Starting phenix.real_space_refine on Sat Feb 7 00:14:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ujk_64215/02_2026/9ujk_64215.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ujk_64215/02_2026/9ujk_64215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ujk_64215/02_2026/9ujk_64215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ujk_64215/02_2026/9ujk_64215.map" model { file = "/net/cci-nas-00/data/ceres_data/9ujk_64215/02_2026/9ujk_64215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ujk_64215/02_2026/9ujk_64215.cif" } resolution = 2.49 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= 0.030 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 89 5.49 5 Mg 3 5.21 5 S 70 5.16 5 C 17749 2.51 5 N 5066 2.21 5 O 5501 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 28480 Number of models: 1 Model: "" Number of chains: 10 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: "B" Number of atoms: 1776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1776 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 210} 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: 10753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1362, 10753 Classifications: {'peptide': 1362} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1293} Chain breaks: 2 Chain: "E" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 754 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain: "F" Number of atoms: 2739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2739 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 13, 'TRANS': 324} Chain breaks: 1 Chain: "G" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 881 Classifications: {'DNA': 43} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 42} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 34 Unusual residues: {' MG': 2, ' ZN': 2, '1N7': 1} Classifications: {'undetermined': 5, 'water': 1} Link IDs: {None: 5} 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 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20156 SG CYS D1112 22.483 59.594 119.817 1.00 35.77 S ATOM 20800 SG CYS D1194 26.303 59.886 118.943 1.00 24.77 S ATOM 20856 SG CYS D1201 24.891 61.495 122.044 1.00 25.67 S ATOM 20880 SG CYS D1204 25.430 58.053 122.004 1.00 41.49 S ATOM 12800 SG CYS D 58 54.836 103.833 82.919 1.00 74.32 S ATOM 12811 SG CYS D 60 56.242 104.679 79.838 1.00 86.28 S ATOM 12922 SG CYS D 73 52.934 104.389 79.522 1.00 77.64 S ATOM 12948 SG CYS D 76 54.461 101.002 80.273 1.00 73.26 S Time building chain proxies: 6.11, per 1000 atoms: 0.21 Number of scatterers: 28480 At special positions: 0 Unit cell: (131.61, 157.29, 207.58, 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 89 15.00 Mg 3 11.99 O 5501 8.00 N 5066 7.00 C 17749 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: 2.59 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1601 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1201 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1112 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1194 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1204 " pdb=" ZN D1602 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 73 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 60 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 58 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 76 " Number of angles added : 12 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6214 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 50 sheets defined 44.1% alpha, 17.6% beta 31 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 3.77 Creating SS restraints... Processing helix chain 'A' and resid 31 through 47 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 Processing helix chain 'A' and resid 206 through 223 Processing helix chain 'B' and resid 31 through 47 Proline residue: B 39 - end of helix 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 Processing helix chain 'B' and resid 206 through 223 Processing helix chain 'C' and resid 19 through 31 removed outlier: 3.969A pdb=" N SER C 25 " --> pdb=" O ILE C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 39 removed outlier: 3.531A pdb=" N ARG C 39 " --> pdb=" O PRO C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 52 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 removed outlier: 3.764A pdb=" N MET C 222 " --> pdb=" O GLN C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 228 removed outlier: 3.736A pdb=" N PHE C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 223 through 228' Processing helix chain 'C' and resid 230 through 243 Processing helix chain 'C' and resid 249 through 262 Processing helix chain 'C' and resid 270 through 282 Processing helix chain 'C' and resid 302 through 316 Processing helix chain 'C' and resid 335 through 360 removed outlier: 3.556A pdb=" N LEU C 360 " --> pdb=" O ARG C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 375 through 389 removed outlier: 3.592A pdb=" N SER C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 408 removed outlier: 3.537A pdb=" N SER C 403 " --> pdb=" O ASN C 399 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 429 removed outlier: 3.529A pdb=" N ARG C 428 " --> pdb=" O GLY C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 435 removed outlier: 3.561A 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 Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 554 through 565 removed outlier: 3.842A pdb=" N MET C 560 " --> pdb=" O ASN C 556 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN C 565 " --> pdb=" O GLY C 561 " (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 592 removed outlier: 3.532A pdb=" N VAL C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 592 " --> pdb=" O VAL C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 687 removed outlier: 3.857A 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 854 through 858 removed outlier: 3.583A pdb=" N MET C 858 " --> pdb=" O VAL C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 874 through 880 removed outlier: 4.721A pdb=" N SER C 878 " --> pdb=" O LEU C 874 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG C 879 " --> pdb=" O GLY C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 898 removed outlier: 3.503A pdb=" N PHE C 896 " --> pdb=" O LEU C 892 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 933 removed outlier: 4.296A pdb=" N ARG C 929 " --> pdb=" O TYR C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 950 removed outlier: 3.533A pdb=" N LYS C 949 " --> pdb=" O ARG C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 969 removed outlier: 3.529A 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 1023 through 1027 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: 3.618A 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 65 through 69 Processing helix chain 'D' and resid 82 through 88 removed outlier: 3.554A pdb=" N VAL D 85 " --> pdb=" O LYS D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.570A pdb=" N ASP D 107 " --> pdb=" O TRP D 103 " (cutoff:3.500A) 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 456 through 468 removed outlier: 3.808A pdb=" N ALA D 460 " --> pdb=" O MET D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 481 Processing helix chain 'D' and resid 485 through 506 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: 4.146A 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 Processing helix chain 'D' and resid 612 through 618 Processing helix chain 'D' and resid 646 through 653 removed outlier: 3.526A 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: 4.018A pdb=" N ARG D 679 " --> pdb=" O ARG D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 683 Processing helix chain 'D' and resid 685 through 695 removed outlier: 3.789A pdb=" N ASP D 689 " --> pdb=" O ASP D 685 " (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 764 through 768 Processing helix chain 'D' and resid 782 through 794 removed outlier: 3.552A pdb=" N ILE D 792 " --> pdb=" O GLY D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 808 through 818 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: 3.591A pdb=" N GLU D 898 " --> pdb=" O LYS D 894 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 907 through 923 Processing helix chain 'D' and resid 923 through 946 removed outlier: 3.595A pdb=" N THR D 944 " --> pdb=" O THR D 940 " (cutoff:3.500A) removed outlier: 4.428A 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: 4.029A 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 1103 removed outlier: 