Starting phenix.real_space_refine on Sat Feb 7 00:05:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ukn_64250/02_2026/9ukn_64250.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ukn_64250/02_2026/9ukn_64250.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ukn_64250/02_2026/9ukn_64250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ukn_64250/02_2026/9ukn_64250.map" model { file = "/net/cci-nas-00/data/ceres_data/9ukn_64250/02_2026/9ukn_64250.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ukn_64250/02_2026/9ukn_64250.cif" } resolution = 2.97 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= 0.029 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 88 5.49 5 Mg 3 5.21 5 S 70 5.16 5 C 17733 2.51 5 N 5058 2.21 5 O 5494 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28448 Number of models: 1 Model: "" Number of chains: 10 Chain: "G" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 859 Classifications: {'DNA': 42} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 41} Chain breaks: 1 Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1767 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 209} Chain: "C" Number of atoms: 8783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1113, 8783 Classifications: {'peptide': 1113} Link IDs: {'PCIS': 1, 'PTRANS': 71, 'TRANS': 1040} Chain breaks: 1 Chain: "D" Number of atoms: 10744 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1360, 10733 Classifications: {'peptide': 1360} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1291} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1360, 10733 Classifications: {'peptide': 1360} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1291} Chain breaks: 2 bond proxies already assigned to first conformer: 10904 Chain: "E" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 761 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 6, 'TRANS': 87} Chain: "F" Number of atoms: 2741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2741 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 13, 'TRANS': 324} Chain breaks: 1 Chain: "H" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 987 Classifications: {'DNA': 48} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 47} Chain: "A" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1772 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 210} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 33 Unusual residues: {' MG': 2, ' ZN': 2, '1N7': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19245 SG CYS D1112 21.943 60.454 120.451 1.00 37.03 S ATOM 19889 SG CYS D1194 25.986 60.367 119.544 1.00 22.39 S ATOM 19945 SG CYS D1201 24.548 62.054 122.499 1.00 28.53 S ATOM 19969 SG CYS D1204 24.821 58.929 122.734 1.00 40.00 S ATOM 11878 SG CYS D 58 54.382 105.292 82.759 1.00 78.44 S ATOM 11889 SG CYS D 60 55.477 105.179 79.643 1.00 73.02 S ATOM 12000 SG CYS D 73 52.081 105.354 79.233 1.00 75.79 S ATOM 12026 SG CYS D 76 53.879 102.342 79.711 1.00 80.08 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG D1096 " occ=0.65 ... (20 atoms not shown) pdb=" NH2BARG D1096 " occ=0.35 Time building chain proxies: 8.21, per 1000 atoms: 0.29 Number of scatterers: 28448 At special positions: 0 Unit cell: (131.664, 157.828, 206.78, 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 70 16.00 P 88 15.00 Mg 3 11.99 O 5494 8.00 N 5058 7.00 C 17733 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: 2.49 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1601 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1112 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1201 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1204 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1194 " pdb=" ZN D1602 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 60 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 73 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 58 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 76 " Number of angles added : 12 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6212 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 52 sheets defined 43.8% alpha, 17.8% beta 24 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 3.78 Creating SS restraints... Processing helix chain 'B' and resid 31 through 47 removed outlier: 3.512A pdb=" N THR B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Proline residue: B 39 - end of helix removed outlier: 3.511A pdb=" N SER B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 83 Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 152 through 157 removed outlier: 3.705A pdb=" N HIS B 156 " --> pdb=" O PRO B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 223 removed outlier: 3.593A pdb=" N THR B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 31 removed outlier: 3.829A pdb=" N SER C 25 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR C 26 " --> pdb=" O GLN C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 39 removed outlier: 3.530A pdb=" N ARG C 39 " --> pdb=" O PRO C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 52 removed outlier: 3.536A pdb=" N ALA C 47 " --> pdb=" O GLY C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 87 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 203 through 212 Processing helix chain 'C' and resid 217 through 222 Processing helix chain 'C' and resid 223 through 229 removed outlier: 3.520A pdb=" N MET C 229 " --> pdb=" O SER C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 243 Processing helix chain 'C' and resid 249 through 262 Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 302 through 316 Processing helix chain 'C' and resid 335 through 360 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 375 through 388 Processing helix chain 'C' and resid 399 through 407 removed outlier: 3.545A pdb=" N SER C 403 " --> pdb=" O ASN C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 429 Processing helix chain 'C' and resid 431 through 435 removed outlier: 3.760A pdb=" N TYR C 435 " --> pdb=" O ARG C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 525 through 529 Processing helix chain 'C' and resid 535 through 540 Processing helix chain 'C' and resid 543 through 547 removed outlier: 3.668A pdb=" N LEU C 546 " --> pdb=" O ASN C 543 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE C 547 " --> pdb=" O THR C 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 543 through 547' Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 554 through 565 removed outlier: 3.951A pdb=" N MET C 560 " --> pdb=" O ASN C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 568 No H-bonds generated for 'chain 'C' and resid 566 through 568' Processing helix chain 'C' and resid 583 through 591 removed outlier: 3.732A pdb=" N VAL C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 687 removed outlier: 3.657A pdb=" N ASP C 686 " --> pdb=" O ASN C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 697 Processing helix chain 'C' and resid 768 through 779 Processing helix chain 'C' and resid 874 through 880 removed outlier: 4.580A pdb=" N SER C 878 " --> pdb=" O LEU C 874 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG C 879 " --> pdb=" O GLY C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 898 removed outlier: 3.560A pdb=" N PHE C 896 " --> pdb=" O LEU C 892 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 933 removed outlier: 3.624A pdb=" N GLU C 923 " --> pdb=" O ALA C 919 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL C 924 " --> pdb=" O GLN C 920 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS C 928 " --> pdb=" O VAL C 924 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ARG C 929 " --> pdb=" O TYR C 925 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY C 933 " --> pdb=" O ARG C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 950 Processing helix chain 'C' and resid 958 through 969 removed outlier: 3.502A pdb=" N GLN C 969 " --> pdb=" O GLU C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1004 Processing helix chain 'C' and resid 1033 through 1044 Processing helix chain 'C' and resid 1045 through 1054 Processing helix chain 'C' and resid 1059 through 1072 Processing helix chain 'C' and resid 1082 through 1094 removed outlier: 3.664A pdb=" N ARG C1086 " --> pdb=" O PRO C1082 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 46 through 51 Processing helix chain 'D' and resid 82 through 88 removed outlier: 3.636A pdb=" N VAL D 85 " --> pdb=" O LYS D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 105 Processing helix chain 'D' and resid 110 through 117 Processing helix chain 'D' and resid 119 through 128 Processing helix chain 'D' and resid 154 through 164 Processing helix chain 'D' and resid 372 through 376 Processing helix chain 'D' and resid 457 through 468 removed outlier: 3.515A pdb=" N GLN D 463 " --> pdb=" O GLU D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 481 Processing helix chain 'D' and resid 485 through 506 removed outlier: 3.610A pdb=" N ARG D 495 " --> pdb=" O LYS D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 511 Processing helix chain 'D' and resid 521 through 525 Processing helix chain 'D' and resid 538 through 560 removed outlier: 4.285A pdb=" N ASP D 542 " --> pdb=" O SER D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 583 Processing helix chain 'D' and resid 602 through 608 removed outlier: 3.523A pdb=" N LEU D 607 " --> pdb=" O LEU D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 618 removed outlier: 3.565A pdb=" N LEU D 618 " --> pdb=" O PHE D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 653 removed outlier: 3.580A pdb=" N GLU D 651 " --> pdb=" O ARG D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 664 Processing helix chain 'D' and resid 669 through 679 removed outlier: 3.521A pdb=" N GLU D 678 " --> pdb=" O ARG D 674 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG D 679 " --> pdb=" O ARG D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 683 removed outlier: 3.775A pdb=" N ILE D 683 " --> pdb=" O GLN D 680 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 680 through 683' Processing helix chain 'D' and resid 685 through 695 removed outlier: 3.834A pdb=" N ASP D 689 " --> pdb=" O ASP D 685 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE D 695 " --> pdb=" O LEU D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 711 No H-bonds generated for 'chain 'D' and resid 709 through 711' Processing helix chain 'D' and resid 729 through 731 No H-bonds generated for 'chain 'D' and resid 729 through 731' Processing helix chain 'D' and resid 732 through 737 Processing helix chain 'D' and resid 752 through 762 Processing helix chain 'D' and resid 782 through 794 removed outlier: 3.553A pdb=" N ILE D 792 " --> pdb=" O GLY D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 808 through 819 removed outlier: 3.529A pdb=" N ALA D 812 " --> pdb=" O THR D 808 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 841 Processing helix chain 'D' and resid 845 through 855 Processing helix chain 'D' and resid 876 through 891 Processing helix chain 'D' and resid 892 through 900 removed outlier: 3.765A pdb=" N GLU D 898 " --> pdb=" O LYS D 894 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 907 through 922 Processing helix chain 'D' and resid 923 through 946 removed outlier: 3.868A pdb=" N THR D 944 " --> pdb=" O THR D 940 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLY D 946 " --> pdb=" O SER D 942 " (cutoff:3.500A) Processing helix chain 'D' and resid 950 through 954 Processing helix chain 'D' and resid 958 through 980 removed outlier: 4.329A pdb=" N GLN D 962 " --> pdb=" O GLU D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 984 through 1015 Processing helix chain 'D' and resid 1018 through 1026 Processing helix chain 'D' and resid 1031 through 1040 Processing helix chain 'D' and resid 1066 through 1102 removed outlier: 3.823A pdb=" N HIS D1075 " --> pdb=" O PHE D1071 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY D1076 " --> pdb=" O ILE D1072 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA D1077 " --> pdb=" O SER D1073 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA D1089 " --> pdb=" O ALA D1085 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP D1090 " --> pdb=" O LEU D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 1136 through 1145 Processing helix chain 'D' and resid 1167 through 1180 Processing helix chain 'D' and resid 1190 through 1194 Processing helix chain 'D' and resid 1202 through 1206 Processing helix chain 'D' and resid 1220 through 1231 removed outlier: 3.544A pdb=" N VAL D1224 " --> pdb=" O ALA D1220 " (cutoff:3.500A) Processing helix chain 'D' and resid 1232 through 1236 Processing helix chain 'D' and resid 1255 through 1264 Processing helix chain 'D' and resid 1331 through 1339 Processing helix chain 'D' and resid 1340 through 1359 removed outlier: 3.755A pdb=" N VAL D1355 " --> pdb=" O GLU D1351 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR D1356 " --> pdb=" O ILE D1352 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN D1359 " --> pdb=" O VAL D1355 " (cutoff:3.500A) Processing helix chain 'D' and resid 1364 through 1376 removed outlier: 4.195A pdb=" N ILE D1368 " --> pdb=" O HIS D1364 " (cutoff:3.500A) Processing helix chain 'D' and resid 1397 through 1410 Processing helix chain 'D' and resid 1423 through 1430 Processing helix chain 'D' and resid 1433 through 1441 removed outlier: 3.515A pdb=" N GLN D1441 " --> pdb=" O ALA D1437 " (cutoff:3.500A) Processing helix chain 'D' and resid 1442 through 1454 removed outlier: 3.611A pdb=" N ALA D1453 " --> pdb=" O GLU D1449 " (cutoff:3.500A) Processing helix chain 'D' and resid 1461 through 1469 removed outlier: 4.206A pdb=" N ASN D1465 " --> pdb=" O GLY D1461 " (cutoff:3.500A) Processing helix chain 'D' and resid 1474 through 1478 Processing helix chain 'D' and resid 1489 through 1499 Processing helix chain 'E' and resid 5 through 11 Processing helix chain 'E' and resid 15 through 33 removed outlier: 3.582A pdb=" N THR E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 71 removed outlier: 3.545A pdb=" N TRP E 63 " --> pdb=" O ASN E 59 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY E 71 " --> pdb=" O GLU E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 93 Processing helix chain 'F' and resid 79 through 89 Processing helix chain 'F' and resid 95 through 121 Processing helix chain 'F' and resid 123 through 137 Processing helix chain 'F' and resid 138 through 140 No H-bonds generated for 'chain 'F' and resid 138 through 140' Processing helix chain 'F' and resid 152 through 165 Processing helix chain 'F' and resid 167 through 190 removed outlier: 4.690A pdb=" N TYR F 173 " --> pdb=" O GLU F 169 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU F 174 " --> pdb=" O HIS