Starting phenix.real_space_refine on Thu Mar 5 21:56:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ac1_15330/03_2026/8ac1_15330.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ac1_15330/03_2026/8ac1_15330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ac1_15330/03_2026/8ac1_15330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ac1_15330/03_2026/8ac1_15330.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ac1_15330/03_2026/8ac1_15330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ac1_15330/03_2026/8ac1_15330.map" } resolution = 4.06 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 32 5.49 5 Mg 1 5.21 5 S 105 5.16 5 C 15685 2.51 5 N 4452 2.21 5 O 4911 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25188 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1767 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 219} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1759 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 10402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1319, 10402 Classifications: {'peptide': 1319} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1263} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 10377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10377 Classifications: {'peptide': 1337} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 55, 'TRANS': 1281} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 221 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "N" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 142 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "R" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 186 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 7} Link IDs: {'rna3p': 8} Chain: "T" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 331 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain breaks: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14377 SG CYS D 70 116.551 122.400 57.270 1.00337.21 S ATOM 14391 SG CYS D 72 115.803 125.875 58.684 1.00341.59 S ATOM 14499 SG CYS D 85 119.257 124.455 58.901 1.00344.86 S ATOM 14523 SG CYS D 88 116.486 122.957 61.027 1.00335.75 S ATOM 20211 SG CYS D 814 126.871 62.404 78.926 1.00110.73 S ATOM 20776 SG CYS D 888 123.060 63.440 78.654 1.00109.50 S ATOM 20827 SG CYS D 895 125.495 63.763 75.864 1.00 97.92 S ATOM 20848 SG CYS D 898 124.228 60.335 76.989 1.00101.02 S Time building chain proxies: 5.44, per 1000 atoms: 0.22 Number of scatterers: 25188 At special positions: 0 Unit cell: (149.988, 140.506, 160.332, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 105 16.00 P 32 15.00 Mg 1 11.99 O 4911 8.00 N 4452 7.00 C 15685 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " Number of angles added : 12 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5798 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 43 sheets defined 37.4% alpha, 15.2% beta 15 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 3.88 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.702A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 88 removed outlier: 3.560A pdb=" N ILE A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 212 through 232 Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.510A pdb=" N SER B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.764A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 removed outlier: 4.211A pdb=" N THR B 116 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 230 removed outlier: 4.121A pdb=" N ARG B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.859A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.904A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 163 through 167 removed outlier: 4.115A pdb=" N SER C 166 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER C 167 " --> pdb=" O THR C 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 163 through 167' Processing helix chain 'C' and resid 207 through 213 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 288 through 293 removed outlier: 4.188A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 removed outlier: 3.698A pdb=" N ARG C 371 " --> pdb=" O TYR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 391 removed outlier: 3.880A pdb=" N SER C 391 " --> pdb=" O ASN C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.592A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 3.726A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 545 through 549 Processing helix chain 'C' and resid 609 through 612 Processing helix chain 'C' and resid 657 through 661 removed outlier: 4.011A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 668 removed outlier: 4.053A pdb=" N LEU C 667 " --> pdb=" O GLY C 664 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE C 668 " --> pdb=" O ALA C 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 664 through 668' Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.611A pdb=" N HIS C 673 " --> pdb=" O PHE C 670 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP C 674 " --> pdb=" O LEU C 671 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 670 through 674' Processing helix chain 'C' and resid 675 through 688 Processing helix chain 'C' and resid 703 through 712 removed outlier: 4.717A pdb=" N ALA C 707 " --> pdb=" O GLY C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 864 removed outlier: 4.033A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 980 Processing helix chain 'C' and resid 985 through 991 Processing helix chain 'C' and resid 993 through 999 Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.517A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1133 removed outlier: 