3.737A pdb=" N HIS D1075 " --> pdb=" O PHE D1071 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY D1076 " --> pdb=" O ILE D1072 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA D1089 " --> pdb=" O ALA D1085 " (cutoff:3.500A) removed outlier: 4.034A 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 1202 through 1206 Processing helix chain 'D' and resid 1220 through 1231 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: 3.714A pdb=" N VAL D1355 " --> pdb=" O GLU D1351 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR D1356 " --> pdb=" O ILE D1352 " (cutoff:3.500A) Processing helix chain 'D' and resid 1364 through 1376 removed outlier: 4.079A pdb=" N ILE D1368 " --> pdb=" O HIS D1364 " (cutoff:3.500A) Processing helix chain 'D' and resid 1397 through 1410 removed outlier: 3.527A pdb=" N GLU D1410 " --> pdb=" O ARG D1406 " (cutoff:3.500A) Processing helix chain 'D' and resid 1423 through 1430 Processing helix chain 'D' and resid 1433 through 1439 Processing helix chain 'D' and resid 1442 through 1454 Processing helix chain 'D' and resid 1461 through 1469 removed outlier: 4.070A 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 1500 Processing helix chain 'E' and resid 5 through 11 Processing helix chain 'E' and resid 15 through 33 removed outlier: 3.602A pdb=" N LEU E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 71 removed outlier: 3.706A 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 152 through 165 Processing helix chain 'F' and resid 167 through 190 removed outlier: 4.328A pdb=" N TYR F 173 " --> pdb=" O GLU F 169 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU F 174 " --> pdb=" O HIS F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 200 removed outlier: 3.774A pdb=" N VAL F 195 " --> pdb=" O ASN F 191 " (cutoff:3.500A) removed outlier: 3.609A 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 Processing helix chain 'F' and resid 228 through 232 removed outlier: 3.637A pdb=" N ARG F 231 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 255 removed outlier: 3.720A pdb=" N TYR F 238 " --> pdb=" O LYS F 234 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TRP F 241 " --> pdb=" O THR F 237 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TRP F 242 " --> pdb=" O TYR F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 283 Processing helix chain 'F' and resid 287 through 296 Processing helix chain 'F' and resid 300 through 311 Processing helix chain 'F' and resid 328 through 333 removed outlier: 3.663A pdb=" N ILE F 333 " --> pdb=" O GLY F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 360 removed outlier: 3.797A pdb=" N LYS F 360 " --> pdb=" O LYS F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 373 removed outlier: 3.626A pdb=" N MET F 367 " --> pdb=" O GLU F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 391 Processing helix chain 'F' and resid 393 through 416 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 16 removed outlier: 6.124A pdb=" N ASP A 193 " --> pdb=" O PRO A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 104 removed outlier: 3.521A pdb=" N SER A 55 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASP A 145 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL A 53 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLY A 147 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N THR A 51 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 107 through 110 removed outlier: 6.641A pdb=" N LYS A 107 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N THR A 131 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL A 109 " --> pdb=" O ILE A 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 150 through 151 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 16 removed outlier: 3.688A pdb=" N TYR B 20 " --> pdb=" O GLN B 16 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP B 193 " --> pdb=" O PRO B 27 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N THR B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU B 186 " --> pdb=" O THR B 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 104 removed outlier: 3.678A pdb=" N SER B 55 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP B 145 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N VAL B 53 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY B 147 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N THR B 51 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 89 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 110 removed outlier: 6.864A pdb=" N VAL B 109 " --> pdb=" O ILE B 129 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 150 through 151 Processing sheet with id=AB2, first strand: chain 'C' and resid 2 through 5 Processing sheet with id=AB3, first strand: chain 'C' and resid 54 through 55 removed outlier: 5.534A pdb=" N LEU C 66 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ILE C 101 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N PHE C 68 " --> pdb=" O GLN C 99 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLN C 99 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU C 70 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA C 96 " --> pdb=" O PHE C 114 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N PHE C 114 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU C 98 " --> pdb=" O GLU C 112 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N GLU C 112 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU C 100 " --> pdb=" O GLU C 110 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N GLU C 110 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N HIS C 102 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE C 108 " --> pdb=" O HIS C 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AB5, first strand: chain 'C' and resid 331 through 334 removed outlier: 6.377A pdb=" N SER C 138 " --> pdb=" O SER C 411 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 145 through 150 removed outlier: 6.633A pdb=" N TYR C 158 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL C 176 " --> pdb=" O TYR C 158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 291 through 294 Processing sheet with id=AB8, first strand: chain 'C' and resid 460 through 461 removed outlier: 5.441A pdb=" N GLU C 482 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL C 475 " --> pdb=" O THR C 480 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR C 480 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 460 through 461 Processing sheet with id=AC1, first strand: chain 'C' and resid 503 through 504 removed outlier: 3.655A pdb=" N ARG C 507 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 595 through 596 removed outlier: 6.390A pdb=" N LEU C 595 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 620 through 624 removed outlier: 6.877A pdb=" N ARG C 610 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N VAL C 606 " --> pdb=" O ARG C 610 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL C 612 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 629 through 630 Processing sheet with id=AC5, first strand: chain 'C' and resid 661 through 662 Processing sheet with id=AC6, first strand: chain 'C' and resid 971 through 972 removed outlier: 6.843A pdb=" N ILE C 688 " --> pdb=" O LYS C 851 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N LEU C 853 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE C 690 " --> pdb=" O LEU C 853 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 689 " --> pdb=" O ILE C 870 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N VAL C 869 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU C 673 " --> pdb=" O VAL C 869 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU C 871 " --> pdb=" O LEU C 673 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA C 675 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL C 988 " --> pdb=" O ILE C 676 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 702 through 713 removed outlier: 3.588A pdb=" N ARG C 802 " --> pdb=" O TYR C 826 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA C 828 " --> pdb=" O VAL C 800 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N VAL C 800 " --> pdb=" O ALA C 828 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N LYS C 830 " --> pdb=" O GLY C 798 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N GLY C 798 " --> pdb=" O LYS C 830 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 721 through 722 Processing sheet with id=AC9, first strand: chain 'C' and resid 754 through 756 removed outlier: 