Starting phenix.real_space_refine on Sat Feb 7 00:08:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ujp_64219/02_2026/9ujp_64219.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ujp_64219/02_2026/9ujp_64219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ujp_64219/02_2026/9ujp_64219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ujp_64219/02_2026/9ujp_64219.map" model { file = "/net/cci-nas-00/data/ceres_data/9ujp_64219/02_2026/9ujp_64219.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ujp_64219/02_2026/9ujp_64219.cif" } resolution = 2.53 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= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 88 5.49 5 Mg 3 5.21 5 S 70 5.16 5 C 17727 2.51 5 N 5059 2.21 5 O 5489 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s 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: 28438 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1767 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 209} Chain: "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: 8794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8794 Classifications: {'peptide': 1114} Link IDs: {'PCIS': 1, 'PTRANS': 71, 'TRANS': 1041} Chain breaks: 1 Chain: "D" Number of atoms: 10755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1362, 10747 Classifications: {'peptide': 1362} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1293} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 1362, 10747 Classifications: {'peptide': 1362} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1293} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 10921 Chain: "E" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 761 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 6, 'TRANS': 87} Chain: "G" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 861 Classifications: {'DNA': 42} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 41} 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: "F" Number of atoms: 2703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2703 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 13, 'TRANS': 319} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20166 SG CYS D1112 106.838 97.276 118.832 1.00 45.13 S ATOM 20810 SG CYS D1194 103.065 97.105 118.012 1.00 41.30 S ATOM 20866 SG CYS D1201 104.542 95.693 121.383 1.00 45.37 S ATOM 20890 SG CYS D1204 104.248 98.991 121.120 1.00 51.07 S ATOM 12814 SG CYS D 58 75.792 52.098 83.014 1.00 92.93 S ATOM 12825 SG CYS D 60 74.586 51.927 80.006 1.00 96.96 S ATOM 12936 SG CYS D 73 77.944 51.857 79.290 1.00 84.55 S ATOM 12962 SG CYS D 76 76.612 54.981 80.347 1.00 88.30 S Time building chain proxies: 8.39, per 1000 atoms: 0.30 Number of scatterers: 28438 At special positions: 0 Unit cell: (129.525, 156.75, 204.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 70 16.00 P 88 15.00 Mg 3 11.99 O 5489 8.00 N 5059 7.00 C 17727 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: 2.43 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1601 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1112 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1204 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1194 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1201 " 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 76 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 58 " Number of angles added : 12 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6208 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 49 sheets defined 44.4% alpha, 17.8% beta 32 base pairs and 73 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 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' 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: 4.255A pdb=" N SER C 25 " --> pdb=" O ILE C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 39 Processing helix chain 'C' and resid 42 through 52 Processing helix chain 'C' and resid 79 through 86 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 203 through 212 removed outlier: 3.787A pdb=" N LEU C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 222 removed outlier: 3.600A pdb=" N MET C 222 " --> pdb=" O GLN C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 228 removed outlier: 3.693A pdb=" N PHE C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 3.669A 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 359 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 375 through 389 removed outlier: 3.850A pdb=" N SER C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 408 Processing helix chain 'C' and resid 419 through 423 Processing helix chain 'C' and resid 431 through 435 removed outlier: 3.629A 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 removed outlier: 3.536A pdb=" N VAL C 539 " --> pdb=" O PRO C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 554 through 567 removed outlier: 3.657A pdb=" N MET C 560 " --> pdb=" O ASN C 556 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR C 566 " --> pdb=" O SER C 562 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN C 567 " --> pdb=" O ASN C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 591 Processing helix chain 'C' and resid 683 through 687 removed outlier: 3.719A pdb=" N ASP C 686 " --> pdb=" O ASN C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 697 Processing helix chain 'C' and resid 768 through 779 Processing helix chain 'C' and resid 874 through 880 removed outlier: 4.761A pdb=" N SER C 878 " --> pdb=" O LEU C 874 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG C 879 " --> pdb=" O GLY C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 898 removed outlier: 3.515A pdb=" N PHE C 896 " --> pdb=" O LEU C 892 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 926 removed outlier: 3.663A pdb=" N VAL C 924 " --> pdb=" O GLN C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 932 Processing helix chain 'C' and resid 937 through 950 removed outlier: 3.604A pdb=" N LYS C 949 " --> pdb=" O ARG C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 969 Processing helix chain 'C' and resid 1000 through 1005 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 1095 removed outlier: 3.508A 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 removed outlier: 3.712A pdb=" N PHE D 68 " --> pdb=" O ARG D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 102 through 107 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 163 Processing helix