3.633A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE C1124 " --> pdb=" O ALA C1120 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY C1125 " --> pdb=" O ALA C1121 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LYS C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.634A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN C1146 " --> pdb=" O ARG C1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 1166 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1272 through 1281 Processing helix chain 'C' and resid 1284 through 1293 Processing helix chain 'C' and resid 1298 through 1310 removed outlier: 3.843A pdb=" N ASP C1310 " --> pdb=" O LYS C1306 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1334 removed outlier: 3.700A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY C1334 " --> pdb=" O ILE C1330 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 113 through 119 removed outlier: 3.781A pdb=" N LEU D 117 " --> pdb=" O HIS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 132 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 180 through 192 Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 211 through 231 removed outlier: 3.549A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 246 through 250 removed outlier: 3.507A pdb=" N LEU D 249 " --> pdb=" O PRO D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 283 Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.535A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASN D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 370 through 389 Proline residue: D 379 - end of helix Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 406 through 417 removed outlier: 4.236A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 453 through 458 removed outlier: 3.730A pdb=" N TYR D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN D 458 " --> pdb=" O CYS D 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 453 through 458' Processing helix chain 'D' and resid 473 through 484 Processing helix chain 'D' and resid 505 through 514 removed outlier: 3.512A pdb=" N GLY D 509 " --> pdb=" O ASP D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.864A pdb=" N GLU D 534 " --> pdb=" O PRO D 530 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 583 removed outlier: 3.875A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 593 removed outlier: 3.675A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 610 Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 648 through 670 removed outlier: 4.041A pdb=" N GLU D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.753A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 4.306A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY D 782 " --> pdb=" O GLY D 778 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY D 794 " --> pdb=" O THR D 790 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 removed outlier: 3.875A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 876 removed outlier: 4.525A pdb=" N GLU D 873 " --> pdb=" O ASP D 870 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLU D 874 " --> pdb=" O LEU D 871 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER D 876 " --> pdb=" O GLU D 873 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 900 Processing helix chain 'D' and resid 915 through 925 Processing helix chain 'D' and resid 926 through 928 No H-bonds generated for 'chain 'D' and resid 926 through 928' Processing helix chain 'D' and resid 1136 through 1147 Processing helix chain 'D' and resid 1216 through 1225 removed outlier: 4.084A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY D1225 " --> pdb=" O LEU D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 4.176A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL D1234 " --> pdb=" O THR D1230 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.093A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU D1254 " --> pdb=" O ASP D1250 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL D1257 " --> pdb=" O ILE D1253 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1294 removed outlier: 3.944A pdb=" N LEU D1292 " --> pdb=" O ALA D1288 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.659A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE D1325 " --> pdb=" O SER D1321 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1337 removed outlier: 3.784A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D1332 " --> pdb=" O THR D1328 " (cutoff:3.500A) Processing helix chain 'D' and resid 1347 through 1353 Processing helix chain 'D' and resid 1360 through 1373 removed outlier: 3.553A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 17 through 28 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 removed outlier: 4.570A pdb=" N HIS A 23 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR A 207 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LYS A 25 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N MET A 205 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N THR A 27 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE A 203 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU A 29 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LEU A 201 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 104 removed outlier: 3.711A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.506A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 152 Processing sheet with id=AA6, first strand: chain 'B' and resid 23 through 31 removed outlier: 5.759A pdb=" N HIS B 23 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR B 207 " --> pdb=" O HIS B 23 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LYS