F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 200 removed outlier: 3.869A pdb=" N VAL F 195 " --> pdb=" O ASN F 191 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL F 196 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 203 No H-bonds generated for 'chain 'F' and resid 201 through 203' Processing helix chain 'F' and resid 208 through 227 removed outlier: 3.658A pdb=" N GLU F 225 " --> pdb=" O ILE F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 232 removed outlier: 3.602A pdb=" N ARG F 231 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 255 removed outlier: 3.735A pdb=" N TYR F 238 " --> pdb=" O LYS F 234 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TRP F 241 " --> pdb=" O THR F 237 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TRP F 242 " --> pdb=" O TYR F 238 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE F 251 " --> pdb=" O ILE F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 283 removed outlier: 3.724A pdb=" N GLN F 279 " --> pdb=" O ALA F 275 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN F 280 " --> pdb=" O ARG F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 296 removed outlier: 3.542A pdb=" N GLY F 296 " --> pdb=" O ALA F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 311 Processing helix chain 'F' and resid 328 through 333 removed outlier: 3.742A pdb=" N ILE F 333 " --> pdb=" O GLY F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 360 removed outlier: 3.643A pdb=" N LYS F 360 " --> pdb=" O LYS F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 373 Processing helix chain 'F' and resid 382 through 391 Processing helix chain 'F' and resid 395 through 416 Processing helix chain 'F' and resid 419 through 423 removed outlier: 4.123A pdb=" N ASP F 423 " --> pdb=" O ASP F 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 47 removed outlier: 3.709A pdb=" N THR A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 74 through 83 Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 152 through 157 removed outlier: 3.610A pdb=" N HIS A 156 " --> pdb=" O PRO A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 223 removed outlier: 3.623A pdb=" N THR A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing sheet with id=AA1, first strand: chain 'B' and resid 10 through 16 removed outlier: 3.745A pdb=" N TYR B 20 " --> pdb=" O GLN B 16 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASP B 193 " --> pdb=" O PRO B 27 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N THR B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU B 186 " --> pdb=" O THR B 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 104 removed outlier: 3.590A pdb=" N ALA B 103 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER B 55 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP B 145 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N VAL B 53 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLY B 147 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N THR B 51 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'B' and resid 108 through 110 removed outlier: 6.979A pdb=" N VAL B 109 " --> pdb=" O ILE B 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 150 through 151 Processing sheet with id=AA6, first strand: chain 'C' and resid 2 through 5 Processing sheet with id=AA7, first strand: chain 'C' and resid 54 through 55 removed outlier: 5.426A pdb=" N LEU C 66 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE C 101 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N PHE C 68 " --> pdb=" O GLN C 99 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLN C 99 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU C 70 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ALA C 92 " --> pdb=" O HIS C 117 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N HIS C 117 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU C 94 " --> pdb=" O LEU C 115 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AA9, first strand: chain 'C' and resid 331 through 334 removed outlier: 6.382A pdb=" N SER C 138 " --> pdb=" O SER C 411 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 145 through 150 removed outlier: 6.964A pdb=" N TYR C 158 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL C 176 " --> pdb=" O TYR C 158 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 291 through 293 Processing sheet with id=AB3, first strand: chain 'C' and resid 460 through 461 removed outlier: 5.308A pdb=" N GLU C 482 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL C 475 " --> pdb=" O THR C 480 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR C 480 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 460 through 461 Processing sheet with id=AB5, first strand: chain 'C' and resid 495 through 497 Processing sheet with id=AB6, first strand: chain 'C' and resid 503 through 504 removed outlier: 4.138A pdb=" N ARG C 507 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 595 through 596 removed outlier: 6.516A pdb=" N LEU C 595 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 620 through 624 removed outlier: 6.809A pdb=" N ARG C 610 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL C 606 " --> pdb=" O ARG C 610 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL C 612 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 629 through 630 Processing sheet with id=AC1, first strand: chain 'C' and resid 661 through 662 Processing sheet with id=AC2, first strand: chain 'C' and resid 971 through 972 removed outlier: 6.996A pdb=" N ILE C 688 " --> pdb=" O ALA C 850 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE C 852 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE C 690 " --> pdb=" O ILE C 852 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL C 689 " --> pdb=" O ILE C 870 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N VAL C 869 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU C 673 " --> pdb=" O VAL C 869 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N LEU C 871 " --> pdb=" O LEU C 673 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA C 675 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL C 988 " --> pdb=" O ILE C 676 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 702 through 713 removed outlier: 3.636A pdb=" N ARG C 802 " --> pdb=" O TYR C 826 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA C 828 " --> pdb=" O VAL C 800 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL C 800 " --> pdb=" O ALA C 828 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N LYS C 830 " --> pdb=" O GLY C 798 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N GLY C 798 " --> pdb=" O LYS C 830 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 721 through 722 Processing sheet with id=AC5, first strand: chain 'C' and resid 754 through 756 removed outlier: 6.804A pdb=" N LEU C 790 " --> pdb=" O LEU C 755 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1006 through 1008 Processing sheet with id=AC7, first strand: chain 'C' and resid 1030 through 1032 removed outlier: 3.635A pdb=" N GLN C1030 " --> pdb=" O VAL D 623 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1097 through 1102 Processing sheet with id=AC9, first strand: chain 'D' and resid 22 through 25 removed outlier: 7.711A pdb=" N HIS D 92 " --> pdb=" O TYR D 23 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU D 25 " --> pdb=" O HIS D 92 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLU D 94 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 10.037A pdb=" N LEU D 95 " --> pdb=" O PRO D 518 " (cutoff:3.500A) removed outlier: 10.836A pdb=" N THR D 97 " --> pdb=" O ALA D 516 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ALA D 516 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 71 through 72 removed outlier: 4.170A pdb=" N LYS D 71 " --> pdb=" O VAL D 80 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 152 through 153 removed outlier: 6.782A pdb=" N ASP D 453 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AD4, first strand: chain 'D' and resid 166 through 170 removed outlier: 3.747A pdb=" N GLU D 183 " --> pdb=" O ALA D 203 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 342 through 346 Processing sheet with id=AD6, first strand: chain 'D' and resid 342 through 346 removed outlier: 3.506A pdb=" N ARG D 210 " --> pdb=" O HIS D 388 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 366 through 368 removed outlier: 6.978A pdb=" N VAL D 377 " --> pdb=" O ILE D 367 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 398 through 402 removed outlier: 3.865A pdb=" N ASP D 413 " --> pdb=" O VAL D 435 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 420 through 422 removed outlier: 7.098A pdb=" N VAL D 427 " --> pdb=" O LEU D 421 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 527 through 529 removed outlier: 6.332A pdb=" N PHE D 535 " --> pdb=" O VAL F 315 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 827 through 828 Processing sheet with id=AE3, first strand: chain 'D' and resid 842 through 843 Processing sheet with id=AE4, first strand: chain 'D' and resid 1106 through 1109 Processing sheet with id=AE5, first strand: chain 'D' and resid 1118 through 1121 Processing sheet with id=AE6, first strand: chain 'D' and resid 1123 through 1126 Processing sheet with id=AE7, first strand: chain 'D' and resid 1153 through 1155 Processing sheet with id=AE8, first strand: chain 'D' and resid 1300 through 1305 removed outlier: 4.244A pdb=" N LEU D1290 " --> pdb=" O LEU D1305 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1394 through 1396 removed outlier: 6.731A pdb=" N ALA D1416 " --> pdb=" O THR D1382 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1485 through 1488 Processing sheet with id=AF2, first strand: chain 'E' and resid 47 through 49 Processing sheet with id=AF3, first strand: chain 'A' and resid 10 through 16 removed outlier: 3.582A pdb=" N GLU A 26 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR A 20 " --> pdb=" O GLN A 16 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ASP A 193 " --> pdb=" O PRO A 27 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N THR A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU A 186 " --> pdb=" O THR A 190 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 96 through 104 removed outlier: 7.262A pdb=" N ASN A 139 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE A 58 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLU A 141 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL A 56 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ARG A 143 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AF6, first strand: chain 'A' and resid 107 through 110 Processing sheet with id=AF7, first strand: chain 'A' and resid 150 through 151 1228 hydrogen bonds defined for protein. 3433 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 8.13 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4690 1.31 - 1.43: 7458 1.43 - 1.56: 16687 1.56 - 1.68: 180 1.68 - 1.81: 127 Bond restraints: 29142 Sorted by residual: bond pdb=" CA GLN D 529 " pdb=" C GLN D 529 " ideal model delta sigma weight residual 1.525 1.483 0.042 1.29e-02 6.01e+03 1.08e+01 bond pdb=" C23 1N7 D1605 " pdb=" C24 1N7 D1605 " ideal model delta sigma weight residual 1.512 1.574 -0.062 2.00e-02 2.50e+03 9.69e+00 bond pdb=" N VAL B 142 " pdb=" CA VAL B 142 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.22e-02 6.72e+03 8.78e+00 bond pdb=" N ILE C 611 " pdb=" CA ILE C 611 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.19e-02 7.06e+03 8.03e+00 bond pdb=" N VAL C 612 " pdb=" CA VAL C 612 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.24e-02 6.50e+03 7.42e+00 ... (remaining 29137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 39329 1.84 - 3.68: 447 3.68 - 5.52: 23 5.52 - 7.35: 4 7.35 - 9.19: 1 Bond angle restraints: 39804 Sorted by residual: angle pdb=" N VAL D 528 " pdb=" CA VAL D 528 " pdb=" C VAL D 528 " ideal model delta sigma weight residual 109.45 116.15 -6.70 1.39e+00 5.18e-01 2.32e+01 angle pdb=" N GLY D 532 " pdb=" CA GLY D 532 " pdb=" C GLY D 532 " ideal model delta sigma weight residual 113.18 103.99 9.19 2.37e+00 1.78e-01 1.50e+01 angle pdb=" CA GLU D1109 " pdb=" C GLU D1109 " pdb=" O GLU D1109 " ideal model delta sigma weight residual 121.36 117.48 3.88 1.06e+00 8.90e-01 1.34e+01 angle pdb=" CA GLY B 136 " pdb=" C GLY B 136 " pdb=" O GLY B 136 " ideal model delta sigma weight residual 121.41 118.21 3.20 8.80e-01 1.29e+00 1.32e+01 angle pdb=" CA GLU B 133 " pdb=" C GLU B 133 " pdb=" O GLU B 133 " ideal model delta sigma weight residual 121.94 117.93 4.01 1.15e+00 7.56e-01 1.21e+01 ... (remaining 39799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.03: 16569 26.03 - 52.07: 959 52.07 - 78.10: 199 78.10 - 104.13: 18 104.13 - 130.17: 1 Dihedral angle restraints: 17746 sinusoidal: 8093 harmonic: 9653 Sorted by residual: dihedral pdb=" C4' DT H 2 " pdb=" C3' DT H 2 " pdb=" O3' DT H 2 " pdb=" P DT H 3 " ideal model delta sinusoidal sigma weight residual 220.00 89.83 130.17 1 3.50e+01 8.16e-04 1.29e+01 dihedral pdb=" CA ASN D 569 " pdb=" CB ASN D 569 " pdb=" CG ASN D 569 " pdb=" OD1 ASN D 569 " ideal model delta sinusoidal sigma weight residual -90.00 -162.39 72.39 2 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA ASP D 685 " pdb=" CB ASP D 685 " pdb=" CG ASP D 685 " pdb=" OD1 ASP D 685 " ideal model delta sinusoidal sigma weight residual -30.00 -86.88 56.88 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 17743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3534 0.045 - 0.090: 652 0.090 - 0.135: 290 0.135 - 0.180: 10 0.180 - 0.225: 3 Chirality restraints: 4489 Sorted by residual: chirality pdb=" CA ILE C 611 " pdb=" N ILE C 611 " pdb=" C ILE C 611 " pdb=" CB ILE C 611 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA MET D 527 " pdb=" N MET D 527 " pdb=" C MET D 527 " pdb=" CB MET D 527 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C20 1N7 D1605 " pdb=" C21 1N7 D1605 " pdb=" C22 1N7 D1605 " pdb=" C9 1N7 D1605 " both_signs ideal model delta sigma weight residual False 2.59 2.79 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 4486 not shown) Planarity restraints: 4893 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D1231 " 0.058 5.00e-02 4.00e+02 8.90e-02 1.27e+01 pdb=" N PRO D1232 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO D1232 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO D1232 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD AARG D1096 " -0.203 9.50e-02 1.11e+02 9.10e-02 5.24e+00 pdb=" NE AARG D1096 " 0.014 2.00e-02 2.50e+03 pdb=" CZ AARG D1096 " -0.005 2.00e-02 2.50e+03 pdb=" NH1AARG D1096 " 0.004 2.00e-02 2.50e+03 pdb=" NH2AARG D1096 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 394 " 0.188 9.50e-02 1.11e+02 8.43e-02 4.43e+00 pdb=" NE ARG F 394 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG F 394 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG F 394 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG F 394 " 0.005 2.00e-02 2.50e+03 ... (remaining 4890 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 124 2.54 - 3.13: 21530 3.13 - 3.72: 41232 3.72 - 4.31: 62236 4.31 - 4.90: 104943 Nonbonded interactions: 230065 Sorted by model distance: nonbonded pdb=" OD1 ASP D 739 " pdb="MG MG D1603 " model vdw 1.955 2.170 nonbonded pdb=" OD1 ASP D 741 " pdb="MG MG D1603 " model vdw 2.136 2.170 nonbonded pdb=" O VAL E 39 " pdb=" NH1 ARG E 72 " model vdw 2.218 3.120 nonbonded pdb=" OE1 GLU D 898 " pdb=" NH2 ARG D 921 " model vdw 2.223 3.120 nonbonded pdb=" NZ LYS B 83 " pdb=" OE2 GLU D 848 " model vdw 2.224 3.120 ... (remaining 230060 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 229) 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=0.05 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 37.480 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:6.