'peptide': 1406} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 50, 'TRANS': 1355} Chain breaks: 2 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 43 bond proxies already assigned to first conformer: 11318 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE A1127 " occ=0.48 ... (20 atoms not shown) pdb=" CZ BPHE A1127 " occ=0.52 Time building chain proxies: 4.50, per 1000 atoms: 0.40 Number of scatterers: 11128 At special positions: 0 Unit cell: (83, 120.35, 159.36, 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 59 16.00 O 2008 8.00 N 1850 7.00 C 7211 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS A 32 " distance=2.03 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 Links applied NAG-ASN " NAG A1701 " - " ASN A 23 " " NAG A1702 " - " ASN A 19 " Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 903.0 milliseconds 2806 Ramachandran restraints generated. 1403 Oldfield, 0 Emsley, 1403 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2662 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 7 sheets defined 71.1% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 removed outlier: 3.768A pdb=" N SER A 8 " --> pdb=" O ARG A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 22 Processing helix chain 'A' and resid 30 through 59 removed outlier: 5.108A pdb=" N VAL A 39 " --> pdb=" O ASN A 35 " (cutoff:3.500A) Proline residue: A 42 - end of helix Proline residue: A 51 - end of helix Processing helix chain 'A' and resid 68 through 99 removed outlier: 3.999A pdb=" N ASP A 88 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU A 89 " --> pdb=" O CYS A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 131 removed outlier: 3.799A pdb=" N LEU A 107 " --> pdb=" O ALA A 103 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 135 through 162 removed outlier: 3.535A pdb=" N LEU A 139 " --> pdb=" O SER A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 190 Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.837A pdb=" N ASN A 203 " --> pdb=" O GLU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 removed outlier: 3.629A pdb=" N ALA A 213 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 220 Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 224 through 234 Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.516A pdb=" N LEU A 241 " --> pdb=" O SER A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 269 Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 312 through 322 removed outlier: 3.528A pdb=" N VAL A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 340 removed outlier: 3.563A pdb=" N PHE A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE A 340 " --> pdb=" O ASP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 355 removed outlier: 3.700A pdb=" N GLU A 344 " --> pdb=" O PHE A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 408 removed outlier: 3.892A pdb=" N TYR A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 408 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 removed outlier: 3.910A pdb=" N SER A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 429 removed outlier: 3.504A pdb=" N ASN A 425 " --> pdb=" O GLY A 421 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N MET A 427 " --> pdb=" O ILE A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 438 removed outlier: 3.637A pdb=" N ALA A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 442 through 463 Proline residue: A 448 - end of helix Processing helix chain 'A' and resid 466 through 509 removed outlier: 3.783A pdb=" N VAL A 472 " --> pdb=" O ALA A 468 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Proline residue: A 478 - end of helix removed outlier: 3.679A pdb=" N TYR A 490 " --> pdb=" O LYS A 486 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN A 500 " --> pdb=" O LYS A 496 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 Processing helix chain 'A' and resid 520 through 572 removed outlier: 3.522A pdb=" N PHE A 524 " --> pdb=" O TRP A 520 " (cutoff:3.500A) Proline residue: A 557 - end of helix removed outlier: 3.986A pdb=" N ASP A 572 " --> pdb=" O TYR A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 598 removed outlier: 4.101A pdb=" N VAL A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER A 585 " --> pdb=" O LYS A 581 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 591 " --> pdb=" O ALA A 587 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE A 594 " --> pdb=" O ASN A 590 " (cutoff:3.500A) Proline residue: A 595 - end of helix Processing helix chain 'A' and resid 598 through 621 Processing helix chain 'A' and resid 626 through 630 removed outlier: 3.867A pdb=" N ILE A 630 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 685 No H-bonds generated for 'chain 'A' and resid 683 through 685' Processing helix chain 'A' and resid 686 through 692 Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 733 through 744 Processing helix chain 'A' and resid 746 through 753 removed outlier: 3.625A pdb=" N GLU A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 752 " --> pdb=" O PRO A 748 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 759 removed outlier: 3.612A pdb=" N ARG A 758 " --> pdb=" O SER A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 785 removed outlier: 3.704A pdb=" N ASP A 785 " --> pdb=" O ALA A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 810 Processing helix chain 'A' and resid 851 through 859 Processing helix chain 'A' and resid 860 through 868 removed outlier: 3.828A pdb=" N GLU A 864 " --> pdb=" O GLY A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 970 removed outlier: 4.019A pdb=" N TYR A 962 " --> pdb=" O LYS A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 1000 Processing helix chain 'A' and resid 1010 through 1058 Processing helix chain 'A' and resid 1059 through 1066 removed outlier: 3.714A pdb=" N PHE A1063 " --> pdb=" O PRO A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1085 removed outlier: 3.788A pdb=" N LEU A1071 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU A1078 " --> pdb=" O ARG A1074 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU A1079 " --> pdb=" O PHE A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1111 Processing helix chain 'A' and resid 1113 through 1122 Proline residue: A1119 - end of helix Processing helix chain 'A' and resid 1128 through 1160 removed outlier: 3.922A pdb=" N ALA A1134 " --> pdb=" O ARG A1130 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG A1137 " --> pdb=" O VAL A1133 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN A1138 " --> pdb=" O ALA A1134 " (cutoff:3.500A) Proline residue: A1149 - end of helix removed outlier: 3.630A pdb=" N GLY A1160 " --> pdb=" O GLU A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1168 Processing helix chain 'A' and resid 1169 through 1220 removed outlier: 3.609A pdb=" N ALA A1187 " --> pdb=" O GLU A1183 " (cutoff:3.500A) Proline residue: A1190 - end of helix Processing helix chain 'A' and resid 1227 through 1264 removed outlier: 3.563A pdb=" N GLN A1238 " --> pdb=" O SER A1234 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR A1240 " --> pdb=" O SER A1236 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N THR A1241 " --> pdb=" O LEU A1237 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN A1256 " --> pdb=" O GLU A1252 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL A1258 " --> pdb=" O GLU A1254 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ALA A1259 " --> pdb=" O THR A1255 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N VAL A1260 " --> pdb=" O ASN A1256 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU A1261 " --> pdb=" O ILE A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1268 removed outlier: 4.150A pdb=" N GLU A1268 " --> pdb=" O GLU A1265 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1265 through 1268' Processing helix chain 'A' and resid 1331 through 1340 removed outlier: 4.294A pdb=" N PHE A1340 " --> pdb=" O THR A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1362 through 1367 removed outlier: 3.861A pdb=" N PHE A1367 " --> pdb=" O HIS A1363 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1388 Processing helix chain 'A' and resid 1394 through 1405 Processing helix chain 'A' and resid 1407 through 1414 Processing helix chain 'A' and resid 1423 through 1427 Processing helix chain 'A' and resid 1430 through 1445 Processing helix chain 'A' and resid 1454 through 1458 Processing helix chain 'A' and resid 1462 through 1474 Processing helix chain 'A' and resid 1486 through 1490 Processing helix chain 'A' and resid 1509 through 1516 removed outlier: 3.592A pdb=" N LEU A1513 " --> pdb=" O SER A1509 " (cutoff:3.500A) Processing helix chain 'A' and resid 1518 through 1526 Processing sheet with id=AA1, first strand: chain 'A' and resid 631 through 633 removed outlier: 6.286A pdb=" N GLN A 631 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LYS A 697 " --> pdb=" O THR A 652 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N THR A 652 " --> pdb=" O LYS A 697 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU A 699 " --> pdb=" O THR A 650 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N HIS A 701 " --> pdb=" O ASN A 648 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ASN A 648 " --> pdb=" O HIS A 701 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N THR A 703 " --> pdb=" O VAL A 646 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N VAL A 646 " --> pdb=" O THR A 703 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LYS A 705 " --> pdb=" O ILE A 644 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A 644 " --> pdb=" O LYS A 705 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N PHE A 651 " --> pdb=" O HIS A 662 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N HIS A 662 " --> pdb=" O PHE A 651 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 631 through 633 removed outlier: 6.286A pdb=" N GLN A 631 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LYS A 697 " --> pdb=" O THR A 652 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N THR A 652 " --> pdb=" O LYS A 697 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU A 699 " --> pdb=" O THR A 650 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N HIS A 701 " --> pdb=" O ASN A 648 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ASN A 648 " --> pdb=" O HIS A 701 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N THR A 703 " --> pdb=" O VAL A 646 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N VAL A 646 " --> pdb=" O THR A 703 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LYS A 705 " --> pdb=" O ILE A 644 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A 644 " --> pdb=" O LYS A 705 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 708 through 711 removed outlier: 6.309A pdb=" N ALA A 709 " --> pdb=" O LEU A 790 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TYR A 789 " --> pdb=" O LEU A 823 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N VAL A 825 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU A 791 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU A 673 " --> pdb=" O VAL A 837 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE A 839 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ALA A 675 " --> pdb=" O ILE A 839 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N MET A 841 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL A 677 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A 848 " --> pdb=" O VAL A 840 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1309 through 1316 removed outlier: 6.760A pdb=" N LYS A1310 " --> pdb=" O GLY A1298 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLY A1298 " --> pdb=" O LYS A1310 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE A1312 " --> pdb=" O ASP A1296 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A1292 " --> pdb=" O ILE A1316 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N TYR A1297 " --> pdb=" O GLU A1347 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU A1347 " --> pdb=" O TYR A1297 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1322 through 1325 removed outlier: 6.702A pdb=" N GLY A1323 " --> pdb=" O ILE A1497 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LEU A1499 " --> pdb=" O GLY A1323 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL A1325 " --> pdb=" O LEU A1499 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL A1496 " --> pdb=" O TRP A1507 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N TRP A1507 " --> pdb=" O VAL A1496 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N VAL A1498 " --> pdb=" O GLN A1505 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1381 through 1382 Processing sheet with id=AA7, first strand: chain 'A' and resid 1449 through 1450 690 hydrogen bonds defined for protein. 