B 25 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N MET B 205 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N THR B 27 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE B 203 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N GLU B 29 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU B 201 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 105 removed outlier: 3.613A pdb=" N GLU B 58 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 108 through 110 removed outlier: 3.734A pdb=" N GLY B 108 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.914A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.553A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU C 100 " --> pdb=" O GLN C 120 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLN C 120 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU C 102 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LYS C 118 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE C 104 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB3, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 160 Processing sheet with id=AB5, first strand: chain 'C' and resid 284 through 286 removed outlier: 4.499A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.834A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 296 through 297 removed outlier: 3.530A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 removed outlier: 6.937A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC1, first strand: chain 'C' and resid 633 through 637 removed outlier: 3.743A pdb=" N SER C 643 " --> pdb=" O CYS C 636 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 716 through 718 removed outlier: 7.314A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 783 " --> pdb=" O ALA C 716 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 749 through 752 removed outlier: 6.874A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.701A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC6, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.548A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 830 through 838 removed outlier: 5.948A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.715A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 6.246A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 8.002A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1268 through 1270 Processing sheet with id=AD3, first strand: chain 'C' and resid 1335 through 1341 removed outlier: 3.568A pdb=" N LYS D 21 " --> pdb=" O GLU C1338 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ALA D 19 " --> pdb=" O GLU C1340 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 104 through 106 Processing sheet with id=AD5, first strand: chain 'D' and resid 144 through 145 Processing sheet with id=AD6, first strand: chain 'D' and resid 254 through 255 removed outlier: 3.534A pdb=" N ARG D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.642A pdb=" N ARG D 551 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE D 552 " --> pdb=" O SER D 568 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL D 564 " --> pdb=" O GLU D 556 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 842 through 843 removed outlier: 4.218A pdb=" N ARG D 842 " --> pdb=" O LEU D 864 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 949 through 951 removed outlier: 4.453A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 991 through 997 removed outlier: 3.662A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1025 through 1028 Processing sheet with id=AE3, first strand: chain 'D' and resid 1034 through 1036 removed outlier: 3.622A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1046 through 1047 Processing sheet with id=AE5, first strand: chain 'D' and resid 1156 through 1157 removed outlier: 3.576A pdb=" N ASP D1208 " --> pdb=" O ALA D1157 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1162 through 1163 removed outlier: 4.022A pdb=" N TYR D1186 " --> pdb=" O ILE D1177 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1278 through 1279 957 hydrogen bonds defined for protein. 2700 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 35 hydrogen bonds 70 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 6.72 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8293 1.34 - 1.45: 3146 1.45 - 1.57: 13943 1.57 - 1.69: 61 1.69 - 1.81: 182 Bond restraints: 25625 Sorted by residual: bond pdb=" CB MET C 805 " pdb=" CG MET C 805 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.62e+00 bond pdb=" CB GLN D 504 " pdb=" CG GLN D 504 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.49e+00 bond pdb=" SD MET C1290 " pdb=" CE MET C1290 " ideal model delta sigma weight residual 1.791 1.760 0.031 2.50e-02 1.60e+03 1.58e+00 bond pdb=" CB GLU C1274 " pdb=" CG GLU C1274 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.57e+00 bond pdb=" CB ARG D 77 " pdb=" CG ARG D 77 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.50e+00 ... (remaining 25620 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 33791 1.69 - 3.39: 805 3.39 - 5.08: 109 5.08 - 6.77: 29 6.77 - 8.47: 6 Bond angle restraints: 34740 Sorted by residual: angle pdb=" N ILE D 499 " pdb=" CA ILE D 499 " pdb=" C ILE D 499 " ideal model delta sigma weight residual 112.80 106.77 6.03 1.15e+00 7.56e-01 2.75e+01 angle pdb=" CA ARG D 77 " pdb=" CB ARG D 77 " pdb=" CG ARG D 77 " ideal model delta sigma weight residual 114.10 120.90 -6.80 2.00e+00 2.50e-01 1.16e+01 angle pdb=" C ILE C 198 " pdb=" N ASP C 199 " pdb=" CA ASP C 199 " ideal model delta sigma weight residual 121.54 127.47 -5.93 1.91e+00 2.74e-01 9.64e+00 angle pdb=" N GLY D 496 " pdb=" CA GLY D 496 " pdb=" C GLY D 496 " ideal model delta sigma weight residual 113.18 120.25 -7.07 2.37e+00 1.78e-01 8.89e+00 angle pdb=" N GLU C1024 " pdb=" CA GLU C1024 " pdb=" CB GLU C1024 " ideal model delta sigma weight residual 110.28 114.77 -4.49 1.55e+00 4.16e-01 8.38e+00 ... (remaining 34735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 13971 17.87 - 35.73: 1412 35.73 - 53.60: 265 53.60 - 71.46: 80 71.46 - 89.33: 22 Dihedral angle restraints: 15750 sinusoidal: 6736 harmonic: 9014 Sorted by residual: dihedral pdb=" CA LYS D 76 " pdb=" C LYS D 76 " pdb=" N ARG D 77 " pdb=" CA ARG D 77 " ideal model delta harmonic sigma weight residual 180.00 147.41 32.59 0 5.00e+00 4.00e-02 4.25e+01 dihedral pdb=" CA ASN D 341 " pdb=" C ASN D 341 " pdb=" N LEU D 342 " pdb=" CA LEU D 342 " ideal model delta harmonic sigma weight residual 180.00 152.62 27.38 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA ILE D 820 " pdb=" C ILE D 820 " pdb=" N MET D 821 " pdb=" CA MET D 821 " ideal model delta harmonic sigma weight residual 180.00 154.08 25.92 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 15747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2802 0.042 - 0.083: 869 0.083 - 0.125: 267 0.125 - 0.167: 34 0.167 - 0.209: 3 Chirality restraints: 3975 Sorted by residual: chirality pdb=" CA ARG D 77 " pdb=" N ARG D 77 " pdb=" C ARG D 77 " pdb=" CB ARG D 77 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB THR D 514 " pdb=" CA THR D 514 " pdb=" OG1 THR D 514 " pdb=" CG2 THR D 514 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.72e-01 chirality pdb=" CA ILE D1090 " pdb=" N ILE D1090 " pdb=" C ILE D1090 " pdb=" CB ILE D1090 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.19e-01 ... (remaining 3972 not shown) Planarity restraints: 4443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C1276 " -0.039 2.00e-02 2.50e+03 2.63e-02 1.73e+01 pdb=" CG TRP C1276 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP C1276 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP C1276 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C1276 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C1276 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C1276 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1276 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1276 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C1276 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C1229 " 0.020 2.00e-02 2.50e+03 1.47e-02 4.31e+00 pdb=" CG TYR C1229 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR C1229 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR C1229 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C1229 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR C1229 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C1229 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR C1229 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 338 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" C PHE D 338 " 0.031 2.00e-02 2.50e+03 pdb=" O PHE D 338 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG D 339 " -0.011 2.00e-02 2.50e+03 ... (remaining 4440 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 305 2.52 - 3.12: 20779 3.12 - 3.71: 42539 3.71 - 4.31: 55060 4.31 - 4.90: 88490 Nonbonded interactions: 207173 Sorted by model distance: nonbonded pdb=" N ASP D 464 " pdb="MG MG D1501 " model vdw 1.927 2.250 nonbonded pdb=" N GLY D 463 " pdb="MG MG D1501 " model vdw 2.091 2.250 nonbonded pdb=" O GLU D 652 " pdb=" OG SER D 655 " model vdw 2.135 3.040 nonbonded pdb=" NH1 ARG D1290 " pdb=" O LYS D1297 " model vdw 2.145 3.120 nonbonded pdb=" O GLU D1158 " pdb=" NH2 ARG D1206 " model vdw 2.147 3.120 ... (remaining 207168 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 158 or resid 160 through 234)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.690 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: 0.040 Extract box with map and model: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 32.670 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 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:1.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 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 0.049 25633 Z= 0.210 Angle : 0.652 8.465 34752 Z= 0.342 Chirality : 0.044 0.209 3975 Planarity : 0.004 0.039 4443 Dihedral : 15.157 89.329 9952 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.15), residues: 3121 helix: 0.26 (0.16), residues: 1055 sheet: -0.28 (0.27), residues: 391 loop : -1.58 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1290 TYR 0.034 0.002 TYR C1229 PHE 0.012 0.002 PHE C 188 TRP 0.068 0.002 TRP C1276 HIS 0.005 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00456 (25625) covalent geometry : angle 0.64887 (34740) hydrogen bonds : bond 0.20563 ( 986) hydrogen bonds : angle 7.91910 ( 2770) metal coordination : bond 0.00992 ( 8) metal coordination : angle 3.47536 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 1.017 Fit side-chains REVERT: B 185 TYR cc_start: 0.9175 (p90) cc_final: 0.8804 (p90) REVERT: B 199 ASP cc_start: 0.8046 (m-30) cc_final: 0.7785 (m-30) REVERT: C 183 TRP cc_start: 0.8782 (m-10) cc_final: 0.8146 (m-10) REVERT: C 429 MET cc_start: 0.9183 (mpp) cc_final: 0.8724 (mpp) REVERT: C 1131 MET cc_start: 0.7696 (ppp) cc_final: 0.7454 (ppp) REVERT: D 466 MET cc_start: 0.7499 (mtp) cc_final: 0.7239 (mtp) REVERT: D 484 MET cc_start: 0.7261 (mpp) cc_final: 0.6954 (mpp) REVERT: D 1189 MET cc_start: 0.8653 (tpt) cc_final: 0.7999 (tpp) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1553 time to fit residues: 33.5986 Evaluate side-chains 105 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 0.1980 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 20.0000 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS C 69 GLN C 133 ASN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1209 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 665 GLN D 907 HIS ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.060484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.045057 restraints weight = 180056.