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 29150 Z= 0.158 Angle : 0.531 23.851 39816 Z= 0.260 Chirality : 0.041 0.225 4489 Planarity : 0.004 0.091 4893 Dihedral : 15.979 130.166 11534 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.77 % Favored : 98.20 % Rotamer: Outliers : 0.10 % Allowed : 7.73 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.15), residues: 3337 helix: 1.12 (0.15), residues: 1255 sheet: 0.37 (0.25), residues: 445 loop : 0.26 (0.16), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 345 TYR 0.009 0.001 TYR C 998 PHE 0.018 0.001 PHE C 425 TRP 0.014 0.001 TRP F 242 HIS 0.005 0.001 HIS C 434 Details of bonding type rmsd covalent geometry : bond 0.00302 (29142) covalent geometry : angle 0.45332 (39804) hydrogen bonds : bond 0.24311 ( 1282) hydrogen bonds : angle 7.79253 ( 3553) metal coordination : bond 0.01166 ( 8) metal coordination : angle 15.90501 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 162 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 165 average time/residue: 1.0768 time to fit residues: 198.0975 Evaluate side-chains 92 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 ASN C 99 GLN C 141 HIS C 834 GLN D 569 ASN D 724 GLN D 901 GLN D 976 GLN D1031 ASN D1441 GLN E 86 GLN F 381 HIS A 180 GLN A 229 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.049763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.034829 restraints weight = 169093.198| |-----------------------------------------------------------------------------| r_work (start): 0.2555 rms_B_bonded: 3.92 r_work: 0.2393 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2379 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2379 r_free = 0.2379 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2379 r_free = 0.2379 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29150 Z= 0.140 Angle : 0.579 9.082 39816 Z= 0.307 Chirality : 0.043 0.152 4489 Planarity : 0.004 0.059 4893 Dihedral : 15.248 135.845 4789 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.62 % Favored : 98.35 % Rotamer: Outliers : 0.84 % Allowed : 9.30 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % 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: 1.28 (0.15), residues: 3337 helix: 1.62 (0.14), residues: 1310 sheet: 0.60 (0.25), residues: 424 loop : 0.40 (0.16), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 360 TYR 0.022 0.001 TYR D 791 PHE 0.013 0.001 PHE F 389 TRP 0.011 0.001 TRP B 200 HIS 0.007 0.001 HIS F 381 Details of bonding type rmsd covalent geometry : bond 0.00313 (29142) covalent geometry : angle 0.57473 (39804) hydrogen bonds : bond 0.05252 ( 1282) hydrogen bonds : angle 4.96538 ( 3553) metal coordination : bond 0.00707 ( 8) metal coordination : angle 3.88015 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 222 MET cc_start: 0.8404 (mtm) cc_final: 0.7884 (mpp) REVERT: C 419 THR cc_start: 0.9003 (OUTLIER) cc_final: 0.8669 (p) REVERT: A 180 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8609 (tt0) outliers start: 24 outliers final: 2 residues processed: 118 average time/residue: 0.9236 time to fit residues: 124.3595 Evaluate side-chains 92 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain D residue 980 MET Chi-restraints excluded: chain A residue 180 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 261 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 254 optimal weight: 1.9990 chunk 304 optimal weight: 7.9990 chunk 255 optimal weight: 0.0980 chunk 340 optimal weight: 5.9990 chunk 158 optimal weight: 0.1980 chunk 258 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.048384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.033312 restraints weight = 198369.086| |-----------------------------------------------------------------------------| r_work (start): 0.2502 rms_B_bonded: 4.19 r_work: 0.2330 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2346 r_free = 0.2346 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2346 r_free = 0.2346 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 29150 Z= 0.182 Angle : 0.529 8.571 39816 Z= 0.280 Chirality : 0.042 0.149 4489 Planarity : 0.004 0.044 4893 Dihedral : 15.252 136.784 4789 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.74 % Favored : 98.23 % Rotamer: Outliers : 0.59 % Allowed : 9.79 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % 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: 1.49 (0.15), residues: 3337 helix: 1.94 (0.15), residues: 1314 sheet: 0.61 (0.25), residues: 422 loop : 0.39 (0.16), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG F 416 TYR 0.013 0.001 TYR D 791 PHE 0.020 0.001 PHE A 179 TRP 0.009 0.001 TRP B 200 HIS 0.005 0.001 HIS F 381 Details of bonding type rmsd covalent geometry : bond 0.00423 (29142) covalent geometry : angle 0.52594 (39804) hydrogen bonds : bond 0.04749 ( 1282) hydrogen bonds : angle 4.59155 ( 3553) metal coordination : bond 0.01077 ( 8) metal coordination : angle 3.54023 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 7 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8533 (ptmm) REVERT: C 121 MET cc_start: 0.9224 (ttm) cc_final: 0.8999 (ttp) REVERT: C 222 MET cc_start: 0.8640 (mtm) cc_final: 0.8099 (mpp) REVERT: C 419 THR cc_start: 0.9110 (OUTLIER) cc_final: 0.8783 (p) REVERT: E 50 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8503 (p) REVERT: A 180 GLN cc_start: 0.8809 (tt0) cc_final: 0.8455 (tt0) REVERT: A 201 THR cc_start: 0.9544 (OUTLIER) cc_final: 0.9254 (t) outliers start: 17 outliers final: 3 residues processed: 100 average time/residue: 0.8475 time to fit residues: 97.9407 Evaluate side-chains 92 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain D residue 1207 TYR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain A residue 201 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 205 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 322 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 240 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 272 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 263 HIS A 180 GLN A 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.049295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.034471 restraints weight = 171281.747| |-----------------------------------------------------------------------------| r_work (start): 0.2557 rms_B_bonded: 3.94 r_work: 0.2394 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2381 r_free = 0.2381 