2028 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: 2.02 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1777 1.31 - 1.43: 2994 1.43 - 1.56: 6505 1.56 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 11372 Sorted by residual: bond pdb=" C7 NAG A1701 " pdb=" N2 NAG A1701 " ideal model delta sigma weight residual 1.346 1.474 -0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C7 NAG A1702 " pdb=" N2 NAG A1702 " ideal model delta sigma weight residual 1.346 1.471 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" C1 NAG A1702 " pdb=" O5 NAG A1702 " ideal model delta sigma weight residual 1.406 1.527 -0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" C1 NAG A1701 " pdb=" O5 NAG A1701 " ideal model delta sigma weight residual 1.406 1.518 -0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" C2 NAG A1702 " pdb=" N2 NAG A1702 " ideal model delta sigma weight residual 1.439 1.515 -0.076 2.00e-02 2.50e+03 1.43e+01 ... (remaining 11367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 15029 1.88 - 3.76: 329 3.76 - 5.64: 64 5.64 - 7.52: 14 7.52 - 9.40: 9 Bond angle restraints: 15445 Sorted by residual: angle pdb=" C GLN A1288 " pdb=" N VAL A1289 " pdb=" CA VAL A1289 " ideal model delta sigma weight residual 121.97 130.41 -8.44 1.80e+00 3.09e-01 2.20e+01 angle pdb=" CB LYS A 967 " pdb=" CG LYS A 967 " pdb=" CD LYS A 967 " ideal model delta sigma weight residual 111.30 120.50 -9.20 2.30e+00 1.89e-01 1.60e+01 angle pdb=" CA CYS A 32 " pdb=" CB CYS A 32 " pdb=" SG CYS A 32 " ideal model delta sigma weight residual 114.40 122.23 -7.83 2.30e+00 1.89e-01 1.16e+01 angle pdb=" CA GLU A1156 " pdb=" CB GLU A1156 " pdb=" CG GLU A1156 " ideal model delta sigma weight residual 114.10 120.74 -6.64 2.00e+00 2.50e-01 1.10e+01 angle pdb=" N ASN A 19 " pdb=" CA ASN A 19 " pdb=" CB ASN A 19 " ideal model delta sigma weight residual 110.49 104.88 5.61 1.69e+00 3.50e-01 1.10e+01 ... (remaining 15440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.53: 6207 23.53 - 47.06: 531 47.06 - 70.59: 53 70.59 - 94.12: 11 94.12 - 117.65: 3 Dihedral angle restraints: 6805 sinusoidal: 2694 harmonic: 4111 Sorted by residual: dihedral pdb=" CB CYS A 7 " pdb=" SG CYS A 7 " pdb=" SG CYS A 32 " pdb=" CB CYS A 32 " ideal model delta sinusoidal sigma weight residual 93.00 126.17 -33.17 1 1.00e+01 1.00e-02 1.56e+01 dihedral pdb=" N2 NAG A1702 " pdb=" C1 NAG A1702 " pdb=" C2 NAG A1702 " pdb=" O5 NAG A1702 " ideal model delta sinusoidal sigma weight residual -178.19 -60.54 -117.65 1 3.00e+01 1.11e-03 1.56e+01 dihedral pdb=" CA MET A 835 " pdb=" C MET A 835 " pdb=" N ASP A 836 " pdb=" CA ASP A 836 " ideal model delta harmonic sigma weight residual -180.00 -160.41 -19.59 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 6802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1523 0.062 - 0.124: 254 0.124 - 0.186: 24 0.186 - 0.248: 2 0.248 - 0.310: 2 Chirality restraints: 1805 Sorted by residual: chirality pdb=" C1 NAG A1702 " pdb=" ND2 ASN A 19 " pdb=" C2 NAG A1702 " pdb=" O5 NAG A1702 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C2 NAG A1702 " pdb=" C1 NAG A1702 " pdb=" C3 NAG A1702 " pdb=" N2 NAG A1702 " both_signs ideal model delta sigma weight residual False -2.49 -2.75 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB VAL A 20 " pdb=" CA VAL A 20 " pdb=" CG1 VAL A 20 " pdb=" CG2 VAL A 20 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1802 not shown) Planarity restraints: 1928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 322 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO A 323 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 323 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 323 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1354 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.94e+00 pdb=" C ASP A1354 " 0.034 2.00e-02 2.50e+03 pdb=" O ASP A1354 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE A1355 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 34 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.89e+00 pdb=" C GLN A 34 " 0.034 2.00e-02 2.50e+03 pdb=" O GLN A 34 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN A 35 " -0.011 2.00e-02 2.50e+03 ... (remaining 1925 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 218 2.68 - 3.24: 11718 3.24 - 3.79: 18158 3.79 - 4.35: 23169 4.35 - 4.90: 37789 Nonbonded interactions: 91052 Sorted by model distance: nonbonded pdb=" OD1 ASP A 430 " pdb=" OG SER A 612 " model vdw 2.129 3.040 nonbonded pdb=" O ILE A1467 " pdb=" OG1 THR A1470 " model vdw 2.167 3.040 nonbonded pdb=" OG1 THR A 378 " pdb=" OE1 GLU A1203 " model vdw 2.173 3.040 nonbonded pdb=" OG SER A 328 " pdb=" ND2 ASN A 442 " model vdw 2.199 3.120 nonbonded pdb=" OG1 THR A 367 " pdb=" OG SER A1214 " model vdw 2.240 3.040 ... (remaining 91047 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.48 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.570 Find NCS groups from input model: 0.060 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 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 : 0.005 0.128 11375 Z= 0.238 Angle : 0.730 9.400 15453 Z= 0.378 Chirality : 0.047 0.310 1805 Planarity : 0.004 0.051 1926 Dihedral : 16.526 117.648 4140 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.14 % Favored : 96.71 % Rotamer: Outliers : 2.87 % Allowed : 21.16 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.23), residues: 1403 helix: 1.02 (0.17), residues: 886 sheet: -0.86 (0.63), residues: 64 loop : -0.77 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1065 TYR 0.028 0.002 TYR A 178 PHE 0.029 0.002 PHE A 50 TRP 0.018 0.002 TRP A1197 HIS 0.011 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00519 (11372) covalent geometry : angle 0.72537 (15445) SS BOND : bond 0.00204 ( 1) SS BOND : angle 4.82518 ( 2) hydrogen bonds : bond 0.13489 ( 689) hydrogen bonds : angle 5.58595 ( 2028) link_NAG-ASN : bond 0.01793 ( 2) link_NAG-ASN : angle 3.16034 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2806 Ramachandran restraints generated. 1403 Oldfield, 0 Emsley, 1403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2806 Ramachandran restraints generated. 1403 Oldfield, 0 Emsley, 1403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 261 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.6798 (OUTLIER) cc_final: 0.6321 (mt) REVERT: A 129 ARG cc_start: 0.8082 (mtt180) cc_final: 0.7575 (mtp-110) REVERT: A 176 TYR cc_start: 0.7657 (m-80) cc_final: 0.7339 (m-80) REVERT: A 262 LYS cc_start: 0.7984 (tttt) cc_final: 0.7669 (tttt) REVERT: A 264 GLU cc_start: 0.7474 (tt0) cc_final: 0.7262 (tt0) REVERT: A 338 MET cc_start: 0.8461 (mmt) cc_final: 0.8141 (mmt) REVERT: A 540 LYS cc_start: 0.8396 (ttmm) cc_final: 0.8104 (ttmm) REVERT: A 593 ARG cc_start: 0.8199 (ttm-80) cc_final: 0.7907 (ttm-80) REVERT: A 643 SER cc_start: 0.8289 (p) cc_final: 0.8082 (t) REVERT: A 735 ARG cc_start: 0.7984 (tmm-80) cc_final: 0.7757 (tmm-80) REVERT: A 744 CYS cc_start: 0.7862 (m) cc_final: 0.7389 (m) REVERT: A 778 LEU cc_start: 0.8658 (tp) cc_final: 0.8404 (tt) REVERT: A 809 ASN cc_start: 0.8067 (m110) cc_final: 0.7831 (m110) REVERT: A 849 MET cc_start: 0.7380 (ptt) cc_final: 0.7103 (ptt) REVERT: A 1311 HIS cc_start: 0.7580 (m-70) cc_final: 0.7156 (m-70) REVERT: A 1376 PRO cc_start: 0.6981 (Cg_exo) cc_final: 0.6762 (Cg_endo) REVERT: A 1387 LEU cc_start: 0.7781 (pp) cc_final: 0.7433 (pp) outliers start: 33 outliers final: 25 residues processed: 279 average time/residue: 0.1074 time to fit residues: 42.3847 Evaluate side-chains 280 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 254 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 642 ASN Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1064 GLU Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1252 