6.699A pdb=" N LEU C 790 " --> pdb=" O LEU C 755 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1006 through 1008 removed outlier: 6.478A pdb=" N CYS D 642 " --> pdb=" O VAL D 719 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL D 721 " --> pdb=" O CYS D 642 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU D 644 " --> pdb=" O VAL D 721 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1030 through 1032 removed outlier: 3.633A pdb=" N GLN C1030 " --> pdb=" O VAL D 623 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1097 through 1102 Processing sheet with id=AD4, first strand: chain 'D' and resid 22 through 25 removed outlier: 7.638A pdb=" N HIS D 92 " --> pdb=" O TYR D 23 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU D 25 " --> pdb=" O HIS D 92 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N GLU D 94 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 10.147A pdb=" N LEU D 95 " --> pdb=" O PRO D 518 " (cutoff:3.500A) removed outlier: 10.676A pdb=" N THR D 97 " --> pdb=" O ALA D 516 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ALA D 516 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 71 through 72 removed outlier: 4.143A pdb=" N LYS D 71 " --> pdb=" O VAL D 80 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 152 through 153 removed outlier: 6.652A pdb=" N ASP D 453 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AD8, first strand: chain 'D' and resid 166 through 170 removed outlier: 3.839A pdb=" N GLU D 183 " --> pdb=" O ALA D 203 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 344 through 346 removed outlier: 7.095A pdb=" N GLU D 389 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL D 211 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU D 387 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL D 213 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL D 385 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TYR D 215 " --> pdb=" O GLY D 383 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY D 383 " --> pdb=" O TYR D 215 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA D 359 " --> pdb=" O VAL D 385 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 351 through 353 Processing sheet with id=AE2, first strand: chain 'D' and resid 398 through 402 removed outlier: 3.593A pdb=" N GLY D 433 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP D 413 " --> pdb=" O VAL D 435 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 420 through 422 removed outlier: 7.148A pdb=" N VAL D 427 " --> pdb=" O LEU D 421 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 527 through 529 removed outlier: 6.676A pdb=" N PHE D 535 " --> pdb=" O VAL F 315 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 827 through 828 Processing sheet with id=AE6, first strand: chain 'D' and resid 842 through 843 Processing sheet with id=AE7, first strand: chain 'D' and resid 1106 through 1109 Processing sheet with id=AE8, first strand: chain 'D' and resid 1118 through 1121 Processing sheet with id=AE9, first strand: chain 'D' and resid 1123 through 1126 Processing sheet with id=AF1, first strand: chain 'D' and resid 1153 through 1155 Processing sheet with id=AF2, first strand: chain 'D' and resid 1300 through 1305 removed outlier: 4.198A pdb=" N LEU D1290 " --> pdb=" O LEU D1305 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 1394 through 1396 removed outlier: 4.515A pdb=" N TYR D1378 " --> pdb=" O LEU D1420 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA D1416 " --> pdb=" O THR D1382 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 1485 through 1488 Processing sheet with id=AF5, first strand: chain 'E' and resid 47 through 49 1250 hydrogen bonds defined for protein. 3477 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 73 hydrogen bonds 146 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 7.85 Time building geometry restraints manager: 3.41 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: 4692 1.31 - 1.43: 7477 1.43 - 1.56: 16698 1.56 - 1.69: 181 1.69 - 1.81: 127 Bond restraints: 29175 Sorted by residual: 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 9.58e+00 bond pdb=" CA LYS F 407 " pdb=" C LYS F 407 " ideal model delta sigma weight residual 1.524 1.485 0.039 1.27e-02 6.20e+03 9.50e+00 bond pdb=" N ILE F 260 " pdb=" CA ILE F 260 " ideal model delta sigma weight residual 1.462 1.431 0.030 1.01e-02 9.80e+03 9.00e+00 bond pdb=" C SER C1009 " pdb=" O SER C1009 " ideal model delta sigma weight residual 1.235 1.207 0.028 1.26e-02 6.30e+03 5.04e+00 bond pdb=" CA ARG C 775 " pdb=" C ARG C 775 " ideal model delta sigma weight residual 1.524 1.495 0.029 1.29e-02 6.01e+03 4.98e+00 ... (remaining 29170 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 38815 1.19 - 2.38: 780 2.38 - 3.57: 222 3.57 - 4.77: 29 4.77 - 5.96: 3 Bond angle restraints: 39849 Sorted by residual: angle pdb=" N GLU C 442 " pdb=" CA GLU C 442 " pdb=" C GLU C 442 " ideal model delta sigma weight residual 108.63 114.59 -5.96 1.60e+00 3.91e-01 1.39e+01 angle pdb=" N ARG F 259 " pdb=" CA ARG F 259 " pdb=" C ARG F 259 " ideal model delta sigma weight residual 109.96 115.09 -5.13 1.50e+00 4.44e-01 1.17e+01 angle pdb=" O ILE F 258 " pdb=" C ILE F 258 " pdb=" N ARG F 259 " ideal model delta sigma weight residual 122.59 117.97 4.62 1.39e+00 5.18e-01 1.11e+01 angle pdb=" N VAL E 39 " pdb=" CA VAL E 39 " pdb=" C VAL E 39 " ideal model delta sigma weight residual 112.29 109.17 3.12 9.40e-01 1.13e+00 1.11e+01 angle pdb=" CA HIS D 709 " pdb=" C HIS D 709 " pdb=" O HIS D 709 " ideal model delta sigma weight residual 121.40 117.75 3.65 1.11e+00 8.12e-01 1.08e+01 ... (remaining 39844 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.79: 16266 19.79 - 39.58: 1070 39.58 - 59.37: 359 59.37 - 79.16: 54 79.16 - 98.94: 15 Dihedral angle restraints: 17764 sinusoidal: 8109 harmonic: 9655 Sorted by residual: dihedral pdb=" CA TYR D1207 " pdb=" C TYR D1207 " pdb=" N ASP D1208 " pdb=" CA ASP D1208 " ideal model delta harmonic sigma weight residual 180.00 150.78 29.22 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA SER A 46 " pdb=" C SER A 46 " pdb=" N SER A 47 " pdb=" CA SER A 47 " ideal model delta harmonic sigma weight residual -180.00 -161.90 -18.10 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA SER D 782 " pdb=" C SER D 782 " pdb=" N ARG D 783 " pdb=" CA ARG D 783 " ideal model delta harmonic sigma weight residual -180.00 -162.68 -17.32 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 17761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3485 0.043 - 0.085: 693 0.085 - 0.127: 306 0.127 - 0.170: 7 0.170 - 0.212: 2 Chirality restraints: 4493 Sorted by residual: 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 2.80 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ILE F 260 " pdb=" N ILE F 260 " pdb=" C ILE F 260 " pdb=" CB ILE F 260 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.98e-01 chirality pdb=" CA ARG F 259 " pdb=" N ARG F 259 " pdb=" C ARG F 259 " pdb=" CB ARG F 259 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 4490 not shown) Planarity restraints: 4893 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP D 743 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" CG ASP D 743 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP D 743 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP D 743 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D1207 " 0.020 2.00e-02 2.50e+03 1.31e-02 3.42e+00 pdb=" CG TYR D1207 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR D1207 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D1207 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR D1207 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D1207 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D1207 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR D1207 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 145 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO D 146 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 146 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 146 " -0.023 5.00e-02 4.00e+02 ... (remaining 4890 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 255 2.63 - 3.19: 24776 3.19 - 3.76: 43600 3.76 - 4.33: 65959 4.33 - 4.90: 105776 Nonbonded interactions: 240366 Sorted by model distance: nonbonded pdb="MG MG D1603 " pdb=" O HOH D1701 " model vdw 2.057 2.170 nonbonded pdb=" OD1 ASP D 741 " pdb="MG MG D1603 " model vdw 2.057 2.170 nonbonded pdb=" OD1 ASP D 739 " pdb="MG MG D1603 " model vdw 2.126 2.170 nonbonded