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2381 r_free = 0.2381 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 29150 Z= 0.103 Angle : 0.482 8.099 39816 Z= 0.255 Chirality : 0.041 0.147 4489 Planarity : 0.004 0.041 4893 Dihedral : 15.104 135.708 4789 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.56 % Favored : 98.41 % Rotamer: Outliers : 0.80 % Allowed : 10.07 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % 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: 1.64 (0.15), residues: 3337 helix: 2.12 (0.15), residues: 1307 sheet: 0.71 (0.25), residues: 429 loop : 0.43 (0.16), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 209 TYR 0.012 0.001 TYR D 989 PHE 0.009 0.001 PHE B 179 TRP 0.009 0.001 TRP B 200 HIS 0.003 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00231 (29142) covalent geometry : angle 0.48037 (39804) hydrogen bonds : bond 0.03590 ( 1282) hydrogen bonds : angle 4.28359 ( 3553) metal coordination : bond 0.00577 ( 8) metal coordination : angle 2.43341 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 1.066 Fit side-chains revert: symmetry clash REVERT: B 123 MET cc_start: 0.9455 (tpp) cc_final: 0.9051 (mmt) REVERT: C 121 MET cc_start: 0.9212 (ttm) cc_final: 0.8986 (ttp) REVERT: C 222 MET cc_start: 0.8701 (mtm) cc_final: 0.8207 (mpp) REVERT: C 340 MET cc_start: 0.9517 (OUTLIER) cc_final: 0.8971 (tmm) REVERT: C 390 GLN cc_start: 0.9384 (tt0) cc_final: 0.8825 (tm-30) REVERT: F 324 GLU cc_start: 0.9580 (mp0) cc_final: 0.9364 (pm20) REVERT: A 180 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: A 201 THR cc_start: 0.9486 (OUTLIER) cc_final: 0.9267 (t) outliers start: 23 outliers final: 6 residues processed: 104 average time/residue: 0.8246 time to fit residues: 99.6997 Evaluate side-chains 94 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain C residue 361 MET Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain D residue 980 MET Chi-restraints excluded: chain D residue 1207 TYR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 201 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 211 optimal weight: 6.9990 chunk 271 optimal weight: 0.8980 chunk 174 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 chunk 261 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 264 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 253 optimal weight: 9.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN A 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.049100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.034111 restraints weight = 199070.102| |-----------------------------------------------------------------------------| r_work (start): 0.2548 rms_B_bonded: 4.22 r_work: 0.2379 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2369 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2369 r_free = 0.2369 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2369 r_free = 0.2369 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2369 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29150 Z= 0.111 Angle : 0.473 8.099 39816 Z= 0.250 Chirality : 0.040 0.140 4489 Planarity : 0.004 0.041 4893 Dihedral : 15.050 135.176 4789 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.80 % Allowed : 10.14 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % 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: 1.72 (0.15), residues: 3337 helix: 2.22 (0.15), residues: 1309 sheet: 0.73 (0.25), residues: 423 loop : 0.45 (0.16), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 900 TYR 0.011 0.001 TYR D 989 PHE 0.007 0.001 PHE C 227 TRP 0.008 0.001 TRP B 200 HIS 0.003 0.001 HIS F 381 Details of bonding type rmsd covalent geometry : bond 0.00252 (29142) covalent geometry : angle 0.47153 (39804) hydrogen bonds : bond 0.03538 ( 1282) hydrogen bonds : angle 4.19270 ( 3553) metal coordination : bond 0.00597 ( 8) metal coordination : angle 2.35076 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 1.178 Fit side-chains revert: symmetry clash REVERT: B 123 MET cc_start: 0.9475 (tpp) cc_final: 0.9020 (mmt) REVERT: C 121 MET cc_start: 0.9241 (ttm) cc_final: 0.9015 (ttp) REVERT: C 222 MET cc_start: 0.8672 (mtm) cc_final: 0.8205 (mpp) REVERT: C 390 GLN cc_start: 0.9358 (tt0) cc_final: 0.8804 (tm-30) REVERT: C 419 THR cc_start: 0.9131 (OUTLIER) cc_final: 0.8812 (p) REVERT: C 858 MET cc_start: 0.9479 (OUTLIER) cc_final: 0.8596 (mmm) REVERT: D 576 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8588 (tm-30) REVERT: E 50 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8586 (p) REVERT: F 324 GLU cc_start: 0.9582 (mp0) cc_final: 0.9305 (pm20) REVERT: A 180 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8632 (tt0) REVERT: A 201 THR cc_start: 0.9491 (OUTLIER) cc_final: 0.9252 (t) outliers start: 23 outliers final: 5 residues processed: 102 average time/residue: 0.8201 time to fit residues: 97.1162 Evaluate side-chains 95 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 858 MET Chi-restraints excluded: chain D residue 1207 TYR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 201 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 132 optimal weight: 0.0370 chunk 230 optimal weight: 4.9990 chunk 160 optimal weight: 0.2980 chunk 122 optimal weight: 3.9990 chunk 269 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 182 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 240 optimal weight: 0.9980 chunk 335 optimal weight: 0.9980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 976 GLN A 180 GLN A 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.049611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.035009 restraints weight = 149343.736| |-----------------------------------------------------------------------------| r_work (start): 0.2582 rms_B_bonded: 3.67 r_work: 0.2428 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2417 r_free = 0.2417 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2417 r_free = 0.2417 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 29150 Z= 0.093 Angle : 0.461 8.455 39816 Z= 0.243 Chirality : 0.040 0.137 4489 Planarity : 0.004 0.041 4893 Dihedral : 14.980 134.370 4789 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.73 % Allowed : 10.28 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % 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: 1.82 (0.15), residues: 3337 helix: 2.29 (0.15), residues: 1310 sheet: 0.81 (0.25), residues: 433 loop : 0.51 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 209 TYR 0.012 0.001 TYR D 989 PHE 0.007 0.001 PHE B 179 TRP 0.008 0.001 TRP B 200 HIS 0.003 0.000 HIS F 381 Details of bonding type rmsd covalent geometry : bond 0.00204 (29142) covalent geometry : angle 0.45971 (39804) hydrogen bonds : bond 0.03207 ( 1282) hydrogen bonds : angle 4.07177 ( 3553) metal coordination : bond 0.00417 ( 8) metal coordination : angle 2.03833 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 1.219 Fit side-chains revert: symmetry clash REVERT: B 123 MET cc_start: 0.9447 (tpp) cc_final: 0.9016 (mmt) REVERT: C 121 MET cc_start: 0.9238 (ttm) cc_final: 0.9014 (ttp) REVERT: C 222 MET cc_start: 0.8684 (mtm) cc_final: 0.8293 (mpp) REVERT: C 361 MET cc_start: 0.8315 (tmm) cc_final: 0.8057 (tmm) REVERT: C 390 GLN cc_start: 0.9319 (tt0) cc_final: 0.8782 (tm-30) REVERT: C 419 THR cc_start: 0.9127 (OUTLIER) cc_final: 0.8803 (p) REVERT: C 560 MET cc_start: 0.9396 (mtp) cc_final: 0.9171 (mtm) REVERT: C 858 MET cc_start: 0.9429 (OUTLIER) cc_final: 0.8573 (mmm) REVERT: D 351 MET cc_start: 0.8998 (mtp) cc_final: 0.8456 (ptm) REVERT: D 576 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8532 (tm-30) REVERT: E 50 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8600 (p) REVERT: F 324 GLU cc_start: 0.9563 (mp0) cc_final: 0.9249 (pm20) REVERT: A 201 THR cc_start: 0.9470 (OUTLIER) cc_final: 0.9244 (t) outliers start: 21 outliers final: 7 residues processed: 104 average time/residue: 0.8736 time to fit residues: 105.4215 Evaluate side-chains 97 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 858 MET Chi-restraints excluded: chain D residue 1207 TYR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 201 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 168 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 211 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 118 optimal weight: 0.0570 chunk 326 optimal weight: 2.9990 chunk 288 optimal weight: 0.2980 chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 overall best weight: 1.6704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1227 GLN A 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.048329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.033576 restraints weight = 178164.965| |-----------------------------------------------------------------------------| r_work (start): 0.2546 rms_B_bonded: 3.97 r_work: 0.2381 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2376 r_free = 0.2376 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2376 r_free = 0.2376 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9014 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29150 Z= 0.137 Angle : 0.477 8.648 39816 Z= 0.251 Chirality : 0.040 0.136 4489 Planarity : 0.004 0.040 4893 Dihedral : 14.978 133.260 4789 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.77 % Allowed : 10.60 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % 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: 1.87 (0.15), residues: 3337 helix: 2.35 (0.15), residues: 1311 sheet: 0.78 (0.25), residues: 424 loop : 0.53 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 416 TYR 0.011 0.001 TYR F 410 PHE 0.008 0.001 PHE D 656 TRP 0.009 0.001 TRP B 200 HIS 0.004 0.001 HIS F 381 Details of bonding type rmsd covalent geometry : bond 0.00319 (29142) covalent geometry : angle 0.47558 (39804) hydrogen bonds : bond 0.03541 ( 1282) hydrogen bonds : angle 4.09204 ( 3553) metal coordination : bond 0.00785 ( 8) metal coordination : angle 2.25535 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 1.272 Fit side-chains revert: symmetry clash REVERT: B 123 MET cc_start: 0.9467 (tpp) cc_final: 0.9038 (mmt) REVERT: C 121 MET cc_start: 0.9285 (ttm) cc_final: 0.9077 (ttp) REVERT: C 222 MET cc_start: 0.8699 (mtm) cc_final: 0.8283 (mpp) REVERT: C 390 GLN cc_start: 0.9310 (tt0) cc_final: 0.8790 (tm-30) REVERT: C 419 THR cc_start: 0.9143 (OUTLIER) cc_final: 0.8810 (p) REVERT: C 837 ASP cc_start: 0.9215 (m-30) cc_final: 0.8859 (m-30) REVERT: C 858 MET cc_start: 0.9498 (OUTLIER) cc_final: 0.8654 (mmm) REVERT: D 351 MET cc_start: 0.9030 (mtp) cc_final: 0.8486 (ptm) REVERT: D 576 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8613 (tm-30) REVERT: F 324 GLU cc_start: 0.9576 (mp0) cc_final: 0.9267 (pm20) REVERT: A 201 THR cc_start: 0.9480 (OUTLIER) cc_final: 0.9211 (t) outliers start: 22 outliers final: 9 residues processed: 103 average time/residue: 0.8488 time to fit residues: 101.4908 Evaluate side-chains 97 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 858 MET Chi-restraints excluded: chain D residue 1207 TYR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 201 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 1 optimal weight: 10.0000 chunk 139 optimal weight: 8.9990 chunk 172 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 275 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 299 optimal weight: 0.9990 chunk 317 optimal weight: 6.9990 chunk 206 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.047697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.033299 restraints weight = 140721.650| |-----------------------------------------------------------------------------| r_work (start): 0.2539 rms_B_bonded: 3.51 r_work: 0.2384 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2384 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2390 r_free = 0.2390 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2390 r_free = 0.2390 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 29150 Z= 0.161 Angle : 0.496 9.806 39816 Z= 0.259 Chirality : 0.041 0.137 4489 Planarity : 0.004 0.043 4893 Dihedral : 14.992 131.458 4789 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.73 % Allowed : 10.74 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % 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: 1.86 (0.15), residues: 3337 helix: 2.36 (0.15), residues: 1312 sheet: 0.74 (0.25), residues: 433 loop : 0.51 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 416 TYR 0.044 0.001 TYR F 410 PHE 0.009 0.001 PHE C 227 TRP 0.009 0.001 TRP B 200 HIS 0.004 0.001 HIS F 381 Details of bonding type rmsd covalent geometry : bond 0.00377 (29142) covalent geometry : angle 0.49418 (39804) hydrogen bonds : bond 0.03717 ( 1282) hydrogen bonds : angle 4.11637 ( 3553) metal coordination : bond 0.00925 ( 8) metal coordination : angle 2.23277 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.9446 (tpp) cc_final: 0.9018 (mmt) REVERT: B 201 THR cc_start: 0.9596 (OUTLIER) cc_final: 0.9302 (t) REVERT: C 222 MET cc_start: 0.8710 (mtm) cc_final: 0.8322 (mpp) REVERT: C 390 GLN cc_start: 0.9291 (tt0) cc_final: 0.8768 (tm-30) REVERT: C 419 THR cc_start: 0.9139 (OUTLIER) cc_final: 0.8805 (p) REVERT: C 560 MET cc_start: 0.9414 (mtp) cc_final: 0.9200 (mtm) REVERT: C 837 ASP cc_start: 0.9190 (m-30) cc_final: 0.8822 (m-30) REVERT: C 858 MET cc_start: 0.9506 (OUTLIER) cc_final: 0.8610 (mmm) REVERT: D 351 MET cc_start: 0.9061 (mtp) cc_final: 0.8520 (ptm) REVERT: D 579 ASP cc_start: 0.8836 (m-30) cc_final: 0.8556 (m-30) REVERT: D 804 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8730 (mp) REVERT: D 987 GLU cc_start: 0.9267 (OUTLIER) cc_final: 0.9052 (pm20) REVERT: F 324 GLU cc_start: 0.9583 (mp0) cc_final: 0.9212 (pm20) REVERT: A 201 THR cc_start: 0.9500 (OUTLIER) cc_final: 0.9213 (t) outliers start: 21 outliers final: 10 residues processed: 104 average time/residue: 0.8206 time to fit residues: 98.8887 Evaluate side-chains 101 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 858 MET Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 987 GLU Chi-restraints excluded: chain D residue 1207 TYR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 201 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 188 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 276 optimal weight: 0.9980 chunk 268 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 340 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 191 optimal weight: 0.0770 chunk 318 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 chunk 304 optimal weight: 4.9990 overall best weight: 2.