chain 'D' and resid 372 through 376 Processing helix chain 'D' and resid 456 through 467 removed outlier: 3.767A 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: 4.174A 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 Processing helix chain 'D' and resid 653 through 664 Processing helix chain 'D' and resid 669 through 679 removed outlier: 4.053A 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 684 through 695 removed outlier: 4.173A pdb=" N TRP D 688 " --> pdb=" O LYS D 684 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP D 689 " --> pdb=" O ASP D 685 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU D 693 " --> pdb=" O ASP D 689 " (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 783 through 794 Processing helix chain 'D' and resid 808 through 819 Processing helix chain 'D' and resid 835 through 841 removed outlier: 3.529A pdb=" N LEU D 839 " --> pdb=" O SER D 835 " (cutoff:3.500A) 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: 3.545A pdb=" N ILE D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 907 through 946 removed outlier: 7.778A pdb=" N MET D 924 " --> pdb=" O LEU D 920 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N GLU D 925 " --> pdb=" O ARG D 921 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS D 926 " --> pdb=" O LEU D 922 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR D 944 " --> pdb=" O THR D 940 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY D 946 " --> pdb=" O SER D 942 " (cutoff:3.500A) Processing helix chain 'D' and resid 950 through 954 removed outlier: 3.518A pdb=" N ALA D 954 " --> pdb=" O ILE D 951 " (cutoff:3.500A) Processing helix chain 'D' and resid 958 through 980 removed outlier: 3.896A 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 1027 Processing helix chain 'D' and resid 1031 through 1040 Processing helix chain 'D' and resid 1066 through 1103 removed outlier: 3.752A pdb=" N HIS D1075 " --> pdb=" O PHE D1071 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY D1076 " --> pdb=" O ILE D1072 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA D1089 " --> pdb=" O ALA D1085 " (cutoff:3.500A) Processing helix chain 'D' and resid 1136 through 1145 Processing helix chain 'D' and resid 1167 through 1180 Processing helix chain 'D' and resid 1190 through 1194 Processing helix chain 'D' and resid 1202 through 1206 Processing helix chain 'D' and resid 1220 through 1231 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 1340 Processing helix chain 'D' and resid 1340 through 1359 removed outlier: 3.515A pdb=" N VAL D1355 " --> pdb=" O GLU D1351 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN D1359 " --> pdb=" O VAL D1355 " (cutoff:3.500A) Processing helix chain 'D' and resid 1364 through 1376 removed outlier: 4.139A pdb=" N ILE D1368 " --> pdb=" O HIS D1364 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL D1371 " --> pdb=" O HIS D1367 " (cutoff:3.500A) Processing helix chain 'D' and resid 1397 through 1410 Processing helix chain 'D' and resid 1423 through 1430 Processing helix chain 'D' and resid 1433 through 1439 Processing helix chain 'D' and resid 1442 through 1454 Processing helix chain 'D' and resid 1461 through 1468 removed outlier: 4.008A pdb=" N ASN D1465 " --> pdb=" O GLY D1461 " (cutoff:3.500A) Processing helix chain 'D' and resid 1474 through 1477 Processing helix chain 'D' and resid 1478 through 1483 removed outlier: 4.519A pdb=" N PHE D1483 " --> pdb=" O ASP D1479 " (cutoff:3.500A) Processing helix chain 'D' and resid 1489 through 1500 Processing helix chain 'E' and resid 5 through 12 Processing helix chain 'E' and resid 15 through 33 removed outlier: 3.587A pdb=" N LEU E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 45 removed outlier: 3.729A pdb=" N ARG E 45 " --> pdb=" O PRO E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 71 removed outlier: 3.507A pdb=" N THR E 70 " --> pdb=" O LYS E 66 " (cutoff:3.500A) removed outlier: 3.655A 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 153 through 165 removed outlier: 3.708A pdb=" N GLU F 157 " --> pdb=" O PRO F 153 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU F 158 " --> pdb=" O LYS F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 190 removed outlier: 4.250A pdb=" N TYR F 173 " --> pdb=" O GLU F 169 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU F 174 " --> pdb=" O HIS F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 200 removed outlier: 3.687A pdb=" N VAL F 195 " --> pdb=" O ASN F 191 " (cutoff:3.500A) removed outlier: 3.733A 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: 3.705A pdb=" N ARG F 231 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 255 removed outlier: 3.638A pdb=" N TYR F 238 " --> pdb=" O LYS F 234 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TRP F 241 " --> pdb=" O THR F 237 " (cutoff:3.500A) removed outlier: 3.833A 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: 3.655A pdb=" N ILE F 333 " --> pdb=" O GLY F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 360 removed outlier: 3.984A pdb=" N LYS F 360 " --> pdb=" O LYS F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 373 removed outlier: 3.544A pdb=" N MET F 367 " --> pdb=" O GLU F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 390 removed outlier: 3.898A pdb=" N PHE F 389 " --> pdb=" O GLU F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 416 removed outlier: 3.629A pdb=" N ASN F 402 " --> pdb=" O ARG F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 423 removed outlier: 3.728A pdb=" N ASP F 423 " --> pdb=" O ASP F 420 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 16 removed outlier: 5.224A pdb=" N TYR A 20 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N THR A 201 " --> pdb=" O TYR A 20 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N GLU A 22 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ILE A 199 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N VAL A 24 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU A 197 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLU A 26 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU A 195 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N THR A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU A 186 " --> pdb=" O THR A 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 104 removed outlier: 3.590A pdb=" N SER A 55 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASP A 145 