pdb=" OD1 ASP D 743 " pdb="MG MG D1603 " model vdw 2.141 2.170 nonbonded pdb=" O GLU C 55 " pdb=" NH1 ARG C 356 " model vdw 2.197 3.120 ... (remaining 240361 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' and resid 6 through 229) } 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: 1.830 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: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 34.420 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.780 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 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 29183 Z= 0.153 Angle : 0.487 17.258 39861 Z= 0.262 Chirality : 0.040 0.212 4493 Planarity : 0.003 0.041 4893 Dihedral : 14.899 98.944 11550 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: 0.83 (0.14), residues: 3336 helix: 1.04 (0.15), residues: 1273 sheet: 0.30 (0.24), residues: 460 loop : 0.39 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 589 TYR 0.031 0.001 TYR D1207 PHE 0.019 0.001 PHE C 699 TRP 0.010 0.001 TRP B 200 HIS 0.006 0.001 HIS C 434 Details of bonding type rmsd covalent geometry : bond 0.00313 (29175) covalent geometry : angle 0.45967 (39849) hydrogen bonds : bond 0.21305 ( 1321) hydrogen bonds : angle 7.29535 ( 3623) metal coordination : bond 0.01322 ( 8) metal coordination : angle 9.26174 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 179 VAL cc_start: 0.8582 (t) cc_final: 0.7865 (m) REVERT: D 483 HIS cc_start: 0.8117 (t-90) cc_final: 0.7836 (t-90) outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 1.0809 time to fit residues: 422.1084 Evaluate side-chains 185 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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: 5.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.1980 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN C 538 GLN C 670 GLN C 829 GLN ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 HIS F 269 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.091453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.061223 restraints weight = 51757.011| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 2.35 r_work: 0.2571 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2439 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2535 r_free = 0.2535 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2535 r_free = 0.2535 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2535 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29183 Z= 0.180 Angle : 0.592 9.239 39861 Z= 0.317 Chirality : 0.044 0.160 4493 Planarity : 0.005 0.046 4893 Dihedral : 15.384 73.999 4799 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.15 % Allowed : 7.17 % Favored : 91.68 % 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: 1.14 (0.14), residues: 3336 helix: 1.43 (0.14), residues: 1299 sheet: 0.34 (0.24), residues: 448 loop : 0.46 (0.16), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 137 TYR 0.021 0.001 TYR D1207 PHE 0.015 0.002 PHE D 740 TRP 0.012 0.001 TRP B 200 HIS 0.008 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00415 (29175) covalent geometry : angle 0.59012 (39849) hydrogen bonds : bond 0.04834 ( 1321) hydrogen bonds : angle 4.87782 ( 3623) metal coordination : bond 0.00449 ( 8) metal coordination : angle 2.94418 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: A 108 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8412 (mp0) REVERT: A 154 GLU cc_start: 0.8624 (pm20) cc_final: 0.8361 (pm20) REVERT: B 185 ARG cc_start: 0.8319 (ptt90) cc_final: 0.7936 (ptm-80) REVERT: C 154 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7482 (ptm-80) REVERT: C 216 GLU cc_start: 0.8214 (pm20) cc_final: 0.7214 (tm-30) REVERT: C 229 MET cc_start: 0.7661 (ttp) cc_final: 0.7403 (ttp) REVERT: C 233 GLU cc_start: 0.9091 (mp0) cc_final: 0.8826 (pt0) REVERT: C 361 MET cc_start: 0.7902 (pp-130) cc_final: 0.7641 (pp-130) REVERT: C 384 GLU cc_start: 0.8347 (tp30) cc_final: 0.7898 (mm-30) REVERT: C 420 ARG cc_start: 0.8014 (ttp80) cc_final: 0.7705 (tmm-80) REVERT: C 771 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7686 (tm-30) REVERT: D 124 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8228 (tp30) REVERT: D 190 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7764 (tp30) REVERT: D 366 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7792 (tptm) REVERT: D 386 HIS cc_start: 0.7725 (m-70) cc_final: 0.7401 (m170) REVERT: D 1197 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8227 (ttt-90) REVERT: D 1337 GLU cc_start: 0.7972 (pp20) cc_final: 0.7757 (pp20) REVERT: E 88 GLU cc_start: 0.8904 (tp30) cc_final: 0.8471 (tp30) REVERT: F 367 MET cc_start: 0.9049 (tpp) cc_final: 0.8846 (tpp) REVERT: F 379 ARG cc_start: 0.6815 (ttp80) cc_final: 0.6589 (ttp80) REVERT: F 419 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8290 (tpp80) outliers start: 33 outliers final: 5 residues processed: 224 average time/residue: 0.9606 time to fit residues: 241.2152 Evaluate side-chains 186 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 366 LYS Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain D residue 1131 SER Chi-restraints excluded: chain D residue 1197 ARG Chi-restraints excluded: chain F residue 302 LYS Chi-restraints excluded: chain F residue 419 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 259 optimal weight: 0.6980 chunk 246 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 323 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 195 optimal weight: 0.0770 chunk 186 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 202 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 999 HIS ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.090168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.059907 restraints weight = 51637.096| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 2.35 r_work: 0.2545 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2413 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2507 r_free = 0.2507 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2507 r_free = 0.2507 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 29183 Z= 0.154 Angle : 0.520 10.832 39861 Z= 0.277 Chirality : 0.042 0.147 4493 Planarity : 0.004 0.041 4893 Dihedral : 15.220 75.592 4799 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.08 % Allowed : 8.57 % Favored : 90.35 % 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: 1.29 (0.14), residues: 3336 helix: 1.68 (0.14), residues: 1307 sheet: 0.33 (0.24), residues: 448 loop : 0.45 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 137 TYR 0.014 0.001 TYR D1207 PHE 0.014 0.001 PHE D1008 TRP 0.011 0.001 TRP B 200 HIS 0.005 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00359 (29175) covalent geometry : angle 0.51844 (39849) hydrogen bonds : bond 0.04487 ( 1321) hydrogen bonds : angle 4.55407 ( 3623) metal coordination : bond 0.00406 ( 8) metal coordination : angle 2.63465 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 1.090 Fit side-chains REVERT: A 108 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8506 (mp0) REVERT: A 110 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7460 (mtpp) REVERT: A 145 ASP cc_start: 0.8762 (m-30) cc_final: 0.8517 (m-30) REVERT: A 154 GLU cc_start: 0.8659 (pm20) cc_final: 0.8366 (pm20) REVERT: A 155 LYS cc_start: 0.8763 (mtpp) cc_final: 0.8448 (ttmt) REVERT: B 102 LYS cc_start: 0.8995 (mmpt) cc_final: 0.8727 (mmmt) REVERT: B 185 ARG cc_start: 0.8478 (ptt90) cc_final: 0.8038 (ptm-80) REVERT: C 154 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7335 (ptm-80) REVERT: C 229 MET cc_start: 0.7786 (ttp) cc_final: 0.7263 (ttp) REVERT: C 230 ARG cc_start: 0.8254 (ttm110) cc_final: 0.7697 (ttm110) REVERT: C 233 GLU cc_start: 0.9123 (mp0) cc_final: 0.8867 (pt0) REVERT: C 237 ARG cc_start: 0.8738 (tpp80) cc_final: 0.8496 (ttt90) REVERT: C 353 ARG cc_start: 0.8027 (mtp85) cc_final: 0.7742 (ttm-80) REVERT: C 357 GLU cc_start: 0.8436 (tt0) cc_final: 0.7445 (tp30) REVERT: C 361 MET cc_start: 0.7891 (pp-130) cc_final: 0.7462 (pp-130) REVERT: C 384 GLU cc_start: 0.8394 (tp30) cc_final: 0.7950 (mm-30) REVERT: C 420 ARG cc_start: 0.8131 (ttp80) cc_final: 0.7856 (tmm-80) REVERT: D 65 ARG cc_start: 0.7654 (mmm160) cc_final: 0.7030 (mpt-90) REVERT: D 124 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8275 (tp30) REVERT: D 351 MET cc_start: 0.9063 (mtp) cc_final: 0.8820 (mpp) REVERT: D 594 PRO cc_start: 0.9043 (Cg_exo) cc_final: 0.8818 (Cg_endo) REVERT: D 763 MET cc_start: 0.9475 (mtp) cc_final: 0.9253 (mtm) REVERT: D 1013 