GLU Chi-restraints excluded: chain A residue 1256 ASN Chi-restraints excluded: chain A residue 1504 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.161789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.130911 restraints weight = 20260.268| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.38 r_work: 0.3484 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.0821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11375 Z= 0.171 Angle : 0.677 10.007 15453 Z= 0.342 Chirality : 0.046 0.322 1805 Planarity : 0.004 0.053 1926 Dihedral : 8.467 105.467 1605 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.14 % Favored : 96.71 % Rotamer: Outliers : 3.86 % Allowed : 20.02 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.23), residues: 1403 helix: 1.19 (0.17), residues: 888 sheet: -0.54 (0.69), residues: 58 loop : -0.71 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1165 TYR 0.013 0.002 TYR A 831 PHE 0.021 0.002 PHE A 50 TRP 0.020 0.001 TRP A1197 HIS 0.010 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00385 (11372) covalent geometry : angle 0.67461 (15445) SS BOND : bond 0.00287 ( 1) SS BOND : angle 3.18082 ( 2) hydrogen bonds : bond 0.05331 ( 689) hydrogen bonds : angle 4.68739 ( 2028) link_NAG-ASN : bond 0.01825 ( 2) link_NAG-ASN : angle 2.30122 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2806 Ramachandran restraints generated. 1403 Oldfield, 0 Emsley, 1403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2806 Ramachandran restraints generated. 1403 Oldfield, 0 Emsley, 1403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 265 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4032 (mmm) cc_final: 0.3413 (mmm) REVERT: A 129 ARG cc_start: 0.8051 (mtt180) cc_final: 0.7538 (mtp-110) REVERT: A 158 MET cc_start: 0.7898 (mtp) cc_final: 0.7687 (mtt) REVERT: A 176 TYR cc_start: 0.7647 (m-80) cc_final: 0.7327 (m-80) REVERT: A 262 LYS cc_start: 0.7970 (tttt) cc_final: 0.7664 (tttt) REVERT: A 338 MET cc_start: 0.8400 (mmt) cc_final: 0.8105 (mmt) REVERT: A 418 SER cc_start: 0.8333 (OUTLIER) cc_final: 0.8125 (p) REVERT: A 540 LYS cc_start: 0.8360 (ttmm) cc_final: 0.8069 (ttmm) REVERT: A 542 SER cc_start: 0.7830 (m) cc_final: 0.7626 (t) REVERT: A 672 SER cc_start: 0.8534 (m) cc_final: 0.8057 (p) REVERT: A 744 CYS cc_start: 0.7820 (m) cc_final: 0.7362 (m) REVERT: A 778 LEU cc_start: 0.8716 (tp) cc_final: 0.8450 (tt) REVERT: A 787 ASP cc_start: 0.7896 (m-30) cc_final: 0.7603 (m-30) REVERT: A 809 ASN cc_start: 0.7987 (m110) cc_final: 0.7729 (m110) REVERT: A 845 LYS cc_start: 0.7664 (mttt) cc_final: 0.7424 (mtpp) REVERT: A 1272 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7345 (mt-10) REVERT: A 1311 HIS cc_start: 0.7339 (m-70) cc_final: 0.6924 (m-70) outliers start: 45 outliers final: 23 residues processed: 292 average time/residue: 0.1017 time to fit residues: 42.2675 Evaluate side-chains 284 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 260 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1076 SER Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1251 SER Chi-restraints excluded: chain A residue 1252 GLU Chi-restraints excluded: chain A residue 1332 LYS Chi-restraints excluded: chain A residue 1342 ILE Chi-restraints excluded: chain A residue 1359 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 82 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 701 HIS ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1195 ASN ** A1386 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 = 0.4028 r_free = 0.4028 target = 0.161024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.129555 restraints weight = 22737.941| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.59 r_work: 0.3466 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11375 Z= 0.181 Angle : 0.658 8.777 15453 Z= 0.335 Chirality : 0.046 0.271 1805 Planarity : 0.004 0.053 1926 Dihedral : 7.560 104.216 1569 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.43 % Favored : 96.50 % Rotamer: Outliers : 3.20 % Allowed : 21.41 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.23), residues: 1403 helix: 1.23 (0.17), residues: 889 sheet: -0.64 (0.69), residues: 58 loop : -0.68 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1165 TYR 0.013 0.002 TYR A 852 PHE 0.018 0.002 PHE A 558 TRP 0.020 0.001 TRP A1197 HIS 0.010 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00416 (11372) covalent geometry : angle 0.65657 (15445) SS BOND : bond 0.00851 ( 1) SS BOND : angle 2.93029 ( 2) hydrogen bonds : bond 0.05348 ( 689) hydrogen bonds : angle 4.57106 ( 2028) link_NAG-ASN : bond 0.01698 ( 2) link_NAG-ASN : angle 1.96760 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2806 Ramachandran restraints generated. 1403 Oldfield, 0 Emsley, 1403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2806 Ramachandran restraints generated. 1403 Oldfield, 0 Emsley, 1403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 262 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3554 (mmm) cc_final: 0.3008 (mmm) REVERT: A 89 LEU cc_start: 0.6837 (tp) cc_final: 0.6577 (tt) REVERT: A 93 PHE cc_start: 0.7210 (m-80) cc_final: 0.6687 (m-80) REVERT: A 129 ARG cc_start: 0.7836 (mtt180) cc_final: 0.7415 (mtp-110) REVERT: A 158 MET cc_start: 0.7765 (mtp) cc_final: 0.7523 (mtt) REVERT: A 176 TYR cc_start: 0.7531 (m-80) cc_final: 0.7259 (m-80) REVERT: A 210 GLU cc_start: 0.7994 (tt0) cc_final: 0.7695 (tt0) REVERT: A 262 LYS cc_start: 0.7897 (tttt) cc_final: 0.7596 (tttt) REVERT: A 338 MET cc_start: 0.8031 (mmt) cc_final: 0.7707 (mmt) REVERT: A 418 SER cc_start: 0.8224 (m) cc_final: 0.8023 (p) REVERT: A 437 LEU cc_start: 0.8465 (tp) cc_final: 0.8093 (tp) REVERT: A 540 LYS cc_start: 0.8266 (ttmm) cc_final: 0.7963 (ttmm) REVERT: A 542 SER cc_start: 0.7718 (m) cc_final: 0.7467 (t) REVERT: A 672 SER cc_start: 0.8487 (m) cc_final: 0.7966 (p) REVERT: A 744 CYS cc_start: 0.7687 (m) cc_final: 0.7261 (m) REVERT: A 778 LEU cc_start: 0.8667 (tp) cc_final: 0.8413 (tt) REVERT: A 787 ASP cc_start: 0.7672 (m-30) cc_final: 0.7372 (m-30) REVERT: A 809 ASN cc_start: 0.7874 (m110) cc_final: 0.7611 (m110) REVERT: A 845 LYS cc_start: 0.7493 (mttt) cc_final: 0.7278 (mtpp) REVERT: A 1272 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7261 (mt-10) REVERT: A 1275 TRP cc_start: 0.7391 (OUTLIER) cc_final: 0.7039 (m-10) REVERT: A 1311 HIS cc_start: 0.7203 (m-70) cc_final: 0.6813 (m-70) outliers start: 37 outliers final: 25 residues processed: 282 average time/residue: 0.0935 time to fit residues: 37.9108 Evaluate side-chains 281 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 255 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1252 GLU Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1275 TRP Chi-restraints excluded: chain A residue 1332 LYS Chi-restraints excluded: chain A residue 1342 ILE Chi-restraints excluded: chain A