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VAL A 53 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLY A 147 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 5.067A 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 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: 3.772A pdb=" N TYR B 20 " --> pdb=" O GLN B 16 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ASP B 193 " --> pdb=" O PRO B 27 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N THR B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 6.679A 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: 3.554A pdb=" N SER B 55 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASP B 145 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N VAL B 53 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY B 147 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 4.695A 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: 6.674A 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 3 through 5 Processing sheet with id=AB3, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.909A pdb=" N ARG C 97 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TYR C 71 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TYR C 95 " --> pdb=" O TYR C 71 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU C 73 " --> pdb=" O PRO C 93 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY C 116 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA C 96 " --> pdb=" O PHE C 114 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N PHE C 114 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU C 98 " --> pdb=" O GLU C 112 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLU C 112 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU C 100 " --> pdb=" O GLU C 110 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLU C 110 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N HIS C 102 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 6.274A 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: 6.362A 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: 6.805A pdb=" N TYR C 158 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 4.483A 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: 5.437A pdb=" N GLU C 482 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N VAL C 475 " --> pdb=" O THR C 480 " (cutoff:3.500A) removed outlier: 6.441A 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 Processing sheet with id=AC2, first strand: chain 'C' and resid 595 through 596 removed outlier: 6.534A 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: 3.546A pdb=" N VAL C 621 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG C 610 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL C 606 " --> pdb=" O ARG C 610 " (cutoff:3.500A) removed outlier: 6.446A 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: 7.117A pdb=" N ILE C 688 " --> pdb=" O ALA C 850 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE C 852 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE C 690 " --> pdb=" O ILE C 852 " (cutoff:3.500A) removed outlier: 4.428A 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: 3.550A pdb=" N GLU C 821 " --> pdb=" O ALA C 712 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG C 802 " --> pdb=" O TYR C 826 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA C 828 " --> pdb=" O VAL C 800 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL C 800 " --> pdb=" O ALA C 828 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N LYS C 830 " --> pdb=" O GLY C 798 " (cutoff:3.500A) removed outlier: 9.128A 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: 6.902A 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: 6.314A pdb=" N CYS D 642 " --> pdb=" O VAL D 719 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL D 721 " --> pdb=" O CYS D 642 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU D 644 " --> pdb=" O VAL D 721 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE D 726 " --> pdb=" O ARG D 628 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL D 630 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU D 728 " --> pdb=" O VAL D 630 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL D 632 " --> pdb=" O LEU D 728 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1030 through 1032 removed outlier: 3.588A 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: 7.707A pdb=" N HIS D 92 " --> pdb=" O TYR D 23 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLU D 25 " --> pdb=" O HIS D 92 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N GLU D 94 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 10.137A pdb=" N LEU D 95 " --> pdb=" O PRO D 518 " (cutoff:3.500A) removed outlier: 10.760A pdb=" N THR D 97 " --> pdb=" O ALA D 516 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ALA D 516 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 152 through 153 removed outlier: 6.719A pdb=" N ASP D 453 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AD7, first strand: chain 'D' and resid 166 through 170 Processing sheet with id=AD8, first strand: chain 'D' and resid 190 through 192 removed outlier: 3.545A pdb=" N ALA D 192 " --> pdb=" O VAL D 195 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 342 through 346 Processing sheet with id=AE1, first strand: chain 'D' and resid 352 through 353 Processing sheet with id=AE2, first strand: chain 'D' and resid 398 through 402 removed outlier: 3.628A pdb=" N VAL D 443 " --> pdb=" O ASP D 438 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 527 through 529 removed outlier: 6.600A pdb=" N PHE D 535 " --> pdb=" O VAL F 315 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 827 through 828 Processing sheet with id=AE5, first strand: chain 'D' and resid 842 through 843 Processing sheet with id=AE6, first strand: chain 'D' and resid 1106 through 1109 Processing sheet with id=AE7, first strand: chain 'D' and resid 1118 through 1121 Processing sheet with id=AE8, first strand: chain 'D' and resid 1123 through 1126 Processing sheet with id=AE9, first strand: chain 'D' and resid 1153 through 1155 Processing sheet with id=AF1, first strand: chain 'D' and resid 1300 through 1303 removed outlier: 3.503A pdb=" N LYS D1301 " --> pdb=" O VAL D1294 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER D1291 " --> pdb=" O GLU D1284 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1394 through 1396 removed outlier: 5.513A pdb=" N VAL D1381 " --> pdb=" O LYS D1418 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LYS D1418 " --> pdb=" O VAL D1381 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 1484 through 1488 Processing sheet with id=AF4, first strand: chain 'E' and resid 47 through 49 1250 hydrogen bonds defined for protein. 