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.046304 restraints weight = 118515.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.046750 restraints weight = 79305.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.046963 restraints weight = 65967.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.047060 restraints weight = 61260.182| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25633 Z= 0.204 Angle : 0.637 7.438 34752 Z= 0.333 Chirality : 0.044 0.175 3975 Planarity : 0.004 0.047 4443 Dihedral : 10.212 77.137 3846 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.59 % Favored : 92.37 % Rotamer: Outliers : 0.11 % Allowed : 8.00 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.15), residues: 3121 helix: 0.40 (0.16), residues: 1094 sheet: -0.35 (0.26), residues: 389 loop : -1.61 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1290 TYR 0.018 0.001 TYR C1018 PHE 0.011 0.001 PHE D 763 TRP 0.028 0.002 TRP C1276 HIS 0.004 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00448 (25625) covalent geometry : angle 0.63354 (34740) hydrogen bonds : bond 0.05166 ( 986) hydrogen bonds : angle 5.98350 ( 2770) metal coordination : bond 0.00900 ( 8) metal coordination : angle 3.56745 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 127 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: B 185 TYR cc_start: 0.9140 (p90) cc_final: 0.8898 (p90) REVERT: C 165 HIS cc_start: 0.8717 (t-170) cc_final: 0.8360 (m90) REVERT: C 429 MET cc_start: 0.9229 (mpp) cc_final: 0.8835 (mpp) REVERT: C 1131 MET cc_start: 0.7894 (ppp) cc_final: 0.7510 (tmm) REVERT: D 466 MET cc_start: 0.7610 (mtp) cc_final: 0.7326 (mtp) REVERT: D 484 MET cc_start: 0.7534 (mpp) cc_final: 0.7018 (mpp) REVERT: D 644 MET cc_start: 0.8588 (pmm) cc_final: 0.8349 (pmm) REVERT: D 1189 MET cc_start: 0.8697 (tpt) cc_final: 0.7969 (tpp) outliers start: 3 outliers final: 0 residues processed: 130 average time/residue: 0.1491 time to fit residues: 33.0527 Evaluate side-chains 106 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 191 optimal weight: 8.9990 chunk 69 optimal weight: 20.0000 chunk 75 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 165 optimal weight: 6.9990 chunk 240 optimal weight: 9.9990 chunk 208 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS C 69 GLN C1268 GLN D 232 ASN D 300 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN D 875 ASN D 921 GLN ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.061368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.046295 restraints weight = 181993.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.047897 restraints weight = 112433.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.048119 restraints weight = 69438.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.048238 restraints weight = 63232.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.048337 restraints weight = 58474.966| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25633 Z= 0.141 Angle : 0.597 7.267 34752 Z= 0.309 Chirality : 0.043 0.199 3975 Planarity : 0.004 0.076 4443 Dihedral : 10.069 78.821 3846 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.15), residues: 3121 helix: 0.53 (0.16), residues: 1087 sheet: -0.27 (0.26), residues: 377 loop : -1.64 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 470 TYR 0.016 0.001 TYR C1229 PHE 0.012 0.001 PHE C1270 TRP 0.020 0.002 TRP C1276 HIS 0.004 0.001 HIS D 907 Details of bonding type rmsd covalent geometry : bond 0.00308 (25625) covalent geometry : angle 0.59443 (34740) hydrogen bonds : bond 0.04254 ( 986) hydrogen bonds : angle 5.56581 ( 2770) metal coordination : bond 0.00889 ( 8) metal coordination : angle 3.02990 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.8010 (mtm) cc_final: 0.7568 (mpp) REVERT: B 185 TYR cc_start: 0.9067 (p90) cc_final: 0.8866 (p90) REVERT: C 165 HIS cc_start: 0.8686 (t-170) cc_final: 0.8368 (m90) REVERT: C 429 MET cc_start: 0.9267 (mpp) cc_final: 0.8897 (mpp) REVERT: C 1095 ASP cc_start: 0.8881 (p0) cc_final: 0.8434 (p0) REVERT: C 1131 MET cc_start: 0.7799 (ppp) cc_final: 0.7584 (tmm) REVERT: D 466 MET cc_start: 0.7578 (mtp) cc_final: 0.7307 (mtp) REVERT: D 484 MET cc_start: 0.7488 (mpp) cc_final: 0.7045 (mpp) REVERT: D 644 MET cc_start: 0.8631 (pmm) cc_final: 0.8397 (pmm) REVERT: D 822 MET cc_start: 0.7770 (tpt) cc_final: 0.7553 (tpt) REVERT: D 1189 MET cc_start: 0.8743 (tpt) cc_final: 0.7952 (tpp) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1566 time to fit residues: 35.1013 Evaluate side-chains 111 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 201 optimal weight: 30.0000 chunk 190 optimal weight: 9.9990 chunk 301 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 chunk 108 optimal weight: 20.0000 chunk 80 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 195 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS C 69 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 910 ASN ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.060459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.045087 restraints weight = 179236.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.046479 restraints weight = 115426.