residue 1359 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 102 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 99 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 HIS A1195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.160331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.129953 restraints weight = 32196.416| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 3.12 r_work: 0.3411 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3415 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3415 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11375 Z= 0.163 Angle : 0.635 8.664 15453 Z= 0.323 Chirality : 0.045 0.252 1805 Planarity : 0.004 0.052 1926 Dihedral : 7.430 101.729 1569 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.00 % Favored : 96.93 % Rotamer: Outliers : 3.61 % Allowed : 21.25 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.23), residues: 1403 helix: 1.33 (0.17), residues: 890 sheet: -1.32 (0.66), residues: 60 loop : -0.52 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1065 TYR 0.013 0.001 TYR A 852 PHE 0.016 0.002 PHE A 558 TRP 0.020 0.001 TRP A1197 HIS 0.008 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00373 (11372) covalent geometry : angle 0.63337 (15445) SS BOND : bond 0.00771 ( 1) SS BOND : angle 2.53327 ( 2) hydrogen bonds : bond 0.05072 ( 689) hydrogen bonds : angle 4.40952 ( 2028) link_NAG-ASN : bond 0.01498 ( 2) link_NAG-ASN : angle 1.83003 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2806 Ramachandran restraints generated. 1403 Oldfield, 0 Emsley, 1403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2806 Ramachandran restraints generated. 1403 Oldfield, 0 Emsley, 1403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 264 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3540 (mmm) cc_final: 0.3086 (mmm) REVERT: A 89 LEU cc_start: 0.6837 (tp) cc_final: 0.6574 (tt) REVERT: A 93 PHE cc_start: 0.7289 (m-80) cc_final: 0.6699 (m-80) REVERT: A 129 ARG cc_start: 0.7873 (mtt180) cc_final: 0.7424 (mtp-110) REVERT: A 158 MET cc_start: 0.7771 (mtp) cc_final: 0.7516 (mtt) REVERT: A 176 TYR cc_start: 0.7566 (m-80) cc_final: 0.7277 (m-80) REVERT: A 210 GLU cc_start: 0.8162 (tt0) cc_final: 0.7873 (tt0) REVERT: A 262 LYS cc_start: 0.7908 (tttt) cc_final: 0.7587 (tttt) REVERT: A 337 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8275 (mp) REVERT: A 338 MET cc_start: 0.8206 (mmt) cc_final: 0.7897 (mmt) REVERT: A 437 LEU cc_start: 0.8462 (tp) cc_final: 0.8088 (tp) REVERT: A 540 LYS cc_start: 0.8290 (ttmm) cc_final: 0.8087 (ttmm) REVERT: A 542 SER cc_start: 0.7760 (m) cc_final: 0.7548 (t) REVERT: A 672 SER cc_start: 0.8475 (m) cc_final: 0.7948 (p) REVERT: A 744 CYS cc_start: 0.7821 (m) cc_final: 0.7389 (m) REVERT: A 778 LEU cc_start: 0.8648 (tp) cc_final: 0.8403 (tt) REVERT: A 787 ASP cc_start: 0.7740 (m-30) cc_final: 0.7384 (m-30) REVERT: A 964 ASP cc_start: 0.7263 (p0) cc_final: 0.6677 (p0) REVERT: A 981 PHE cc_start: 0.7991 (t80) cc_final: 0.7786 (t80) REVERT: A 1272 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7497 (mt-10) REVERT: A 1311 HIS cc_start: 0.7320 (m-70) cc_final: 0.6919 (m-70) outliers start: 43 outliers final: 28 residues processed: 289 average time/residue: 0.1012 time to fit residues: 42.2062 Evaluate side-chains 290 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 261 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1076 SER Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1252 GLU Chi-restraints excluded: chain A residue 1332 LYS Chi-restraints excluded: chain A residue 1342 ILE Chi-restraints excluded: chain A residue 1359 LYS Chi-restraints excluded: chain A residue 1504 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 55 optimal weight: 0.0370 chunk 6 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 HIS A1195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.159863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.129758 restraints weight = 31174.072| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 3.15 r_work: 0.3405 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11375 Z= 0.164 Angle : 0.635 8.642 15453 Z= 0.321 Chirality : 0.045 0.241 1805 Planarity : 0.004 0.051 1926 Dihedral : 7.141 99.809 1567 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.00 % Favored : 96.93 % Rotamer: Outliers : 3.36 % Allowed : 22.23 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.23), residues: 1403 helix: 1.39 (0.17), residues: 891 sheet: -1.36 (0.65), residues: 60 loop : -0.55 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1165 TYR 0.015 0.001 TYR A 852 PHE 0.017 0.002 PHE A 558 TRP 0.019 0.001 TRP A1197 HIS 0.009 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00376 (11372) covalent geometry : angle 0.63357 (15445) SS BOND : bond 0.00007 ( 1) SS BOND : angle 2.65041 ( 2) hydrogen bonds : bond 0.05122 ( 689) hydrogen bonds : angle 4.34653 ( 2028) link_NAG-ASN : bond 0.01377 ( 2) link_NAG-ASN : angle 1.78342 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2806 Ramachandran restraints generated. 1403 Oldfield, 0 Emsley, 1403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2806 Ramachandran restraints generated. 1403 Oldfield, 0 Emsley, 1403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 260 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3582 (mmm) cc_final: 0.3200 (mmm) REVERT: A 89 LEU cc_start: 0.6822 (tp) cc_final: 0.6565 (tt) REVERT: A 93 PHE cc_start: 0.7325 (m-80) cc_final: 0.6717 (m-80) REVERT: A 129 ARG cc_start: 0.7943 (mtt180) cc_final: 0.7443 (mtp-110) REVERT: A 158 MET cc_start: 0.7749 (mtp) cc_final: 0.7471 (mtt) REVERT: A 176 TYR cc_start: 0.7565 (m-80) cc_final: 0.7283 (m-80) REVERT: A 262 LYS cc_start: 0.7924 (tttt) cc_final: 0.7594 (tttt) REVERT: A 337 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8274 (mp) REVERT: A 338 MET cc_start: 0.8230 (mmt) cc_final: 0.7935 (mmt) REVERT: A 437 LEU cc_start: 0.8449 (tp) cc_final: 0.8079 (tp) REVERT: A 540 LYS cc_start: 0.8369 (ttmm) cc_final: 0.8139 (ttmm) REVERT: A 542 SER cc_start: 0.7726 (m) cc_final: 0.7516 (t) REVERT: A 544 TYR cc_start: 0.7193 (OUTLIER) cc_final: 0.6752 (t80) REVERT: A 672 SER cc_start: 0.8501 (m) cc_final: 0.7968 (p) REVERT: A 778 LEU cc_start: 0.8614 (tp) cc_final: 0.8361 (tt) REVERT: A 787 ASP cc_start: 0.7768 (m-30) cc_final: 0.7404 (m-30) REVERT: A 809 ASN cc_start: 0.7914 (m110) cc_final: 0.7677 (m110) REVERT: A 964 ASP cc_start: 0.7271 (p0) cc_final: 0.6683 (p0) REVERT: A 1272 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7545 (mt-10) REVERT: A 1275 TRP cc_start: 0.7486 (OUTLIER) cc_final: 0.7128 (m-10) REVERT: A 1311 HIS cc_start: 0.7340 (m-70) cc_final: 0.6932 (m-70) outliers start: 40 outliers final: 27 residues processed: 283 average time/residue: 0.1045 time to fit residues: 42.4459 Evaluate side-chains 284 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 