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.047292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.032948 restraints weight = 134030.100| |-----------------------------------------------------------------------------| r_work (start): 0.2528 rms_B_bonded: 3.42 r_work: 0.2376 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2376 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2378 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2378 r_free = 0.2378 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2378 r_free = 0.2378 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2378 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29150 Z= 0.186 Angle : 0.516 8.924 39816 Z= 0.269 Chirality : 0.041 0.138 4489 Planarity : 0.004 0.046 4893 Dihedral : 15.007 130.084 4789 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.77 % Allowed : 10.74 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % 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: 1.82 (0.15), residues: 3337 helix: 2.33 (0.15), residues: 1319 sheet: 0.61 (0.25), residues: 447 loop : 0.52 (0.16), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 416 TYR 0.038 0.001 TYR F 410 PHE 0.010 0.001 PHE C 227 TRP 0.009 0.001 TRP B 200 HIS 0.004 0.001 HIS F 381 Details of bonding type rmsd covalent geometry : bond 0.00437 (29142) covalent geometry : angle 0.51456 (39804) hydrogen bonds : bond 0.03891 ( 1282) hydrogen bonds : angle 4.15500 ( 3553) metal coordination : bond 0.01073 ( 8) metal coordination : angle 2.31459 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.9423 (tpp) cc_final: 0.8981 (mmt) REVERT: B 201 THR cc_start: 0.9602 (OUTLIER) cc_final: 0.9307 (t) REVERT: C 222 MET cc_start: 0.8714 (mtm) cc_final: 0.8344 (mpp) REVERT: C 361 MET cc_start: 0.8631 (tmm) cc_final: 0.8343 (tmm) REVERT: C 390 GLN cc_start: 0.9303 (tt0) cc_final: 0.8788 (tm-30) REVERT: C 419 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8851 (p) REVERT: C 560 MET cc_start: 0.9434 (mtp) cc_final: 0.9201 (mtm) REVERT: C 837 ASP cc_start: 0.9178 (m-30) cc_final: 0.8816 (m-30) REVERT: C 858 MET cc_start: 0.9519 (OUTLIER) cc_final: 0.8506 (mmm) REVERT: D 351 MET cc_start: 0.9090 (mtp) cc_final: 0.8593 (ptm) REVERT: D 579 ASP cc_start: 0.8847 (m-30) cc_final: 0.8582 (m-30) REVERT: D 804 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8771 (mp) REVERT: D 987 GLU cc_start: 0.9267 (OUTLIER) cc_final: 0.9052 (pm20) REVERT: F 324 GLU cc_start: 0.9582 (mp0) cc_final: 0.9302 (pm20) REVERT: A 201 THR cc_start: 0.9504 (OUTLIER) cc_final: 0.9225 (t) outliers start: 22 outliers final: 8 residues processed: 106 average time/residue: 0.7602 time to fit residues: 92.9192 Evaluate side-chains 101 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 858 MET Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 987 GLU Chi-restraints excluded: chain D residue 1207 TYR Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 163 optimal weight: 0.0870 chunk 292 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 chunk 229 optimal weight: 0.0970 chunk 58 optimal weight: 6.9990 chunk 101 optimal weight: 0.4980 chunk 111 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 294 optimal weight: 5.9990 overall best weight: 1.0758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.048131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.033761 restraints weight = 139899.193| |-----------------------------------------------------------------------------| r_work (start): 0.2556 rms_B_bonded: 3.52 r_work: 0.2397 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2404 r_free = 0.2404 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2404 r_free = 0.2404 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29150 Z= 0.109 Angle : 0.483 8.992 39816 Z= 0.253 Chirality : 0.040 0.135 4489 Planarity : 0.004 0.043 4893 Dihedral : 14.937 129.413 4789 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.52 % Allowed : 11.09 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % 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: 1.89 (0.15), residues: 3337 helix: 2.39 (0.15), residues: 1312 sheet: 0.71 (0.25), residues: 439 loop : 0.56 (0.16), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 209 TYR 0.040 0.001 TYR F 410 PHE 0.008 0.001 PHE C 227 TRP 0.009 0.001 TRP B 200 HIS 0.003 0.001 HIS F 381 Details of bonding type rmsd covalent geometry : bond 0.00252 (29142) covalent geometry : angle 0.48206 (39804) hydrogen bonds : bond 0.03382 ( 1282) hydrogen bonds : angle 4.02312 ( 3553) metal coordination : bond 0.00610 ( 8) metal coordination : angle 1.84492 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.9391 (tpp) cc_final: 0.8991 (mmt) REVERT: B 201 THR cc_start: 0.9592 (OUTLIER) cc_final: 0.9336 (t) REVERT: C 222 MET cc_start: 0.8689 (mtm) cc_final: 0.8361 (mpp) REVERT: C 361 MET cc_start: 0.8665 (tmm) cc_final: 0.8394 (tmm) REVERT: C 390 GLN cc_start: 0.9300 (tt0) cc_final: 0.8766 (tm-30) REVERT: C 419 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8817 (p) REVERT: C 560 MET cc_start: 0.9400 (mtp) cc_final: 0.9189 (mtm) REVERT: C 837 ASP cc_start: 0.9177 (m-30) cc_final: 0.8815 (m-30) REVERT: C 858 MET cc_start: 0.9497 (OUTLIER) cc_final: 0.8597 (mmm) REVERT: D 351 MET cc_start: 0.9083 (mtp) cc_final: 0.8602 (ptm) REVERT: D 579 ASP cc_start: 0.8822 (m-30) cc_final: 0.8567 (m-30) REVERT: D 804 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8763 (mp) REVERT: D 987 GLU cc_start: 0.9248 (OUTLIER) cc_final: 0.9039 (pm20) REVERT: F 324 GLU cc_start: 0.9566 (mp0) cc_final: 0.9167 (pm20) REVERT: A 201 THR cc_start: 0.9492 (OUTLIER) cc_final: 0.9239 (t) outliers start: 15 outliers final: 6 residues processed: 103 average time/residue: 0.8018 time to fit residues: 95.1454 Evaluate side-chains 98 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 858 MET Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 987 GLU Chi-restraints excluded: chain D residue 1207 TYR Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 229 optimal weight: 0.0070 chunk 311 optimal weight: 0.6980 chunk 221 optimal weight: 0.9980 chunk 128 optimal weight: 7.9990 chunk 188 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 152 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 316 optimal weight: 8.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.048560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.034030 restraints weight = 158589.536| |-----------------------------------------------------------------------------| r_work (start): 0.2570 rms_B_bonded: 3.76 r_work: 0.2407 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2407 r_free = 0.2407 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2407 r_free = 0.2407 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 29150 Z= 0.098 Angle : 0.475 9.223 39816 Z= 0.249 Chirality : 0.040 0.133 4489 Planarity : 0.004 0.043 4893 Dihedral : 14.871 128.748 4789 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.49 % Allowed : 11.12 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % 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: 1.95 (0.15), residues: 3337 helix: 2.42 (0.15), residues: 1315 sheet: 0.75 (0.25), residues: 439 loop : 0.60 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 416 TYR 0.039 0.001 TYR F 410 PHE 0.015 0.001 PHE D1440 TRP 0.009 0.001 TRP B 200 HIS 0.007 0.001 HIS D1103 Details of bonding type rmsd covalent geometry : bond 0.00223 (29142) covalent geometry : angle 0.47425 (39804) hydrogen bonds : bond 0.03162 ( 1282) hydrogen bonds : angle 3.94831 ( 3553) metal coordination : bond 0.00480 ( 8) metal coordination : angle 1.84312 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8627.48 seconds wall clock time: 147 minutes 44.16 seconds (8864.16 seconds total)