3474 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 73 hydrogen bonds 146 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 8.55 Time building geometry restraints manager: 3.31 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: 4695 1.31 - 1.43: 7304 1.43 - 1.56: 16825 1.56 - 1.68: 182 1.68 - 1.81: 127 Bond restraints: 29133 Sorted by residual: bond pdb=" C ARG C 376 " pdb=" O ARG C 376 " ideal model delta sigma weight residual 1.244 1.182 0.062 9.80e-03 1.04e+04 3.97e+01 bond pdb=" C ARG D 35 " pdb=" CA BARG D 35 " ideal model delta sigma weight residual 1.524 1.578 -0.054 1.16e-02 7.43e+03 2.20e+01 bond pdb=" C ARG D 35 " pdb=" CA AARG D 35 " ideal model delta sigma weight residual 1.524 1.572 -0.048 1.16e-02 7.43e+03 1.71e+01 bond pdb=" N ARG C 610 " pdb=" CA ARG C 610 " ideal model delta sigma weight residual 1.456 1.409 0.047 1.23e-02 6.61e+03 1.47e+01 bond pdb=" N ARG C 376 " pdb=" CA ARG C 376 " ideal model delta sigma weight residual 1.459 1.422 0.038 1.04e-02 9.25e+03 1.31e+01 ... (remaining 29128 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 38955 1.46 - 2.92: 675 2.92 - 4.38: 128 4.38 - 5.84: 22 5.84 - 7.30: 9 Bond angle restraints: 39789 Sorted by residual: angle pdb=" O ARG D 35 " pdb=" C ARG D 35 " pdb=" CA AARG D 35 " ideal model delta sigma weight residual 120.13 126.95 -6.82 1.40e+00 5.10e-01 2.37e+01 angle pdb=" O ARG D 35 " pdb=" C ARG D 35 " pdb=" CA BARG D 35 " ideal model delta sigma weight residual 120.13 126.90 -6.77 1.40e+00 5.10e-01 2.34e+01 angle pdb=" O3' DG H 38 " pdb=" C3' DG H 38 " pdb=" C2' DG H 38 " ideal model delta sigma weight residual 111.50 104.45 7.05 1.50e+00 4.44e-01 2.21e+01 angle pdb=" N ARG C 610 " pdb=" CA ARG C 610 " pdb=" CB ARG C 610 " ideal model delta sigma weight residual 111.56 105.00 6.56 1.55e+00 4.16e-01 1.79e+01 angle pdb=" N ARG F 396 " pdb=" CA ARG F 396 " pdb=" C ARG F 396 " ideal model delta sigma weight residual 111.07 107.40 3.67 1.07e+00 8.73e-01 1.17e+01 ... (remaining 39784 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 16084 17.48 - 34.95: 1128 34.95 - 52.43: 386 52.43 - 69.91: 117 69.91 - 87.39: 33 Dihedral angle restraints: 17748 sinusoidal: 8101 harmonic: 9647 Sorted by residual: dihedral pdb=" CA ALA D 422 " pdb=" C ALA D 422 " pdb=" N ASP D 423 " pdb=" CA ASP D 423 " ideal model delta harmonic sigma weight residual -180.00 -161.07 -18.93 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ASP D1488 " pdb=" CB ASP D1488 " pdb=" CG ASP D1488 " pdb=" OD1 ASP D1488 " ideal model delta sinusoidal sigma weight residual -30.00 -88.73 58.73 1 2.00e+01 2.50e-03 1.15e+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 -163.13 -16.87 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 17745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 3306 0.041 - 0.081: 810 0.081 - 0.122: 337 0.122 - 0.162: 29 0.162 - 0.203: 2 Chirality restraints: 4484 Sorted by residual: chirality pdb=" CA ARG C 376 " pdb=" N ARG C 376 " pdb=" C ARG C 376 " pdb=" CB ARG C 376 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB ILE F 400 " pdb=" CA ILE F 400 " pdb=" CG1 ILE F 400 " pdb=" CG2 ILE F 400 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA VAL D1215 " pdb=" N VAL D1215 " pdb=" C VAL D1215 " pdb=" CB VAL D1215 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.33e-01 ... (remaining 4481 not shown) Planarity restraints: 4890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D1207 " 0.030 2.00e-02 2.50e+03 2.61e-02 1.37e+01 pdb=" CG TYR D1207 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR D1207 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR D1207 " -0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR D1207 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR D1207 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR D1207 " 0.022 2.00e-02 2.50e+03 pdb=" OH TYR D1207 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA D 192 " 0.037 5.00e-02 4.00e+02 5.66e-02 5.12e+00 pdb=" N PRO D 193 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 193 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 193 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 395 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C GLU F 395 " -0.037 2.00e-02 2.50e+03 pdb=" O GLU F 395 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG F 396 " 0.013 2.00e-02 2.50e+03 ... (remaining 4887 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 397 2.66 - 3.22: 25521 3.22 - 3.78: 45953 3.78 - 4.34: 66319 4.34 - 4.90: 104592 Nonbonded interactions: 242782 Sorted by model distance: nonbonded pdb=" OD1 ASP D 739 " pdb="MG MG D1603 " model vdw 2.099 2.170 nonbonded pdb=" OD1 ASP D 741 " pdb="MG MG D1603 " model vdw 2.099 2.170 nonbonded pdb=" OD1 ASP D 743 " pdb="MG MG D1603 " model vdw 2.100 2.170 nonbonded pdb=" OG SER C 363 " pdb=" OG SER C 366 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR D 132 " pdb=" NH2 ARG D 568 " model vdw 2.203 3.120 ... (remaining 242777 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 37.970 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 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 29141 Z= 0.149 Angle : 0.549 27.296 39801 Z= 0.269 Chirality : 0.042 0.203 4484 Planarity : 0.004 0.079 4890 Dihedral : 14.548 87.386 11540 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.14 % Allowed : 0.10 % Favored : 99.76 % 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: 1.02 (0.15), residues: 3333 helix: 1.01 (0.14), residues: 1293 sheet: 0.51 (0.26), residues: 430 loop : 0.64 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 416 TYR 0.050 0.001 TYR D1207 PHE 0.022 0.002 PHE C 699 TRP 0.024 0.001 TRP D1398 HIS 0.010 0.001 HIS D1333 Details of bonding type rmsd covalent geometry : bond 0.00286 (29133) covalent geometry : angle 0.50236 (39789) hydrogen bonds : bond 0.21540 ( 1321) hydrogen bonds : angle 7.69501 ( 3620) metal coordination : bond 0.01402 ( 8) metal coordination : angle 12.79930 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 353 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 227 PHE cc_start: 0.7583 (m-10) cc_final: 