254 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1251 SER Chi-restraints excluded: chain A residue 1275 TRP Chi-restraints excluded: chain A residue 1332 LYS Chi-restraints excluded: chain A residue 1342 ILE Chi-restraints excluded: chain A residue 1359 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 8 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 137 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 128 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 HIS A 985 HIS A1195 ASN A1386 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.160303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.129702 restraints weight = 19030.984| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.31 r_work: 0.3475 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11375 Z= 0.167 Angle : 0.636 8.558 15453 Z= 0.321 Chirality : 0.045 0.235 1805 Planarity : 0.004 0.051 1926 Dihedral : 6.945 97.783 1564 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.29 % Favored : 96.64 % Rotamer: Outliers : 3.61 % Allowed : 22.40 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.23), residues: 1403 helix: 1.39 (0.17), residues: 894 sheet: -1.32 (0.65), residues: 60 loop : -0.56 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1046 TYR 0.018 0.001 TYR A 852 PHE 0.017 0.002 PHE A 558 TRP 0.019 0.001 TRP A1197 HIS 0.010 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00385 (11372) covalent geometry : angle 0.63452 (15445) SS BOND : bond 0.00488 ( 1) SS BOND : angle 2.65023 ( 2) hydrogen bonds : bond 0.05116 ( 689) hydrogen bonds : angle 4.32479 ( 2028) link_NAG-ASN : bond 0.01284 ( 2) link_NAG-ASN : angle 1.73959 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2806 Ramachandran restraints generated. 1403 Oldfield, 0 Emsley, 1403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2806 Ramachandran restraints generated. 1403 Oldfield, 0 Emsley, 1403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 252 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3552 (mmm) cc_final: 0.3226 (mmm) REVERT: A 129 ARG cc_start: 0.8057 (mtt180) cc_final: 0.7544 (mtp-110) REVERT: A 158 MET cc_start: 0.7841 (mtp) cc_final: 0.7577 (mtt) REVERT: A 176 TYR cc_start: 0.7596 (m-80) cc_final: 0.7342 (m-80) REVERT: A 210 GLU cc_start: 0.8314 (tt0) cc_final: 0.8104 (tt0) REVERT: A 262 LYS cc_start: 0.7940 (tttt) cc_final: 0.7618 (tttt) REVERT: A 337 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8331 (mp) REVERT: A 338 MET cc_start: 0.8354 (mmt) cc_final: 0.8076 (mmt) REVERT: A 437 LEU cc_start: 0.8488 (tp) cc_final: 0.8108 (tp) REVERT: A 540 LYS cc_start: 0.8388 (ttmm) cc_final: 0.8157 (ttmm) REVERT: A 544 TYR cc_start: 0.7416 (OUTLIER) cc_final: 0.6966 (t80) REVERT: A 672 SER cc_start: 0.8551 (m) cc_final: 0.8046 (p) REVERT: A 744 CYS cc_start: 0.7780 (m) cc_final: 0.7235 (m) REVERT: A 778 LEU cc_start: 0.8692 (tp) cc_final: 0.8441 (tt) REVERT: A 787 ASP cc_start: 0.7915 (m-30) cc_final: 0.7570 (m-30) REVERT: A 809 ASN cc_start: 0.7952 (m110) cc_final: 0.7741 (m110) REVERT: A 848 GLU cc_start: 0.6788 (tp30) cc_final: 0.6441 (tp30) REVERT: A 849 MET cc_start: 0.7278 (ptt) cc_final: 0.7056 (ptp) REVERT: A 964 ASP cc_start: 0.7445 (p0) cc_final: 0.6857 (p0) REVERT: A 1272 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7642 (mt-10) REVERT: A 1275 TRP cc_start: 0.7564 (OUTLIER) cc_final: 0.7298 (m-10) REVERT: A 1311 HIS cc_start: 0.7425 (m-70) cc_final: 0.7016 (m-70) REVERT: A 1385 MET cc_start: 0.6578 (tmm) cc_final: 0.6377 (tmm) outliers start: 43 outliers final: 33 residues processed: 281 average time/residue: 0.1091 time to fit residues: 43.8814 Evaluate side-chains 283 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 247 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 1076 SER Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1251 SER Chi-restraints excluded: chain A residue 1275 TRP Chi-restraints excluded: chain A residue 1277 ILE Chi-restraints excluded: chain A residue 1332 LYS Chi-restraints excluded: chain A residue 1359 LYS Chi-restraints excluded: chain A residue 1367 PHE Chi-restraints excluded: chain A residue 1504 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 79 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 10 optimal weight: 0.0050 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS A 701 HIS ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1025 GLN A1195 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.160666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.129227 restraints weight = 26302.107| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 3.00 r_work: 0.3437 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3442 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3442 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11375 Z= 0.155 Angle : 0.641 10.506 15453 Z= 0.321 Chirality : 0.045 0.304 1805 Planarity : 0.004 0.050 1926 Dihedral : 6.892 96.518 1564 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.50 % Favored : 96.43 % Rotamer: Outliers : 3.69 % Allowed : 22.40 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.23), residues: 1403 helix: 1.44 (0.17), residues: 889 sheet: -1.43 (0.61), residues: 65 loop : -0.54 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1046 TYR 0.019 0.001 TYR A 852 PHE 0.028 0.002 PHE A1030 TRP 0.021 0.001 TRP A1197 HIS 0.007 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00353 (11372) covalent geometry : angle 0.63958 (15445) SS BOND : bond 0.00294 ( 1) SS BOND : angle 2.43666 ( 2) hydrogen bonds : bond 0.05039 ( 689) hydrogen bonds : angle 4.28892 ( 2028) link_NAG-ASN : bond 0.01253 ( 2) link_NAG-ASN : angle 1.71536 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2806 Ramachandran restraints generated. 1403 Oldfield, 0 Emsley, 1403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2806 Ramachandran restraints generated. 