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.046768 restraints weight = 75086.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.046937 restraints weight = 65678.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.047039 restraints weight = 60503.411| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 25633 Z= 0.214 Angle : 0.639 7.871 34752 Z= 0.332 Chirality : 0.044 0.188 3975 Planarity : 0.004 0.060 4443 Dihedral : 10.112 82.560 3846 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.15), residues: 3121 helix: 0.41 (0.16), residues: 1096 sheet: -0.47 (0.26), residues: 372 loop : -1.76 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 197 TYR 0.019 0.001 TYR C1229 PHE 0.013 0.002 PHE C1270 TRP 0.016 0.002 TRP C1276 HIS 0.006 0.001 HIS D 907 Details of bonding type rmsd covalent geometry : bond 0.00474 (25625) covalent geometry : angle 0.63627 (34740) hydrogen bonds : bond 0.04399 ( 986) hydrogen bonds : angle 5.52449 ( 2770) metal coordination : bond 0.01041 ( 8) metal coordination : angle 3.38147 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 165 HIS cc_start: 0.8730 (t-170) cc_final: 0.8395 (m170) REVERT: C 429 MET cc_start: 0.9186 (mpp) cc_final: 0.8730 (mpp) REVERT: D 484 MET cc_start: 0.7781 (mpp) cc_final: 0.7161 (mpp) REVERT: D 581 MET cc_start: 0.8777 (tpp) cc_final: 0.8391 (ttm) REVERT: D 644 MET cc_start: 0.8641 (pmm) cc_final: 0.8428 (pmm) REVERT: D 1189 MET cc_start: 0.8779 (tpt) cc_final: 0.7946 (tpp) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1512 time to fit residues: 33.0571 Evaluate side-chains 108 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 199 optimal weight: 30.0000 chunk 32 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 276 optimal weight: 40.0000 chunk 162 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 310 optimal weight: 10.0000 chunk 58 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS C 69 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.060712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.045395 restraints weight = 178870.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.046652 restraints weight = 118246.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.047108 restraints weight = 76995.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.047265 restraints weight = 66232.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.047356 restraints weight = 60853.328| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25633 Z= 0.180 Angle : 0.617 7.067 34752 Z= 0.320 Chirality : 0.044 0.194 3975 Planarity : 0.004 0.053 4443 Dihedral : 10.088 85.060 3846 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.15), residues: 3121 helix: 0.47 (0.16), residues: 1083 sheet: -0.51 (0.26), residues: 372 loop : -1.75 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 470 TYR 0.019 0.001 TYR C1229 PHE 0.012 0.001 PHE D 763 TRP 0.013 0.002 TRP D 580 HIS 0.005 0.001 HIS D 907 Details of bonding type rmsd covalent geometry : bond 0.00401 (25625) covalent geometry : angle 0.61320 (34740) hydrogen bonds : bond 0.04158 ( 986) hydrogen bonds : angle 5.39451 ( 2770) metal coordination : bond 0.00808 ( 8) metal coordination : angle 3.55766 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.8319 (mtm) cc_final: 0.7919 (mpp) REVERT: C 429 MET cc_start: 0.9211 (mpp) cc_final: 0.8811 (mpp) REVERT: C 1095 ASP cc_start: 0.8521 (p0) cc_final: 0.8293 (p0) REVERT: D 484 MET cc_start: 0.7699 (mpp) cc_final: 0.7126 (mpp) REVERT: D 821 MET cc_start: 0.6935 (tpt) cc_final: 0.6363 (ppp) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1490 time to fit residues: 33.6938 Evaluate side-chains 108 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 218 optimal weight: 4.9990 chunk 199 optimal weight: 0.5980 chunk 270 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 107 optimal weight: 20.0000 chunk 310 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 302 optimal weight: 0.8980 chunk 305 optimal weight: 6.9990 chunk 164 optimal weight: 0.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS C 69 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 ASN ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.061149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.045864 restraints weight = 178562.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.047247 restraints weight = 115459.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.047592 restraints weight = 74646.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.047770 restraints weight = 64975.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.047867 restraints weight = 59682.253| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25633 Z= 0.146 Angle : 0.602 7.816 34752 Z= 0.310 Chirality : 0.044 0.229 3975 Planarity : 0.004 0.054 4443 Dihedral : 9.974 84.661 3846 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 0.04 % Allowed : 3.42 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.15), residues: 3121 helix: 0.49 (0.16), residues: 1094 sheet: -0.45 (0.26), residues: 370 loop : -1.74 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D1290 TYR 0.017 0.001 TYR C1229 PHE 0.010 0.001 PHE D 338 TRP 0.018 0.002 TRP C1276 HIS 0.008 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00324 (25625) covalent geometry : angle 0.59873 (34740) hydrogen bonds : bond 0.03921 ( 986) hydrogen bonds : angle 5.21717 ( 2770) metal coordination : bond 0.00627 ( 8) metal coordination : angle 3.24599 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.8265 (mtm) cc_final: 0.8004 (mpp) REVERT: B 185 TYR cc_start: 0.9071 (p90) cc_final: 0.8858 (p90) REVERT: C 1095 ASP cc_start: 0.8586 (p0) cc_final: 0.8358 (p0) REVERT: D 466 MET cc_start: 0.7634 (mtp) cc_final: 0.7072 (mtp) REVERT: D 484 MET cc_start: 0.7792 (mpp) cc_final: 0.7269 (mpp) REVERT: D 625 MET cc_start: 0.8741 (ttp) cc_final: 0.8541 (ttp) REVERT: D 821 MET cc_start: 0.6694 (tpt) cc_final: 0.6374 (ppp) REVERT: D 1189 MET cc_start: 0.8766 (tpt) cc_final: 0.7797 (tpp) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.1568 time to fit residues: 36.6622 Evaluate side-chains 112 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 81 optimal weight: 0.9990 chunk 145 optimal weight: 10.0000 chunk 210 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 282 optimal weight: 10.0000 chunk 253 optimal weight: 0.9980 chunk 174 optimal weight: 9.9990 chunk 6 optimal weight: 0.4980 chunk 235 optimal weight: 1.9990 chunk 299 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS B 41 ASN C 69 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN D 294 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 910 ASN ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1326 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.061797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.046911 restraints weight = 179549.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.048470 restraints weight = 112239.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.048750 restraints weight = 70147.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.048848 restraints weight = 63123.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.048915 restraints weight = 58410.325| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25633 Z= 0.116 Angle : 0.599 8.049 34752 Z= 0.306 Chirality : 0.044 0.231 3975 Planarity : 0.004 0.055 4443 Dihedral : 9.823 83.633 3846 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.08 % Allowed : 2.10 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.15), residues: 3121 helix: 0.56 (0.16), residues: 1099 sheet: -0.52 (0.26), residues: 383 loop : -1.70 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1290 TYR 0.021 0.001 TYR C 26 PHE 0.009 0.001 PHE C1164 TRP 0.015 0.001 TRP C1276 HIS 0.009 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00258 (25625) covalent geometry : angle 0.59682 (34740) hydrogen bonds : bond 0.03686 ( 986) hydrogen bonds : angle 5.12656 ( 2770) metal coordination : bond 0.00436 ( 8) metal coordination : angle 2.86984 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 185 TYR cc_start: 0.9024 (p90) cc_final: 0.8807 (p90) REVERT: C 1095 ASP cc_start: 0.8549 (p0) cc_final: 0.8310 (p0) REVERT: C 1290 MET cc_start: 0.8583 (ptp) cc_final: 0.8361 (ppp) REVERT: D 466 MET cc_start: 0.7543 (mtp) cc_final: 0.7022 (mtp) REVERT: D 484 MET cc_start: 0.7671 (mpp) cc_final: 0.7231 (mpp) REVERT: D 581 MET cc_start: 0.8758 (tpp) cc_final: 0.8330 (ttm) REVERT: D 1189 MET cc_start: 0.8762 (tpt) cc_final: 0.7722 (tpp) outliers start: 2 outliers final: 0 residues processed: 142 average time/residue: 0.1414 time to fit residues: 34.0352 Evaluate side-chains 117 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 59 optimal weight: 8.9990 chunk 157 optimal weight: 0.0770 chunk 149 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 185 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 38 optimal weight: 0.0370 chunk 158 optimal weight: 2.9990 chunk 253 optimal weight: 3.9990 chunk 250 optimal weight: 10.0000 overall best weight: 1.2220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS C 69 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 910 ASN ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1326 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.062242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.047170 restraints weight = 180053.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.048964 restraints weight = 110990.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.049272 restraints weight = 70165.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.049543 restraints weight = 59543.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.049683 restraints weight = 54686.799| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25633 Z= 0.110 Angle : 0.592 8.183 34752 Z= 0.301 Chirality : 0.043 0.214 3975 Planarity : 0.004 0.053 4443 Dihedral : 9.697 82.497 3846 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.04 % Allowed : 1.54 % Favored : 98.42 % 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: -1.01 (0.15), residues: 3121 helix: 0.59 (0.16), residues: 1102 sheet: -0.37 (0.26), residues: 373 loop : -1.67 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1290 TYR 0.018 0.001 TYR C 346 PHE 0.010 0.001 PHE D 338 TRP 0.043 0.002 TRP C1276 HIS 0.011 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00244 (25625) covalent geometry : angle 0.59048 (34740) hydrogen bonds : bond 0.03550 ( 986) hydrogen bonds : angle 4.99783 ( 2770) metal coordination : bond 0.00628 ( 8) metal coordination : angle 2.21100 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 185 ASP cc_start: 0.8001 (p0) cc_final: 0.7557 (p0) REVERT: C 1095 ASP cc_start: 0.8351 (p0) cc_final: 0.8145 (p0) REVERT: D 466 MET cc_start: 0.7666 (mtp) cc_final: 0.7171 (mtp) REVERT: D 1189 MET cc_start: 0.8758 (tpt) cc_final: 0.7696 (tpp) outliers start: 1 outliers final: 0 residues processed: 141 average time/residue: 0.1515 time to fit residues: 36.0120 Evaluate side-chains 114 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 281 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 12 optimal weight: 20.0000 chunk 40 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 217 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 299 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS B 41 ASN C 69 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.061544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.046406 restraints weight = 178022.