0.6803 (m-10) REVERT: C 361 MET cc_start: 0.8414 (ptm) cc_final: 0.8205 (pp-130) REVERT: E 50 THR cc_start: 0.9007 (m) cc_final: 0.8702 (p) outliers start: 4 outliers final: 2 residues processed: 356 average time/residue: 1.0258 time to fit residues: 405.5377 Evaluate side-chains 173 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 979 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS A 180 GLN B 95 GLN B 229 GLN C 390 GLN C 538 GLN D 348 GLN F 83 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.072366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.049948 restraints weight = 82833.718| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 2.65 r_work: 0.2593 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2473 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2476 r_free = 0.2476 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2476 r_free = 0.2476 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 29141 Z= 0.219 Angle : 0.615 9.223 39801 Z= 0.325 Chirality : 0.045 0.176 4484 Planarity : 0.005 0.050 4890 Dihedral : 15.584 147.446 4797 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.01 % Allowed : 6.47 % Favored : 92.51 % 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: 1.27 (0.15), residues: 3333 helix: 1.34 (0.14), residues: 1300 sheet: 0.48 (0.26), residues: 416 loop : 0.71 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 416 TYR 0.018 0.001 TYR D 132 PHE 0.022 0.002 PHE C 699 TRP 0.010 0.001 TRP B 200 HIS 0.009 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00508 (29133) covalent geometry : angle 0.61348 (39789) hydrogen bonds : bond 0.04824 ( 1321) hydrogen bonds : angle 5.08574 ( 3620) metal coordination : bond 0.00804 ( 8) metal coordination : angle 2.63935 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 227 PHE cc_start: 0.8429 (m-10) cc_final: 0.7854 (m-80) REVERT: C 251 ASP cc_start: 0.8566 (p0) cc_final: 0.8339 (p0) REVERT: C 361 MET cc_start: 0.8736 (ptm) cc_final: 0.8343 (pp-130) REVERT: C 771 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8335 (tm-30) REVERT: D 530 VAL cc_start: 0.8431 (t) cc_final: 0.8148 (m) REVERT: E 44 GLU cc_start: 0.9306 (mt-10) cc_final: 0.8979 (mt-10) REVERT: E 50 THR cc_start: 0.8913 (m) cc_final: 0.8467 (p) REVERT: F 110 MET cc_start: 0.9347 (OUTLIER) cc_final: 0.9064 (mtp) REVERT: F 336 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8561 (mt-10) REVERT: F 419 ARG cc_start: 0.8508 (ttm110) cc_final: 0.8290 (ttm110) outliers start: 29 outliers final: 8 residues processed: 201 average time/residue: 0.9438 time to fit residues: 214.7350 Evaluate side-chains 154 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain D residue 1281 VAL Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 336 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 37 optimal weight: 10.0000 chunk 312 optimal weight: 7.9990 chunk 212 optimal weight: 0.4980 chunk 301 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 290 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 261 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN B 163 ASN C 102 HIS C 390 GLN D1359 GLN E 59 ASN ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.072768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.050706 restraints weight = 70865.029| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 2.46 r_work: 0.2580 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2459 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2515 r_free = 0.2515 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2515 r_free = 0.2515 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29141 Z= 0.129 Angle : 0.521 7.929 39801 Z= 0.275 Chirality : 0.042 0.168 4484 Planarity : 0.004 0.036 4890 Dihedral : 15.251 87.008 4791 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.63 % Allowed : 7.94 % Favored : 91.43 % 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: 1.44 (0.15), residues: 3333 helix: 1.56 (0.14), residues: 1308 sheet: 0.46 (0.25), residues: 423 loop : 0.76 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 346 TYR 0.013 0.001 TYR D 128 PHE 0.011 0.001 PHE A 179 TRP 0.009 0.001 TRP B 200 HIS 0.006 0.001 HIS C 434 Details of bonding type rmsd covalent geometry : bond 0.00294 (29133) covalent geometry : angle 0.51845 (39789) hydrogen bonds : bond 0.04205 ( 1321) hydrogen bonds : angle 4.75059 ( 3620) metal coordination : bond 0.00484 ( 8) metal coordination : angle 2.82230 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8788 (tm-30) REVERT: B 107 LYS cc_start: 0.9255 (ptpp) cc_final: 0.8909 (pttm) REVERT: C 216 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8188 (pp20) REVERT: C 227 PHE cc_start: 0.8469 (m-10) cc_final: 0.8033 (m-80) REVERT: C 361 MET cc_start: 0.8745 (ptm) cc_final: 0.8352 (pp-130) REVERT: C 650 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.8027 (mtp85) REVERT: C 771 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8279 (tm-30) REVERT: D 480 GLU cc_start: 0.8923 (tt0) cc_final: 0.8374 (tm-30) REVERT: D 530 VAL cc_start: 0.8308 (t) cc_final: 0.8019 (m) REVERT: E 50 THR cc_start: 0.8884 (m) cc_final: 0.8470 (p) REVERT: E 86 GLN cc_start: 0.8971 (tm-30) cc_final: 0.8713 (tp-100) REVERT: E 90 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8863 (tp30) REVERT: F 110 MET cc_start: 0.9355 (OUTLIER) cc_final: 0.9052 (mtp) outliers start: 18 outliers final: 8 residues processed: 170 average time/residue: 0.8928 time to fit residues: 171.8002 Evaluate side-chains 149 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 650 ARG Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 1281 VAL Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 262 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 290 optimal weight: 8.9990 chunk 214 optimal weight: 3.9990 chunk 320 optimal weight: 5.9990 chunk 325 optimal weight: 0.8980 chunk 116 optimal weight: 9.9990 chunk 323 optimal weight: 2.9990 chunk 88 optimal weight: 0.0270 chunk 233 optimal weight: 2.9990 chunk 38 optimal weight: 0.0050 chunk 200 optimal weight: 0.8980 chunk 319 optimal weight: 0.0970 overall best weight: 0.3850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN C 390 GLN ** 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 = 0.3260 r_free = 0.3260 target = 0.073601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.051651 restraints weight = 66590.310| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 2.41 r_work: 0.2611 