1403 Oldfield, 0 Emsley, 1403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 249 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3443 (mmm) cc_final: 0.3156 (mmm) REVERT: A 93 PHE cc_start: 0.7213 (m-80) cc_final: 0.6872 (m-80) REVERT: A 129 ARG cc_start: 0.7850 (mtt180) cc_final: 0.7432 (mtp-110) REVERT: A 142 TRP cc_start: 0.8209 (m100) cc_final: 0.7850 (m100) REVERT: A 158 MET cc_start: 0.7717 (mtp) cc_final: 0.7448 (mtt) REVERT: A 262 LYS cc_start: 0.7861 (tttt) cc_final: 0.7570 (tttt) REVERT: A 337 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8247 (mp) REVERT: A 338 MET cc_start: 0.8103 (mmt) cc_final: 0.7822 (mmt) REVERT: A 437 LEU cc_start: 0.8470 (tp) cc_final: 0.8125 (tp) REVERT: A 508 ILE cc_start: 0.7019 (tp) cc_final: 0.6760 (tt) REVERT: A 540 LYS cc_start: 0.8320 (ttmm) cc_final: 0.8093 (ttmm) REVERT: A 544 TYR cc_start: 0.7136 (OUTLIER) cc_final: 0.6734 (t80) REVERT: A 672 SER cc_start: 0.8502 (m) cc_final: 0.7997 (p) REVERT: A 744 CYS cc_start: 0.7709 (m) cc_final: 0.7150 (m) REVERT: A 778 LEU cc_start: 0.8656 (tp) cc_final: 0.8394 (tt) REVERT: A 787 ASP cc_start: 0.7735 (m-30) cc_final: 0.7364 (m-30) REVERT: A 809 ASN cc_start: 0.7918 (m110) cc_final: 0.7689 (m110) REVERT: A 964 ASP cc_start: 0.7202 (p0) cc_final: 0.6610 (p0) REVERT: A 1268 GLU cc_start: 0.8009 (tp30) cc_final: 0.7792 (tp30) REVERT: A 1272 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7553 (mt-10) REVERT: A 1275 TRP cc_start: 0.7442 (OUTLIER) cc_final: 0.7159 (m-10) REVERT: A 1311 HIS cc_start: 0.7381 (m-70) cc_final: 0.6989 (m-70) outliers start: 44 outliers final: 31 residues processed: 274 average time/residue: 0.1080 time to fit residues: 42.4173 Evaluate side-chains 280 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 246 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 1076 SER Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1275 TRP Chi-restraints excluded: chain A residue 1332 LYS Chi-restraints excluded: chain A residue 1342 ILE Chi-restraints excluded: chain A residue 1359 LYS Chi-restraints excluded: chain A residue 1367 PHE Chi-restraints excluded: chain A residue 1504 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 59 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 68 optimal weight: 0.0040 chunk 105 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 136 optimal weight: 0.3980 chunk 84 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 701 HIS A 985 HIS A1195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.161198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.130205 restraints weight = 21410.399| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.48 r_work: 0.3482 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11375 Z= 0.141 Angle : 0.628 10.144 15453 Z= 0.315 Chirality : 0.044 0.287 1805 Planarity : 0.004 0.049 1926 Dihedral : 6.850 95.113 1564 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.36 % Favored : 96.57 % Rotamer: Outliers : 2.71 % Allowed : 23.63 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.23), residues: 1403 helix: 1.57 (0.18), residues: 886 sheet: -1.35 (0.62), residues: 65 loop : -0.45 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1046 TYR 0.018 0.001 TYR A 852 PHE 0.023 0.001 PHE A1030 TRP 0.021 0.001 TRP A1197 HIS 0.015 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00312 (11372) covalent geometry : angle 0.62718 (15445) SS BOND : bond 0.00270 ( 1) SS BOND : angle 2.31844 ( 2) hydrogen bonds : bond 0.04782 ( 689) hydrogen bonds : angle 4.24776 ( 2028) link_NAG-ASN : bond 0.01210 ( 2) link_NAG-ASN : angle 1.71349 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2806 Ramachandran restraints generated. 1403 Oldfield, 0 Emsley, 1403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2806 Ramachandran restraints generated. 1403 Oldfield, 0 Emsley, 1403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 243 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3421 (mmm) cc_final: 0.3184 (mmm) REVERT: A 93 PHE cc_start: 0.7355 (m-80) cc_final: 0.6874 (m-80) REVERT: A 129 ARG cc_start: 0.8088 (mtt180) cc_final: 0.7485 (mtp-110) REVERT: A 130 ARG cc_start: 0.8104 (tpp80) cc_final: 0.7666 (mmp80) REVERT: A 158 MET cc_start: 0.7813 (mtp) cc_final: 0.7557 (mtt) REVERT: A 176 TYR cc_start: 0.7705 (m-80) cc_final: 0.7305 (m-80) REVERT: A 262 LYS cc_start: 0.7910 (tttt) cc_final: 0.7619 (tttt) REVERT: A 338 MET cc_start: 0.8374 (mmt) cc_final: 0.8115 (mmt) REVERT: A 437 LEU cc_start: 0.8523 (tp) cc_final: 0.8173 (tp) REVERT: A 540 LYS cc_start: 0.8377 (ttmm) cc_final: 0.8149 (ttmm) REVERT: A 544 TYR cc_start: 0.7369 (OUTLIER) cc_final: 0.6960 (t80) REVERT: A 672 SER cc_start: 0.8553 (m) cc_final: 0.8059 (p) REVERT: A 744 CYS cc_start: 0.7822 (m) cc_final: 0.7248 (m) REVERT: A 778 LEU cc_start: 0.8702 (tp) cc_final: 0.8448 (tt) REVERT: A 787 ASP cc_start: 0.7883 (m-30) cc_final: 0.7552 (m-30) REVERT: A 809 ASN cc_start: 0.7949 (m110) cc_final: 0.7724 (m110) REVERT: A 964 ASP cc_start: 0.7460 (p0) cc_final: 0.6873 (p0) REVERT: A 1272 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7595 (mt-10) REVERT: A 1275 TRP cc_start: 0.7573 (OUTLIER) cc_final: 0.7343 (m-10) REVERT: A 1311 HIS cc_start: 0.7386 (m-70) cc_final: 0.7017 (m-70) outliers start: 32 outliers final: 25 residues processed: 264 average time/residue: 0.1064 time to fit residues: 40.3625 Evaluate side-chains 268 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 241 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1275 TRP Chi-restraints excluded: chain A residue 1332 LYS Chi-restraints excluded: chain A residue 1342 ILE Chi-restraints excluded: chain A residue 1359 LYS Chi-restraints excluded: chain A residue 1504 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 82 optimal weight: 8.9990 chunk 95 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 71 optimal weight: 0.3980 chunk 103 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 135 optimal weight: 0.0770 chunk 18 optimal weight: 0.5980 chunk 127 optimal weight: 0.6980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 701 HIS A1195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.160829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.129862 restraints weight = 20615.534| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.45 r_work: 0.3478 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11375 Z= 0.151 Angle : 0.646 9.832 15453 Z= 0.322 Chirality : 0.044 0.230 1805 Planarity : 0.004 0.048 1926 Dihedral : 6.710 93.364 1564 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.43 % Favored : 96.50 % Rotamer: Outliers : 2.79 % Allowed : 23.71 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.23), residues: 1403 helix: 1.56 (0.18), residues: 887 sheet: -1.24 (0.62), residues: 64 loop : -0.53 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1046 TYR 0.017 0.001 TYR A 852 PHE 0.025 0.001 PHE A1030 TRP 0.017 0.001 TRP A1197 HIS 0.013 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00344 (11372) covalent geometry : angle 0.64485 (15445) SS BOND : bond 0.00285 ( 1) SS BOND : angle 2.24686 ( 2) hydrogen bonds : bond 0.04922 ( 689) hydrogen bonds : angle 4.23553 ( 2028) link_NAG-ASN : bond 0.01170 ( 2) link_NAG-ASN : angle 1.74655 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2806 Ramachandran restraints generated. 1403 Oldfield, 0 Emsley, 1403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2806 Ramachandran restraints generated. 