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8233 (mp0) REVERT: D 1100 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.7985 (m-30) REVERT: D 1124 GLN cc_start: 0.8458 (tt0) cc_final: 0.8193 (tt0) REVERT: D 1197 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7893 (ttt-90) REVERT: D 1198 TYR cc_start: 0.8489 (m-80) cc_final: 0.8273 (m-80) REVERT: D 1337 GLU cc_start: 0.7886 (pp20) cc_final: 0.7664 (pp20) REVERT: E 88 GLU cc_start: 0.8855 (tp30) cc_final: 0.8461 (tp30) REVERT: F 367 MET cc_start: 0.9097 (tpp) cc_final: 0.8843 (tpp) outliers start: 31 outliers final: 2 residues processed: 213 average time/residue: 0.9939 time to fit residues: 238.7827 Evaluate side-chains 184 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 175 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain D residue 1013 GLU Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1197 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 216 optimal weight: 4.9990 chunk 238 optimal weight: 1.9990 chunk 263 optimal weight: 0.0970 chunk 61 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 158 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN B 163 ASN ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.089780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.059475 restraints weight = 51501.691| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 2.34 r_work: 0.2534 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2401 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2401 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2496 r_free = 0.2496 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2496 r_free = 0.2496 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29183 Z= 0.148 Angle : 0.506 8.498 39861 Z= 0.270 Chirality : 0.042 0.150 4493 Planarity : 0.004 0.053 4893 Dihedral : 15.175 73.422 4799 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.91 % Allowed : 9.34 % Favored : 89.76 % 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: 1.39 (0.14), residues: 3336 helix: 1.80 (0.14), residues: 1309 sheet: 0.34 (0.24), residues: 461 loop : 0.49 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 198 TYR 0.013 0.001 TYR D 989 PHE 0.011 0.001 PHE D1008 TRP 0.011 0.001 TRP B 200 HIS 0.005 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00349 (29175) covalent geometry : angle 0.50438 (39849) hydrogen bonds : bond 0.04078 ( 1321) hydrogen bonds : angle 4.39801 ( 3623) metal coordination : bond 0.00434 ( 8) metal coordination : angle 2.19537 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8521 (mp0) REVERT: A 110 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7476 (mtpp) REVERT: A 145 ASP cc_start: 0.8801 (m-30) cc_final: 0.8518 (m-30) REVERT: A 154 GLU cc_start: 0.8719 (pm20) cc_final: 0.8397 (pm20) REVERT: A 155 LYS cc_start: 0.8769 (mtpp) cc_final: 0.8444 (ttmt) REVERT: A 185 ARG cc_start: 0.8924 (ptm160) cc_final: 0.8449 (ttm-80) REVERT: B 91 ASN cc_start: 0.8332 (t0) cc_final: 0.8032 (t0) REVERT: B 102 LYS cc_start: 0.8962 (mmpt) cc_final: 0.8705 (mmmt) REVERT: B 185 ARG cc_start: 0.8617 (ptt90) cc_final: 0.7988 (ptm-80) REVERT: B 190 THR cc_start: 0.8773 (p) cc_final: 0.8490 (t) REVERT: C 154 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7311 (ptm-80) REVERT: C 229 MET cc_start: 0.7804 (ttp) cc_final: 0.7279 (ttp) REVERT: C 233 GLU cc_start: 0.9150 (mp0) cc_final: 0.8919 (pt0) REVERT: C 237 ARG cc_start: 0.8750 (tpp80) cc_final: 0.8508 (ttt90) REVERT: C 353 ARG cc_start: 0.8054 (mtp85) cc_final: 0.7772 (ttm-80) REVERT: C 357 GLU cc_start: 0.8404 (tt0) cc_final: 0.7431 (tp30) REVERT: C 361 MET cc_start: 0.8009 (pp-130) cc_final: 0.7544 (pp-130) REVERT: C 384 GLU cc_start: 0.8395 (tp30) cc_final: 0.7945 (mm-30) REVERT: C 420 ARG cc_start: 0.8122 (ttp80) cc_final: 0.7848 (tmm-80) REVERT: C 1000 MET cc_start: 0.8821 (mtt) cc_final: 0.8368 (mtt) REVERT: D 124 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8317 (tp30) REVERT: D 366 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7859 (tptm) REVERT: D 594 PRO cc_start: 0.9062 (Cg_exo) cc_final: 0.8845 (Cg_endo) REVERT: D 1013 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8347 (mp0) REVERT: D 1124 GLN cc_start: 0.8454 (tt0) cc_final: 0.8195 (tt0) REVERT: D 1197 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8213 (ttt-90) REVERT: E 88 GLU cc_start: 0.8876 (tp30) cc_final: 0.8467 (tp30) REVERT: F 367 MET cc_start: 0.9129 (tpp) cc_final: 0.8898 (tpp) REVERT: F 410 TYR cc_start: 0.8439 (t80) cc_final: 0.7900 (t80) outliers start: 26 outliers final: 7 residues processed: 205 average time/residue: 1.0090 time to fit residues: 232.6677 Evaluate side-chains 187 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 173 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 557 ARG Chi-restraints excluded: chain C residue 928 LYS Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 366 LYS Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain D residue 1013 GLU Chi-restraints excluded: chain D residue 1197 ARG Chi-restraints excluded: chain D residue 1452 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 109 optimal weight: 6.9990 chunk 326 optimal weight: 6.9990 chunk 320 optimal weight: 3.9990 chunk 268 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 315 optimal weight: 3.9990 chunk 171 optimal weight: 9.9990 chunk 284 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 173 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 ASN C 843 HIS D 762 GLN ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.085162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.054670 restraints weight = 52488.561| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 2.35 r_work: 0.2553 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2430 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2430 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2504 r_free = 0.2504 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2504 r_free = 0.2504 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.093 29183 Z= 0.394 Angle : 0.655 9.971 39861 Z= 0.341 Chirality : 0.049 0.164 4493 Planarity : 0.006 0.081 4893 Dihedral : 15.371 75.325 4799 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.47 % Allowed : 9.41 % Favored : 89.13 % 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: 1.12 (0.14), residues: 3336 helix: 1.53 (0.14), residues: 1316 sheet: 0.23 (0.24), residues: 445 loop : 0.34 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 198 TYR 0.020 0.002 TYR D 128 PHE 0.021 0.002 PHE A 179 TRP 0.010 0.002 TRP A 200 HIS 0.010 0.002 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00956 (29175) covalent geometry : angle 0.65255 (39849) hydrogen bonds : bond 0.05617 ( 1321) hydrogen bonds : angle 4.70136 ( 3623) metal coordination : bond 0.01056 ( 8) metal coordination : angle 3.42076 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 183 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8684 (mp0) REVERT: A 110 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7593 (mtpp) REVERT: A 145 ASP cc_start: 0.8840 (m-30) cc_final: 0.8426 (m-30) REVERT: A 154 GLU cc_start: 0.8854 (pm20) cc_final: 0.8511 (pm20) REVERT: B 91 ASN cc_start: 0.8523 (t0) cc_final: 0.8241 (t0) REVERT: B 102 LYS cc_start: 0.9027 (mmpt) cc_final: 0.8760 (mmmt) REVERT: B 185 ARG cc_start: 0.8678 (ptt90) cc_final: 0.8040 (ptm-80) REVERT: B 190 THR cc_start: 0.8774 (p) cc_final: 0.8508 (t) REVERT: C 230 ARG cc_start: 0.8337 (ttm110) cc_final: 0.7861 (ttp-110) REVERT: C 233 GLU cc_start: 0.9161 (mp0) cc_final: 0.8837 (mt-10) REVERT: C 353 ARG cc_start: 0.8121 (mtp85) cc_final: 0.7862 (ttm-80) REVERT: C 357 GLU cc_start: 0.8599 (tt0) cc_final: 0.7666 (tp30) REVERT: C 361 MET cc_start: 0.8063 (pp-130) cc_final: 0.7589 (pp-130) REVERT: C 384 GLU cc_start: 0.8485 (tp30) cc_final: 0.8018 (mm-30) REVERT: D 124 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8638 (tp30) REVERT: D 190 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8052 (tp30) REVERT: D 345 TYR cc_start: 0.7587 (m-10) cc_final: 0.7365 (m-10) REVERT: D 365 ASP cc_start: 0.7745 (m-30) cc_final: 0.7446 (m-30) REVERT: D 366 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8067 (tptm) REVERT: D 386 HIS cc_start: 0.7884 (m-70) cc_final: 0.7493 (m90) REVERT: D 797 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8670 (mppt) REVERT: D 1013 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8513 (mp0) REVERT: D 1100 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.8169 (m-30) REVERT: D 1124 GLN cc_start: 0.8628 (tt0) cc_final: 0.8395 (tt0) REVERT: D 1197 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8281 (ttt-90) REVERT: E 44 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8735 (mt-10) REVERT: E 88 GLU cc_start: 0.8928 (tp30) cc_final: 0.8608 (tp30) REVERT: F 367 MET cc_start: 0.9170 (tpp) cc_final: 0.8920 (tpp) REVERT: F 379 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6846 (ptt90) REVERT: F 410 TYR cc_start: 0.8473 (t80) cc_final: 0.7917 (t80) outliers start: 42 outliers final: 16 residues processed: 214 average time/residue: 1.0009 time to fit residues: 241.1520 Evaluate side-chains 199 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 557 ARG Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 366 LYS Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain D residue 782 SER Chi-restraints excluded: chain D residue 797 LYS Chi-restraints excluded: chain D residue 875 THR Chi-restraints excluded: chain D residue 1013 GLU Chi-restraints excluded: chain D residue 1051 GLU Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1197 ARG Chi-restraints excluded: chain D residue 1452 ILE Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 65 MET Chi-restraints excluded: chain F residue 379 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 109 optimal weight: 0.8980 chunk 287 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 193 optimal weight: 0.6980 chunk 90 optimal weight: 0.0870 chunk 13 optimal weight: 0.9980 chunk 326 optimal weight: 0.9990 chunk 219 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 ASN C 843 HIS ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.088650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.058422 restraints weight = 51925.550| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 2.33 r_work: 0.2643 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2521 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29183 Z= 0.121 Angle : 0.498 7.512 39861 Z= 0.266 Chirality : 0.041 0.145 4493 Planarity : 0.004 0.050 4893 Dihedral : 15.151 72.449 4799 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.91 % Allowed : 10.31 % Favored : 88.78 % 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: 1.32 (0.14), residues: 3336 helix: 1.77 (0.14), residues: 1319 sheet: 0.16 (0.24), residues: 465 loop : 0.46 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG D 65 TYR 0.013 0.001 TYR D 989 PHE 0.012 0.001 PHE B 179 TRP 0.012 0.001 TRP B 200 HIS 0.005 0.001 HIS D 386 Details of bonding type rmsd covalent geometry : bond 0.00279 (29175) covalent geometry : angle 0.49657 (39849) hydrogen bonds : bond 0.03809 ( 1321) hydrogen bonds : angle 4.31246 ( 3623) metal coordination : bond 0.00294 ( 8) metal coordination : angle 1.84457 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8697 (mp0) REVERT: A 110 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7589 (mtpp) REVERT: A 145 ASP cc_start: 0.8853 (m-30) cc_final: 0.8550 (m-30) REVERT: A 154 GLU cc_start: 0.8845 (pm20) cc_final: 0.8528 (pm20) REVERT: A 155 LYS cc_start: 0.8860 (mtpp) cc_final: 0.8568 (ttmt) REVERT: A 229 GLN cc_start: 0.7638 (mt0) cc_final: 0.7374 (mm-40) REVERT: B 91 ASN cc_start: 0.8574 (t0) cc_final: 0.8278 (t0) REVERT: B 102 LYS cc_start: 0.9079 (mmpt) cc_final: 0.8486 (mmmt) REVERT: B 185 ARG cc_start: 0.8701 (ptt90) cc_final: 0.8196 (ptm-80) REVERT: B 190 THR cc_start: 0.8667 (p) cc_final: 0.8418 (t) REVERT: C 154 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7369 (ptm-80) REVERT: C 229 MET cc_start: 0.8094 (ttm) cc_final: 0.7675 (ttp) REVERT: C 230 ARG cc_start: 0.8476 (ttm110) cc_final: 0.7893 (ttp-110) REVERT: C 233 GLU cc_start: 0.9177 (mp0) cc_final: 0.8893 (pt0) REVERT: C 353 ARG cc_start: 0.8079 (mtp85) cc_final: 0.7801 (ttm-80) REVERT: C 357 GLU cc_start: 0.8461 (tt0) cc_final: 0.7583 (tp30) REVERT: C 361 MET cc_start: 0.8155 (pp-130) cc_final: 0.7574 (pp-130) REVERT: C 384 GLU cc_start: 0.8476 (tp30) cc_final: 0.8040 (mm-30) REVERT: C 1000 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8305 (mtt) REVERT: D 30 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8214 (mt-10) REVERT: D 124 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8478 (tp30) REVERT: D 190 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8130 (tp30) REVERT: D 1013 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8432 (mp0) REVERT: D 1197 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8122 (ttt-90) REVERT: E 44 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8743 (mt-10) REVERT: E 88 GLU cc_start: 0.8955 (tp30) cc_final: 0.8554 (tp30) REVERT: F 367 MET cc_start: 0.9133 (tpp) cc_final: 0.8864 (tpp) REVERT: F 410 TYR cc_start: 0.8472 (t80) cc_final: 0.7925 (t80) outliers start: 26 outliers final: 6 residues processed: 202 average time/residue: 0.8671 time to fit residues: 198.3056 Evaluate side-chains 186 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 557 ARG Chi-restraints excluded: chain C residue 928 LYS Chi-restraints excluded: chain C residue 1000 MET Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 1013 GLU Chi-restraints excluded: chain D residue 1197 ARG Chi-restraints excluded: chain D residue 1452 ILE Chi-restraints excluded: chain E residue 44 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 111 optimal weight: 3.9990 chunk 308 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 148 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 181 optimal weight: 9.9990 chunk 266 optimal weight: 0.0040 chunk 18 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 overall best weight: 1.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 402 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.087695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.057394 restraints weight = 52044.326| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 2.33 r_work: 0.2616 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2495 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2485 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2485 r_free = 0.2485 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2485 r_free = 0.2485 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2485 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29183 Z= 0.174 Angle : 0.515 8.213 39861 Z= 0.273 Chirality : 0.042 0.147 4493 Planarity : 0.004 0.070 4893 Dihedral : 15.139 72.032 4799 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.91 % Allowed : 10.70 % 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: 1.39 (0.14), residues: 3336 helix: 1.83 (0.14), residues: 1313 sheet: 0.17 (0.24), residues: 469 loop : 0.51 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 198 TYR 0.013 0.001 TYR D 989 PHE 0.013 0.001 PHE A 179 TRP 0.011 0.001 TRP B 200 HIS 0.005 0.001 HIS D 386 Details of bonding type rmsd covalent geometry : bond 0.00418 (29175) covalent geometry : angle 0.51432 (39849) hydrogen bonds : bond 0.04085 ( 1321) hydrogen bonds : angle 4.30320 ( 3623) metal coordination : bond 0.00498 ( 8) metal coordination : angle 2.03062 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8591 (mp0) REVERT: A 110 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7656 (mtpp) REVERT: A 145 ASP cc_start: 0.8874 (m-30) cc_final: 0.8507 (m-30) REVERT: A 154 GLU cc_start: 0.8860 (pm20) cc_final: 0.8516 (pm20) REVERT: A 155 LYS cc_start: 0.8883 (mtpp) cc_final: 0.8577 (ttmt) REVERT: A 229 GLN cc_start: 0.7673 (mt0) cc_final: 0.7382 (mm-40) REVERT: B 91 ASN cc_start: 0.8606 (t0) cc_final: 0.8319 (t0) REVERT: B 185 ARG cc_start: 0.8697 (ptt90) cc_final: 0.8189 (ptm-80) REVERT: B 190 THR cc_start: 0.8626 (p) cc_final: 0.8370 (t) REVERT: C 154 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7318 (ptm-80) REVERT: C 229 MET cc_start: 0.8091 (ttm) cc_final: 0.7652 (ttp) REVERT: C 230 ARG cc_start: 0.8490 (ttm110) cc_final: 0.7932 (ttp-110) REVERT: C 233 GLU cc_start: 0.9165 (mp0) cc_final: 0.8886 (pt0) REVERT: C 353 ARG cc_start: 0.8116 (mtp85) cc_final: 0.7839 (ttm-80) REVERT: C 357 GLU cc_start: 0.8498 (tt0) cc_final: 0.7639 (tp30) REVERT: C 361 MET cc_start: 0.8159 (pp-130) cc_final: 0.7572 (pp-130) REVERT: C 384 GLU cc_start: 0.8489 (tp30) cc_final: 0.8062 (mm-30) REVERT: C 725 ASP cc_start: 0.8815 (t0) cc_final: 0.8409 (p0) REVERT: C 1000 MET cc_start: 0.8835 (mtt) cc_final: 0.8447 (mtt) REVERT: C 1052 MET cc_start: 0.9266 (mtt) cc_final: 0.9050 (mtt) REVERT: D 30 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8228 (mt-10) REVERT: D 124 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8568 (tp30) REVERT: D 190 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8135 (tp30) REVERT: D 386 HIS cc_start: 0.7966 (m-70) cc_final: 0.7708 (m90) REVERT: D 1013 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8513 (mp0) REVERT: D 1100 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8124 (m-30) REVERT: D 1499 ARG cc_start: 0.8898 (tmm-80) cc_final: 0.8641 (ttp80) REVERT: E 44 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8713 (mt-10) REVERT: E 87 LYS cc_start: 0.9147 (ttpt) cc_final: 0.8879 (pttm) REVERT: E 88 GLU cc_start: 0.8927 (tp30) cc_final: 0.8617 (tp30) REVERT: F 367 MET cc_start: 0.9141 (tpp) cc_final: 0.8860 (tpp) REVERT: F 379 ARG cc_start: 0.7287 (ttt-90) cc_final: 0.7076 (ptt-90) REVERT: F 410 TYR cc_start: 0.8482 (t80) cc_final: 0.7945 (t80) outliers start: 26 outliers final: 10 residues processed: 200 average time/residue: 0.9264 time to fit residues: 209.4817 Evaluate side-chains 189 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 557 ARG Chi-restraints excluded: chain C residue 928 LYS Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 782 SER Chi-restraints excluded: chain D residue 875 THR Chi-restraints excluded: chain D residue 1013 GLU Chi-restraints excluded: chain D residue 1051 GLU Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1452 ILE Chi-restraints excluded: chain E residue 44 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 142 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 329 optimal weight: 9.9990 chunk 222 optimal weight: 3.9990 chunk 306 optimal weight: 9.9990 chunk 187 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 298 optimal weight: 2.9990 chunk 175 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 402 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.086619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.056330 restraints weight = 52362.598| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 2.33 r_work: 0.2599 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2477 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2455 r_free = 0.2455 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2455 r_free = 0.2455 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 29183 Z= 0.253 Angle : 0.560 8.442 39861 Z= 0.295 Chirality : 0.044 0.151 4493 Planarity : 0.005 0.048 4893 Dihedral : 15.205 72.504 4799 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.12 % Allowed : 10.87 % Favored : 88.01 % 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: 1.32 (0.14), residues: 3336 helix: 1.76 (0.14), residues: 1310 sheet: 0.15 (0.24), residues: 469 loop : 0.49 (0.16), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 65 TYR 0.015 0.001 TYR D 128 PHE 0.017 0.002 PHE A 179 TRP 0.011 0.001 TRP B 200 HIS 0.007 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00613 (29175) covalent geometry : angle 0.55841 (39849) hydrogen bonds : bond 0.04544 ( 1321) hydrogen bonds : angle 4.39581 ( 3623) metal coordination : bond 0.00687 ( 8) metal coordination : angle 2.45195 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.8615 (mp0) REVERT: A 145 ASP cc_start: 0.8882 (m-30) cc_final: 0.8481 (m-30) REVERT: A 154 GLU cc_start: 0.8869 (pm20) cc_final: 0.8513 (pm20) REVERT: A 229 GLN cc_start: 0.7692 (mt0) cc_final: 0.7394 (mm-40) REVERT: B 91 ASN cc_start: 0.8641 (t0) cc_final: 0.8356 (t0) REVERT: B 185 ARG cc_start: 0.8698 (ptt90) cc_final: 0.8375 (ptt90) REVERT: B 190 THR cc_start: 0.8625 (p) cc_final: 0.8376 (t) REVERT: C 154 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7299 (ptm-80) REVERT: C 230 ARG cc_start: 0.8486 (ttm110) cc_final: 0.8102 (ttp-110) REVERT: C 233 GLU cc_start: 0.9159 (mp0) cc_final: 0.8897 (pt0) REVERT: C 353 ARG cc_start: 0.8130 (mtp85) cc_final: 0.7880 (ttm-80) REVERT: C 357 GLU cc_start: 0.8557 (tt0) cc_final: 0.7701 (tp30) REVERT: C 361 MET cc_start: 0.8095 (pp-130) cc_final: 0.7482 (pp-130) REVERT: C 384 GLU cc_start: 0.8504 (tp30) cc_final: 0.8078 (mm-30) REVERT: C 486 MET cc_start: 0.9437 (ptp) cc_final: 0.9188 (mtt) REVERT: C 725 ASP cc_start: 0.8825 (t0) cc_final: 0.8356 (p0) REVERT: D 30 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8275 (mt-10) REVERT: D 65 ARG cc_start: 0.7724 (mmm160) cc_final: 0.7035 (mpt-90) REVERT: D 124 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8602 (tp30) REVERT: D 190 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8213 (tp30) REVERT: D 345 TYR cc_start: 0.7789 (m-10) cc_final: 0.7548 (m-10) REVERT: D 366 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8179 (tptm) REVERT: D 1013 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8517 (mp0) REVERT: D 1100 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8122 (m-30) REVERT: D 1499 ARG cc_start: 0.8820 (tmm-80) cc_final: 0.8609 (ttp80) REVERT: E 44 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8797 (mt-10) REVERT: E 87 LYS cc_start: 0.9150 (ttpt) cc_final: 0.8881 (pttm) REVERT: E 88 GLU cc_start: 0.8983 (tp30) cc_final: 0.8683 (tp30) REVERT: F 248 ASN cc_start: 0.8904 (OUTLIER) cc_final: 0.8699 (t0) REVERT: F 367 MET cc_start: 0.9139 (tpp) cc_final: 0.8851 (tpp) REVERT: F 410 TYR cc_start: 0.8469 (t80) cc_final: 0.7957 (t80) outliers start: 32 outliers final: 14 residues processed: 197 average time/residue: 0.8876 time to fit residues: 197.9699 Evaluate side-chains 194 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 557 ARG Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 366 LYS Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain D residue 782 SER Chi-restraints excluded: chain D residue 875 THR Chi-restraints excluded: chain D residue 980 MET Chi-restraints excluded: chain D residue 1013 GLU Chi-restraints excluded: chain D residue 1051 GLU Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1452 ILE Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 65 MET Chi-restraints excluded: chain F residue 248 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 121 optimal weight: 8.9990 chunk 223 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 285 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3339 r_free = 0.3339 target = 0.087653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.057395 restraints weight = 52057.021| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 2.33 r_work: 0.2627 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2490 r_free = 0.2490 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2490 r_free = 0.2490 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29183 Z= 0.159 Angle : 0.521 8.184 39861 Z= 0.276 Chirality : 0.042 0.147 4493 Planarity : 0.004 0.095 4893 Dihedral : 15.162 71.750 4799 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.94 % Allowed : 11.15 % Favored : 87.90 % 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: 1.37 (0.15), residues: 3336 helix: 1.80 (0.14), residues: 1319 sheet: 0.18 (0.24), residues: 469 loop : 0.50 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG D 198 TYR 0.013 0.001 TYR D 989 PHE 0.011 0.001 PHE D1008 TRP 0.012 0.001 TRP B 200 HIS 0.005 0.001 HIS D 386 Details of bonding type rmsd covalent geometry : bond 0.00380 (29175) covalent geometry : angle 0.51972 (39849) hydrogen bonds : bond 0.04029 ( 1321) hydrogen bonds : angle 4.29366 ( 3623) metal coordination : bond 0.00466 ( 8) metal coordination : angle 1.95105 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8572 (mp0) REVERT: A 145 ASP cc_start: 0.8867 (m-30) cc_final: 0.8482 (m-30) REVERT: A 154 GLU cc_start: 0.8867 (pm20) cc_final: 0.8515 (pm20) REVERT: A 155 LYS cc_start: 0.8933 (mtpp) cc_final: 0.8603 (ttmt) REVERT: A 229 GLN cc_start: 0.7688 (mt0) cc_final: 0.7395 (mm-40) REVERT: B 91 ASN cc_start: 0.8655 (t0) cc_final: 0.8351 (t0) REVERT: B 185 ARG cc_start: 0.8712 (ptt90) cc_final: 0.8391 (ptt90) REVERT: B 190 THR cc_start: 0.8578 (p) cc_final: 0.8329 (t) REVERT: C 154 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7295 (ptm-80) REVERT: C 229 MET cc_start: 0.8143 (ttm) cc_final: 0.7912 (ttp) REVERT: C 230 ARG cc_start: 0.8466 (ttm110) cc_final: 0.7909 (ttp-110) REVERT: C 233 GLU cc_start: 0.9155 (mp0) cc_final: 0.8815 (pt0) REVERT: C 284 ARG cc_start: 0.8624 (mmm-85) cc_final: 0.8395 (mmm-85) REVERT: C 353 ARG cc_start: 0.8117 (mtp85) cc_final: 0.7838 (ttm-80) REVERT: C 357 GLU cc_start: 0.8512 (tt0) cc_final: 0.7691 (tp30) REVERT: C 361 MET cc_start: 0.8120 (pp-130) cc_final: 0.7520 (pp-130) REVERT: C 384 GLU cc_start: 0.8494 (tp30) cc_final: 0.8060 (mm-30) REVERT: C 486 MET cc_start: 0.9409 (ptp) cc_final: 0.9179 (mtt) REVERT: C 725 ASP cc_start: 0.8808 (t0) cc_final: 0.8359 (p0) REVERT: C 814 GLU