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2491 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2546 r_free = 0.2546 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2546 r_free = 0.2546 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 29141 Z= 0.104 Angle : 0.492 8.133 39801 Z= 0.259 Chirality : 0.041 0.153 4484 Planarity : 0.004 0.037 4890 Dihedral : 15.213 83.778 4791 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.77 % Allowed : 8.57 % Favored : 90.66 % 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: 1.55 (0.15), residues: 3333 helix: 1.71 (0.14), residues: 1309 sheet: 0.53 (0.26), residues: 403 loop : 0.75 (0.16), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 419 TYR 0.011 0.001 TYR D 128 PHE 0.019 0.001 PHE F 389 TRP 0.009 0.001 TRP B 200 HIS 0.006 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00231 (29133) covalent geometry : angle 0.48994 (39789) hydrogen bonds : bond 0.03564 ( 1321) hydrogen bonds : angle 4.50337 ( 3620) metal coordination : bond 0.00338 ( 8) metal coordination : angle 2.50038 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8803 (tm-30) REVERT: B 107 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8992 (pttm) REVERT: C 227 PHE cc_start: 0.8518 (m-10) cc_final: 0.8236 (m-80) REVERT: C 361 MET cc_start: 0.8724 (ptm) cc_final: 0.8333 (pp-130) REVERT: C 771 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8282 (tm-30) REVERT: D 351 MET cc_start: 0.9176 (mtp) cc_final: 0.8634 (ptp) REVERT: D 480 GLU cc_start: 0.8912 (tt0) cc_final: 0.8428 (tm-30) REVERT: D 530 VAL cc_start: 0.8288 (t) cc_final: 0.7982 (m) REVERT: E 44 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8804 (mt-10) REVERT: E 50 THR cc_start: 0.8860 (m) cc_final: 0.8464 (p) REVERT: F 110 MET cc_start: 0.9319 (OUTLIER) cc_final: 0.9111 (mtt) REVERT: F 419 ARG cc_start: 0.8459 (ttm110) cc_final: 0.8225 (ttm110) outliers start: 22 outliers final: 8 residues processed: 171 average time/residue: 0.8858 time to fit residues: 172.2889 Evaluate side-chains 154 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 1281 VAL Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 262 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 126 optimal weight: 4.9990 chunk 256 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 211 optimal weight: 0.9980 chunk 241 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 200 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 173 optimal weight: 7.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 390 GLN E 28 GLN ** 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 = 0.3184 r_free = 0.3184 target = 0.069946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.047532 restraints weight = 71099.645| |-----------------------------------------------------------------------------| r_work (start): 0.2638 rms_B_bonded: 2.48 r_work: 0.2496 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2377 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2377 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2436 r_free = 0.2436 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2436 r_free = 0.2436 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 29141 Z= 0.219 Angle : 0.553 6.972 39801 Z= 0.291 Chirality : 0.044 0.162 4484 Planarity : 0.004 0.041 4890 Dihedral : 15.329 83.737 4791 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.01 % Allowed : 8.71 % Favored : 90.27 % 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: 1.59 (0.15), residues: 3333 helix: 1.73 (0.14), residues: 1305 sheet: 0.44 (0.25), residues: 422 loop : 0.83 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 360 TYR 0.023 0.001 TYR D 128 PHE 0.026 0.002 PHE D 68 TRP 0.009 0.001 TRP D 688 HIS 0.011 0.001 HIS C 434 Details of bonding type rmsd covalent geometry : bond 0.00519 (29133) covalent geometry : angle 0.55075 (39789) hydrogen bonds : bond 0.04377 ( 1321) hydrogen bonds : angle 4.58844 ( 3620) metal coordination : bond 0.00905 ( 8) metal coordination : angle 3.16885 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8982 (ttpp) cc_final: 0.8535 (ttpp) REVERT: A 155 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.9188 (ttpp) REVERT: A 220 GLU cc_start: 0.9150 (OUTLIER) cc_final: 0.8892 (tm-30) REVERT: B 72 LYS cc_start: 0.9386 (mmtt) cc_final: 0.9177 (mptp) REVERT: B 93 SER cc_start: 0.9508 (t) cc_final: 0.9226 (p) REVERT: B 107 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8917 (pttm) REVERT: C 227 PHE cc_start: 0.8552 (m-10) cc_final: 0.8352 (m-80) REVERT: C 361 MET cc_start: 0.8725 (ptm) cc_final: 0.8379 (pp-130) REVERT: C 409 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8612 (ttp-170) REVERT: C 713 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8503 (mtm180) REVERT: C 771 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8293 (tm-30) REVERT: D 351 MET cc_start: 0.9298 (mtp) cc_final: 0.8805 (ptp) REVERT: D 480 GLU cc_start: 0.8941 (tt0) cc_final: 0.8442 (tm-30) REVERT: D 530 VAL cc_start: 0.8435 (t) cc_final: 0.8146 (m) REVERT: D 1499 ARG cc_start: 0.8544 (tmm-80) cc_final: 0.7931 (tmm-80) REVERT: E 44 GLU cc_start: 0.9285 (mt-10) cc_final: 0.9026 (mt-10) REVERT: E 87 LYS cc_start: 0.9369 (tmmt) cc_final: 0.9074 (tmmt) REVERT: F 390 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.7785 (m-80) REVERT: F 419 ARG cc_start: 0.8352 (ttm110) cc_final: 0.8119 (ttm110) outliers start: 29 outliers final: 7 residues processed: 172 average time/residue: 0.8696 time to fit residues: 169.9477 Evaluate side-chains 155 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 409 ARG Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 713 ARG Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 390 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 40 optimal weight: 0.9980 chunk 330 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 254 optimal weight: 2.9990 chunk 250 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 317 optimal weight: 0.7980 chunk 91 optimal weight: 0.0170 chunk 189 optimal weight: 3.9990 chunk 275 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 ASN B 229 GLN C 390 GLN E 28 GLN E 86 GLN ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.071807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.049531 restraints weight = 74956.518| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 2.54 r_work: 0.2546 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2426 