1403 Oldfield, 0 Emsley, 1403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 251 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3548 (mmm) cc_final: 0.3334 (mmm) REVERT: A 93 PHE cc_start: 0.7340 (m-80) cc_final: 0.6971 (m-80) REVERT: A 129 ARG cc_start: 0.8094 (mtt180) cc_final: 0.7463 (mtp-110) REVERT: A 130 ARG cc_start: 0.8122 (tpp80) cc_final: 0.7722 (mmp80) REVERT: A 158 MET cc_start: 0.7816 (mtp) cc_final: 0.7573 (mtt) REVERT: A 176 TYR cc_start: 0.7666 (m-80) cc_final: 0.7307 (m-80) REVERT: A 262 LYS cc_start: 0.7941 (tttt) cc_final: 0.7634 (tttt) REVERT: A 338 MET cc_start: 0.8384 (mmt) cc_final: 0.8112 (mmt) REVERT: A 437 LEU cc_start: 0.8505 (tp) cc_final: 0.8159 (tp) REVERT: A 540 LYS cc_start: 0.8401 (ttmm) cc_final: 0.8174 (ttmm) REVERT: A 544 TYR cc_start: 0.7342 (OUTLIER) cc_final: 0.6935 (t80) REVERT: A 672 SER cc_start: 0.8551 (m) cc_final: 0.8047 (p) REVERT: A 744 CYS cc_start: 0.7825 (m) cc_final: 0.7231 (m) REVERT: A 778 LEU cc_start: 0.8705 (tp) cc_final: 0.8447 (tt) REVERT: A 787 ASP cc_start: 0.7902 (m-30) cc_final: 0.7570 (m-30) REVERT: A 809 ASN cc_start: 0.7994 (m110) cc_final: 0.7762 (m110) REVERT: A 964 ASP cc_start: 0.7491 (p0) cc_final: 0.6906 (p0) REVERT: A 967 LYS cc_start: 0.8440 (tppt) cc_final: 0.7763 (mttt) REVERT: A 1272 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7596 (mt-10) REVERT: A 1275 TRP cc_start: 0.7610 (OUTLIER) cc_final: 0.7330 (m-10) REVERT: A 1311 HIS cc_start: 0.7425 (m-70) cc_final: 0.7095 (m-70) outliers start: 33 outliers final: 28 residues processed: 271 average time/residue: 0.1037 time to fit residues: 40.3155 Evaluate side-chains 276 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 246 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 1076 SER Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1275 TRP Chi-restraints excluded: chain A residue 1332 LYS Chi-restraints excluded: chain A residue 1342 ILE Chi-restraints excluded: chain A residue 1359 LYS Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1504 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 0.4980 chunk 131 optimal weight: 0.0970 chunk 78 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 701 HIS A1195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.159208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.127844 restraints weight = 22507.601| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.57 r_work: 0.3447 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11375 Z= 0.181 Angle : 0.664 9.790 15453 Z= 0.332 Chirality : 0.045 0.237 1805 Planarity : 0.004 0.049 1926 Dihedral : 6.539 91.969 1564 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.57 % Favored : 96.36 % Rotamer: Outliers : 2.79 % Allowed : 23.54 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.23), residues: 1403 helix: 1.46 (0.17), residues: 886 sheet: -1.30 (0.61), residues: 65 loop : -0.50 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1046 TYR 0.018 0.002 TYR A 831 PHE 0.027 0.002 PHE A1030 TRP 0.015 0.001 TRP A1197 HIS 0.014 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00424 (11372) covalent geometry : angle 0.66325 (15445) SS BOND : bond 0.00297 ( 1) SS BOND : angle 2.27090 ( 2) hydrogen bonds : bond 0.05207 ( 689) hydrogen bonds : angle 4.29080 ( 2028) link_NAG-ASN : bond 0.01169 ( 2) link_NAG-ASN : angle 1.75907 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2806 Ramachandran restraints generated. 1403 Oldfield, 0 Emsley, 1403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2806 Ramachandran restraints generated. 1403 Oldfield, 0 Emsley, 1403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 255 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LEU cc_start: 0.6929 (tp) cc_final: 0.6686 (tt) REVERT: A 93 PHE cc_start: 0.7386 (m-80) cc_final: 0.6891 (m-80) REVERT: A 129 ARG cc_start: 0.8138 (mtt180) cc_final: 0.7514 (mtp-110) REVERT: A 130 ARG cc_start: 0.8113 (tpp80) cc_final: 0.7735 (mmp80) REVERT: A 142 TRP cc_start: 0.8329 (m100) cc_final: 0.7966 (m100) REVERT: A 176 TYR cc_start: 0.7673 (m-80) cc_final: 0.7353 (m-80) REVERT: A 262 LYS cc_start: 0.7946 (tttt) cc_final: 0.7639 (tttt) REVERT: A 338 MET cc_start: 0.8382 (mmt) cc_final: 0.8126 (mmt) REVERT: A 437 LEU cc_start: 0.8526 (tp) cc_final: 0.8186 (tp) REVERT: A 441 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8344 (tp) REVERT: A 540 LYS cc_start: 0.8409 (ttmm) cc_final: 0.8182 (ttmm) REVERT: A 544 TYR cc_start: 0.7430 (OUTLIER) cc_final: 0.7014 (t80) REVERT: A 672 SER cc_start: 0.8543 (m) cc_final: 0.8051 (p) REVERT: A 744 CYS cc_start: 0.7796 (m) cc_final: 0.7205 (m) REVERT: A 778 LEU cc_start: 0.8724 (tp) cc_final: 0.8480 (tt) REVERT: A 787 ASP cc_start: 0.7923 (m-30) cc_final: 0.7591 (m-30) REVERT: A 964 ASP cc_start: 0.7500 (p0) cc_final: 0.6915 (p0) REVERT: A 1272 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7626 (mt-10) REVERT: A 1275 TRP cc_start: 0.7620 (OUTLIER) cc_final: 0.7373 (m-10) REVERT: A 1311 HIS cc_start: 0.7453 (m-70) cc_final: 0.7147 (m-70) outliers start: 33 outliers final: 28 residues processed: 273 average time/residue: 0.1090 time to fit residues: 42.4586 Evaluate side-chains 283 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 252 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1275 TRP Chi-restraints excluded: chain A residue 1332 LYS Chi-restraints excluded: chain A residue 1342 ILE Chi-restraints excluded: chain A residue 1359 LYS Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1367 PHE Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1504 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 16 optimal weight: 7.9990 chunk 97 optimal weight: 0.6980 chunk 122 optimal weight: 0.0040 chunk 7 optimal weight: 0.9980 chunk 123 optimal weight: 0.0020 chunk 63 optimal weight: 0.7980 chunk 130 optimal weight: 0.0670 chunk 27 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.2938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 701 HIS A1195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.161223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.130173 restraints weight = 22427.808| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.56 r_work: 0.3485 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3493 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11375 Z= 0.133 Angle : 0.636 9.044 15453 Z= 0.314 Chirality : 0.043 0.237 1805 Planarity : 0.004 0.057 1926 Dihedral : 6.309 92.228 1562 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.36 % Favored : 96.57 % Rotamer: Outliers : 2.13 % Allowed : 25.02 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.23), residues: 1403 helix: 1.66 (0.18), residues: 890 sheet: -1.12 (0.63), residues: 64 loop : -0.51 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1046 TYR 0.041 0.001 TYR A 831 PHE 0.015 0.001 PHE A 558 TRP 0.022 0.001 TRP A1197 HIS 0.011 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00294 (11372) covalent geometry : angle 0.63446 (15445) SS BOND : bond 0.00282 ( 1) SS BOND : angle 2.01362 ( 2) hydrogen bonds : bond 0.04674 ( 689) hydrogen bonds : angle 4.17425 ( 2028) link_NAG-ASN : bond 0.01174 ( 2) link_NAG-ASN : angle 1.77736 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3429.97 seconds wall clock time: 59 minutes 33.56 seconds (3573.56 seconds total)