cc_start: 0.8184 (tp30) cc_final: 0.7757 (tm-30) REVERT: C 1000 MET cc_start: 0.8761 (mtt) cc_final: 0.8197 (mtt) REVERT: C 1052 MET cc_start: 0.9186 (mtt) cc_final: 0.8895 (mmm) REVERT: D 30 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8268 (mt-10) REVERT: D 124 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8556 (tp30) REVERT: D 190 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8225 (tp30) REVERT: D 366 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8295 (tptm) REVERT: D 483 HIS cc_start: 0.7642 (t-90) cc_final: 0.7434 (t-90) REVERT: D 976 GLN cc_start: 0.8407 (tm-30) cc_final: 0.8171 (tm-30) REVERT: D 980 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8030 (mtm) REVERT: D 1013 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8465 (mp0) REVERT: D 1100 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8015 (m-30) REVERT: D 1499 ARG cc_start: 0.8853 (tmm-80) cc_final: 0.8616 (ttp80) REVERT: E 44 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8700 (mt-10) REVERT: E 87 LYS cc_start: 0.9161 (ttpt) cc_final: 0.8857 (pttm) REVERT: E 88 GLU cc_start: 0.8974 (tp30) cc_final: 0.8659 (tp30) REVERT: F 367 MET cc_start: 0.9141 (tpp) cc_final: 0.8842 (tpp) REVERT: F 410 TYR cc_start: 0.8462 (t80) cc_final: 0.7946 (t80) outliers start: 27 outliers final: 15 residues processed: 194 average time/residue: 0.8856 time to fit residues: 193.7731 Evaluate side-chains 196 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 557 ARG Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 366 LYS Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain D residue 782 SER Chi-restraints excluded: chain D residue 875 THR Chi-restraints excluded: chain D residue 980 MET Chi-restraints excluded: chain D residue 1013 GLU Chi-restraints excluded: chain D residue 1051 GLU Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1452 ILE Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 65 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 276 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 253 optimal weight: 0.8980 chunk 296 optimal weight: 6.9990 chunk 338 optimal weight: 7.9990 chunk 281 optimal weight: 6.9990 chunk 261 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 232 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 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 = 0.3343 r_free = 0.3343 target = 0.087894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.057686 restraints weight = 51611.650| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 2.32 r_work: 0.2628 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2578 r_free = 0.2578 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2578 r_free = 0.2578 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29183 Z= 0.154 Angle : 0.517 8.445 39861 Z= 0.274 Chirality : 0.042 0.145 4493 Planarity : 0.004 0.081 4893 Dihedral : 15.126 70.755 4799 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.87 % Allowed : 11.19 % Favored : 87.94 % 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: 1.43 (0.15), residues: 3336 helix: 1.86 (0.14), residues: 1319 sheet: 0.21 (0.24), residues: 463 loop : 0.52 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 8 TYR 0.012 0.001 TYR D 989 PHE 0.011 0.001 PHE A 179 TRP 0.011 0.001 TRP B 200 HIS 0.005 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00368 (29175) covalent geometry : angle 0.51645 (39849) hydrogen bonds : bond 0.03902 ( 1321) hydrogen bonds : angle 4.24386 ( 3623) metal coordination : bond 0.00434 ( 8) metal coordination : angle 1.88332 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8570 (mp0) REVERT: A 145 ASP cc_start: 0.8885 (m-30) cc_final: 0.8518 (m-30) REVERT: A 154 GLU cc_start: 0.8859 (pm20) cc_final: 0.8532 (pm20) REVERT: A 155 LYS cc_start: 0.8942 (mtpp) cc_final: 0.8614 (ttmt) REVERT: A 229 GLN cc_start: 0.7699 (mt0) cc_final: 0.7403 (mm-40) REVERT: B 72 LYS cc_start: 0.9295 (mtmt) cc_final: 0.9035 (mtpp) REVERT: B 91 ASN cc_start: 0.8683 (t0) cc_final: 0.8370 (t0) REVERT: B 185 ARG cc_start: 0.8705 (ptt90) cc_final: 0.8169 (ptm-80) REVERT: B 190 THR cc_start: 0.8573 (p) cc_final: 0.8328 (t) REVERT: C 108 ILE cc_start: 0.9105 (pp) cc_final: 0.8899 (mp) REVERT: C 154 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7199 (ptm-80) REVERT: C 229 MET cc_start: 0.8147 (ttm) cc_final: 0.7917 (ttp) REVERT: C 230 ARG cc_start: 0.8460 (ttm110) cc_final: 0.7858 (ttp-110) REVERT: C 233 GLU cc_start: 0.9149 (mp0) cc_final: 0.8789 (pt0) REVERT: C 353 ARG cc_start: 0.8109 (mtp85) cc_final: 0.7852 (ttm-80) REVERT: C 357 GLU cc_start: 0.8487 (tt0) cc_final: 0.7692 (tp30) REVERT: C 361 MET cc_start: 0.8120 (pp-130) cc_final: 0.7533 (pp-130) REVERT: C 384 GLU cc_start: 0.8502 (tp30) cc_final: 0.8078 (mm-30) REVERT: C 419 THR cc_start: 0.9182 (m) cc_final: 0.8746 (p) REVERT: C 723 THR cc_start: 0.9165 (t) cc_final: 0.8913 (p) REVERT: C 725 ASP cc_start: 0.8850 (t0) cc_final: 0.8376 (p0) REVERT: C 814 GLU cc_start: 0.8168 (tp30) cc_final: 0.7753 (tm-30) REVERT: C 1000 MET cc_start: 0.8729 (mtt) cc_final: 0.8201 (mtt) REVERT: C 1052 MET cc_start: 0.9186 (mtt) cc_final: 0.8900 (mmm) REVERT: D 30 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8273 (mt-10) REVERT: D 124 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8572 (tp30) REVERT: D 190 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8224 (tp30) REVERT: D 195 VAL cc_start: 0.8894 (m) cc_final: 0.8630 (p) REVERT: D 366 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8376 (tptm) REVERT: D 976 GLN cc_start: 0.8407 (tm-30) cc_final: 0.8146 (tm-30) REVERT: D 980 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.8021 (mtm) REVERT: D 1013 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8497 (mp0) REVERT: D 1100 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.8123 (m-30) REVERT: D 1499 ARG cc_start: 0.8856 (tmm-80) cc_final: 0.8557 (ttp80) REVERT: E 87 LYS cc_start: 0.9143 (ttpt) cc_final: 0.8815 (pttm) REVERT: E 88 GLU cc_start: 0.8990 (tp30) cc_final: 0.8712 (tp30) REVERT: F 367 MET cc_start: 0.9132 (tpp) cc_final: 0.8834 (tpp) REVERT: F 410 TYR cc_start: 0.8481 (t80) cc_final: 0.7969 (t80) outliers start: 25 outliers final: 13 residues processed: 198 average time/residue: 0.8722 time to fit residues: 195.5220 Evaluate side-chains 196 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 557 ARG Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 366 LYS Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain D residue 782 SER Chi-restraints excluded: chain D residue 875 THR Chi-restraints excluded: chain D residue 980 MET Chi-restraints excluded: chain D residue 1013 GLU Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1452 ILE Chi-restraints excluded: chain E residue 65 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 6 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 169 optimal weight: 0.0070 chunk 160 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 15 optimal weight: 0.0070 chunk 81 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.088400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.058255 restraints weight = 51772.084| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 2.32 r_work: 0.2643 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2522 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2511 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2511 r_free = 0.2511 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2511 r_free = 0.2511 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2511 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29183 Z= 0.128 Angle : 0.511 10.346 39861 Z= 0.270 Chirality : 0.041 0.143 4493 Planarity : 0.004 0.092 4893 Dihedral : 15.107 70.247 4799 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.87 % Allowed : 11.33 % Favored : 87.80 % 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: 1.47 (0.15), residues: 3336 helix: 1.88 (0.14), residues: 1325 sheet: 0.20 (0.24), residues: 463 loop : 0.56 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG D 198 TYR 0.012 0.001 TYR D 989 PHE 0.010 0.001 PHE B 179 TRP 0.012 0.001 TRP B 200 HIS 0.005 0.001 HIS D 386 Details of bonding type rmsd covalent geometry : bond 0.00299 (29175) covalent geometry : angle 0.50983 (39849) hydrogen bonds : bond 0.03720 ( 1321) hydrogen bonds : angle 4.20683 ( 3623) metal coordination : bond 0.00337 ( 8) metal coordination : angle 1.71880 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11853.33 seconds wall clock time: 201 minutes 44.20 seconds (12104.20 seconds total)