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2426 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2483 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2483 r_free = 0.2483 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2483 r_free = 0.2483 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29141 Z= 0.112 Angle : 0.492 7.957 39801 Z= 0.260 Chirality : 0.041 0.153 4484 Planarity : 0.004 0.045 4890 Dihedral : 15.154 81.267 4791 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.56 % Allowed : 9.59 % Favored : 89.85 % 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: 1.68 (0.15), residues: 3333 helix: 1.85 (0.14), residues: 1307 sheet: 0.57 (0.26), residues: 413 loop : 0.80 (0.16), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG D 360 TYR 0.014 0.001 TYR D 128 PHE 0.023 0.001 PHE F 389 TRP 0.010 0.001 TRP B 200 HIS 0.006 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00252 (29133) covalent geometry : angle 0.49009 (39789) hydrogen bonds : bond 0.03553 ( 1321) hydrogen bonds : angle 4.40958 ( 3620) metal coordination : bond 0.00410 ( 8) metal coordination : angle 2.60069 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8981 (ttpp) cc_final: 0.8532 (ttpp) REVERT: A 220 GLU cc_start: 0.9141 (OUTLIER) cc_final: 0.8878 (tm-30) REVERT: B 59 GLU cc_start: 0.9161 (tp30) cc_final: 0.8911 (pm20) REVERT: B 93 SER cc_start: 0.9501 (t) cc_final: 0.9233 (p) REVERT: B 107 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.9013 (pttm) REVERT: C 361 MET cc_start: 0.8735 (ptm) cc_final: 0.8368 (pp-130) REVERT: C 409 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8613 (ttp-170) REVERT: C 771 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8273 (tm-30) REVERT: D 68 PHE cc_start: 0.7378 (m-10) cc_final: 0.7113 (m-10) REVERT: D 351 MET cc_start: 0.9349 (mtp) cc_final: 0.8908 (ptp) REVERT: D 480 GLU cc_start: 0.8949 (tt0) cc_final: 0.8486 (tm-30) REVERT: D 530 VAL cc_start: 0.8344 (t) cc_final: 0.8060 (m) REVERT: E 44 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8886 (mt-10) REVERT: E 50 THR cc_start: 0.8866 (m) cc_final: 0.8457 (p) REVERT: F 389 PHE cc_start: 0.8772 (t80) cc_final: 0.8528 (t80) REVERT: F 390 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.7682 (m-80) REVERT: F 419 ARG cc_start: 0.8409 (ttm110) cc_final: 0.8161 (ttm110) outliers start: 16 outliers final: 6 residues processed: 168 average time/residue: 0.8661 time to fit residues: 165.5574 Evaluate side-chains 153 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 409 ARG Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 390 PHE Chi-restraints excluded: chain F residue 417 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 143 optimal weight: 0.5980 chunk 237 optimal weight: 0.0060 chunk 31 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 130 optimal weight: 0.0980 chunk 21 optimal weight: 2.9990 chunk 230 optimal weight: 0.9980 chunk 262 optimal weight: 4.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 ASN B 229 GLN C 390 GLN E 28 GLN ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.072430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.050348 restraints weight = 65984.870| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 2.40 r_work: 0.2575 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2454 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2507 r_free = 0.2507 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2507 r_free = 0.2507 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 29141 Z= 0.104 Angle : 0.481 8.520 39801 Z= 0.253 Chirality : 0.041 0.147 4484 Planarity : 0.004 0.042 4890 Dihedral : 15.031 79.026 4791 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.59 % Allowed : 9.80 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.15), residues: 3333 helix: 1.92 (0.14), residues: 1310 sheet: 0.66 (0.26), residues: 404 loop : 0.80 (0.16), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 420 TYR 0.013 0.001 TYR D 128 PHE 0.022 0.001 PHE F 389 TRP 0.010 0.001 TRP B 200 HIS 0.005 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00234 (29133) covalent geometry : angle 0.47951 (39789) hydrogen bonds : bond 0.03387 ( 1321) hydrogen bonds : angle 4.29186 ( 3620) metal coordination : bond 0.00366 ( 8) metal coordination : angle 2.52883 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8989 (ttpp) cc_final: 0.8588 (ttpp) REVERT: A 220 GLU cc_start: 0.9146 (OUTLIER) cc_final: 0.8879 (tm-30) REVERT: B 93 SER cc_start: 0.9511 (t) cc_final: 0.9249 (p) REVERT: B 107 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8992 (pttm) REVERT: B 139 ASN cc_start: 0.9011 (t0) cc_final: 0.7956 (t0) REVERT: C 227 PHE cc_start: 0.8494 (m-80) cc_final: 0.7944 (m-80) REVERT: C 361 MET cc_start: 0.8762 (ptm) cc_final: 0.8435 (ppp) REVERT: C 771 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8243 (tm-30) REVERT: D 68 PHE cc_start: 0.7469 (m-10) cc_final: 0.7189 (m-10) REVERT: D 351 MET cc_start: 0.9361 (mtp) cc_final: 0.8910 (ptp) REVERT: D 480 GLU cc_start: 0.8936 (tt0) cc_final: 0.8535 (tm-30) REVERT: D 530 VAL cc_start: 0.8314 (t) cc_final: 0.8015 (m) REVERT: E 44 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8839 (mt-10) REVERT: E 50 THR cc_start: 0.8870 (m) cc_final: 0.8428 (p) REVERT: E 84 ARG cc_start: 0.9219 (mmm-85) cc_final: 0.8815 (mmm160) REVERT: E 86 GLN cc_start: 0.9197 (tp-100) cc_final: 0.8312 (mm-40) REVERT: F 367 MET cc_start: 0.9587 (tpp) cc_final: 0.9380 (tpp) REVERT: F 389 PHE cc_start: 0.8813 (t80) cc_final: 0.8585 (t80) REVERT: F 390 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.7687 (m-80) REVERT: F 419 ARG cc_start: 0.8434 (ttm110) cc_final: 0.8213 (ttm110) outliers start: 17 outliers final: 5 residues processed: 163 average time/residue: 0.8694 time to fit residues: 161.2345 Evaluate side-chains 153 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain D residue 1281 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 390 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 273 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 chunk 170 optimal weight: 4.9990 chunk 339 optimal weight: 0.0870 chunk 88 optimal weight: 0.9980 chunk 276 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 261 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 256 optimal weight: 2.