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.047876 restraints weight = 113556.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.048080 restraints weight = 76301.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.048310 restraints weight = 64399.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.048521 restraints weight = 58811.383| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25633 Z= 0.147 Angle : 0.614 7.926 34752 Z= 0.314 Chirality : 0.044 0.254 3975 Planarity : 0.004 0.052 4443 Dihedral : 9.725 83.711 3846 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.15), residues: 3121 helix: 0.56 (0.16), residues: 1101 sheet: -0.49 (0.26), residues: 389 loop : -1.65 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 77 TYR 0.023 0.001 TYR C 26 PHE 0.030 0.001 PHE C1270 TRP 0.052 0.002 TRP C1276 HIS 0.011 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00329 (25625) covalent geometry : angle 0.61206 (34740) hydrogen bonds : bond 0.03794 ( 986) hydrogen bonds : angle 5.07891 ( 2770) metal coordination : bond 0.00712 ( 8) metal coordination : angle 2.49443 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 151 MET cc_start: 0.6027 (mmm) cc_final: 0.5817 (mmp) REVERT: D 466 MET cc_start: 0.7617 (mtp) cc_final: 0.7121 (mtp) REVERT: D 1189 MET cc_start: 0.8754 (tpt) cc_final: 0.7681 (tpp) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1587 time to fit residues: 35.5681 Evaluate side-chains 109 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 133 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 169 optimal weight: 0.9980 chunk 172 optimal weight: 7.9990 chunk 281 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 293 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS C 69 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.061115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.045917 restraints weight = 177471.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.047375 restraints weight = 112940.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.047699 restraints weight = 71848.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.047838 restraints weight = 63546.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.047963 restraints weight = 58165.694| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25633 Z= 0.177 Angle : 0.640 7.524 34752 Z= 0.328 Chirality : 0.044 0.246 3975 Planarity : 0.004 0.049 4443 Dihedral : 9.859 86.737 3846 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.15), residues: 3121 helix: 0.50 (0.16), residues: 1090 sheet: -0.60 (0.26), residues: 375 loop : -1.64 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 77 TYR 0.014 0.001 TYR C1229 PHE 0.014 0.001 PHE D 116 TRP 0.112 0.003 TRP C1276 HIS 0.012 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00395 (25625) covalent geometry : angle 0.63679 (34740) hydrogen bonds : bond 0.03999 ( 986) hydrogen bonds : angle 5.16880 ( 2770) metal coordination : bond 0.00889 ( 8) metal coordination : angle 3.34525 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6242 Ramachandran restraints generated. 3121 Oldfield, 0 Emsley, 3121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.8097 (mtm) cc_final: 0.7854 (mpp) REVERT: C 429 MET cc_start: 0.9161 (mpp) cc_final: 0.8699 (mpp) REVERT: D 151 MET cc_start: 0.6085 (mmm) cc_final: 0.5872 (mmp) REVERT: D 466 MET cc_start: 0.7660 (mtp) cc_final: 0.7084 (mtp) REVERT: D 1189 MET cc_start: 0.8778 (tpt) cc_final: 0.7713 (tpp) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1483 time to fit residues: 32.5568 Evaluate side-chains 107 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 293 optimal weight: 2.9990 chunk 278 optimal weight: 0.0570 chunk 0 optimal weight: 20.0000 chunk 86 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 273 optimal weight: 0.3980 chunk 62 optimal weight: 4.9990 chunk 261 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 chunk 213 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 overall best weight: 1.4702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 910 ASN ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.062190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.047414 restraints weight = 179853.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.048923 restraints weight = 109796.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.049128 restraints weight = 73109.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.049284 restraints weight = 64258.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.049467 restraints weight = 59169.007| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25633 Z= 0.114 Angle : 0.607 8.694 34752 Z= 0.308 Chirality : 0.044 0.232 3975 Planarity : 0.004 0.053 4443 Dihedral : 9.716 86.621 3846 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: -1.00 (0.15), residues: 3121 helix: 0.62 (0.16), residues: 1094 sheet: -0.58 (0.26), residues: 373 loop : -1.61 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 77 TYR 0.019 0.001 TYR C 26 PHE 0.011 0.001 PHE C1270 TRP 0.090 0.003 TRP C1276 HIS 0.011 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00256 (25625) covalent geometry : angle 0.60576 (34740) hydrogen bonds : bond 0.03557 ( 986) hydrogen bonds : angle 4.97954 ( 2770) metal coordination : bond 0.00433 ( 8) metal coordination : angle 2.39204 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3712.03 seconds wall clock time: 65 minutes 17.49 seconds (3917.49 seconds total)