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 ASN B 229 GLN C 390 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 = 0.3235 r_free = 0.3235 target = 0.072278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.049932 restraints weight = 75263.960| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 2.55 r_work: 0.2596 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2482 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2477 r_free = 0.2477 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2477 r_free = 0.2477 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29141 Z= 0.114 Angle : 0.484 7.504 39801 Z= 0.254 Chirality : 0.041 0.148 4484 Planarity : 0.004 0.043 4890 Dihedral : 14.998 77.740 4791 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.49 % Allowed : 10.01 % Favored : 89.50 % 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: 1.76 (0.15), residues: 3333 helix: 1.95 (0.14), residues: 1309 sheet: 0.66 (0.26), residues: 404 loop : 0.81 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 84 TYR 0.013 0.001 TYR D 128 PHE 0.022 0.001 PHE F 389 TRP 0.009 0.001 TRP B 200 HIS 0.005 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00259 (29133) covalent geometry : angle 0.48264 (39789) hydrogen bonds : bond 0.03422 ( 1321) hydrogen bonds : angle 4.26368 ( 3620) metal coordination : bond 0.00400 ( 8) metal coordination : angle 2.44444 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8990 (ttpp) cc_final: 0.8588 (ttpp) REVERT: A 220 GLU cc_start: 0.9158 (OUTLIER) cc_final: 0.8899 (tm-30) REVERT: B 93 SER cc_start: 0.9519 (t) cc_final: 0.9253 (p) REVERT: B 107 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8999 (pttm) REVERT: C 230 ARG cc_start: 0.8817 (ttp-110) cc_final: 0.8573 (ttp-110) REVERT: C 361 MET cc_start: 0.8764 (ptm) cc_final: 0.8462 (ppp) REVERT: C 771 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8272 (tm-30) REVERT: D 68 PHE cc_start: 0.7572 (m-10) cc_final: 0.7254 (m-10) REVERT: D 90 MET cc_start: 0.9287 (mtp) cc_final: 0.8997 (mtp) REVERT: D 351 MET cc_start: 0.9379 (mtp) cc_final: 0.8930 (ptp) REVERT: D 480 GLU cc_start: 0.8959 (tt0) cc_final: 0.8579 (tm-30) REVERT: D 530 VAL cc_start: 0.8313 (t) cc_final: 0.8011 (m) REVERT: D 1086 LEU cc_start: 0.8928 (tt) cc_final: 0.8567 (mt) REVERT: E 44 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8871 (mt-10) REVERT: E 50 THR cc_start: 0.8875 (m) cc_final: 0.8439 (p) REVERT: E 86 GLN cc_start: 0.8965 (tp-100) cc_final: 0.8727 (tp-100) REVERT: F 390 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.7666 (m-80) REVERT: F 419 ARG cc_start: 0.8437 (ttm110) cc_final: 0.7766 (ptp-110) outliers start: 14 outliers final: 5 residues processed: 161 average time/residue: 0.8908 time to fit residues: 162.9426 Evaluate side-chains 152 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain D residue 1281 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 390 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 270 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 251 optimal weight: 5.9990 chunk 246 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 221 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 ASN B 229 GLN C 390 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 = 0.3209 r_free = 0.3209 target = 0.071101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.048404 restraints weight = 84426.333| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 2.71 r_work: 0.2513 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2391 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2451 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2451 r_free = 0.2451 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2451 r_free = 0.2451 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2451 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29141 Z= 0.152 Angle : 0.510 10.259 39801 Z= 0.267 Chirality : 0.042 0.147 4484 Planarity : 0.004 0.044 4890 Dihedral : 15.038 76.298 4791 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.56 % Allowed : 10.11 % Favored : 89.33 % 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: 1.73 (0.15), residues: 3333 helix: 1.90 (0.14), residues: 1316 sheet: 0.60 (0.26), residues: 407 loop : 0.82 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 84 TYR 0.017 0.001 TYR D 128 PHE 0.014 0.001 PHE D 982 TRP 0.008 0.001 TRP D 996 HIS 0.006 0.001 HIS C 434 Details of bonding type rmsd covalent geometry : bond 0.00356 (29133) covalent geometry : angle 0.50834 (39789) hydrogen bonds : bond 0.03656 ( 1321) hydrogen bonds : angle 4.30364 ( 3620) metal coordination : bond 0.00559 ( 8) metal coordination : angle 2.44701 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ASP cc_start: 0.8464 (p0) cc_final: 0.7844 (t0) REVERT: A 220 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.8923 (tm-30) REVERT: B 93 SER cc_start: 0.9542 (t) cc_final: 0.9279 (p) REVERT: B 107 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8924 (pttm) REVERT: C 227 PHE cc_start: 0.8541 (m-80) cc_final: 0.7979 (m-80) REVERT: C 230 ARG cc_start: 0.8794 (ttp-110) cc_final: 0.8542 (ttp-110) REVERT: C 251 ASP cc_start: 0.8696 (p0) cc_final: 0.8427 (p0) REVERT: C 361 MET cc_start: 0.8780 (ptm) cc_final: 0.8446 (ppp) REVERT: C 771 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8290 (tm-30) REVERT: D 68 PHE cc_start: 0.7719 (m-10) cc_final: 0.7503 (m-10) REVERT: D 351 MET cc_start: 0.9440 (mtp) cc_final: 0.9035 (ptp) REVERT: D 480 GLU cc_start: 0.8962 (tt0) cc_final: 0.8611 (tm-30) REVERT: D 530 VAL cc_start: 0.8395 (t) cc_final: 0.8101 (m) REVERT: D 1499 ARG cc_start: 0.8608 (tmm-80) cc_final: 0.8222 (tmm-80) REVERT: E 44 GLU cc_start: 0.9277 (mt-10) cc_final: 0.8975 (mt-10) REVERT: E 86 GLN cc_start: 0.8702 (tp-100) cc_final: 0.8225 (tp-100) REVERT: E 90 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: F 367 MET cc_start: 0.9564 (tpp) cc_final: 0.9356 (tpp) REVERT: F 390 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.7689 (m-80) REVERT: F 419 ARG cc_start: 0.8462 (ttm110) cc_final: 0.7796 (ptp-110) outliers start: 16 outliers final: 7 residues processed: 164 average time/residue: 0.9236 time to fit residues: 172.0831 Evaluate side-chains 154 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain D residue 1281 VAL Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 390 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 234 optimal weight: 0.0970 chunk 159 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 188 optimal weight: 0.3980 chunk 174 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 221 optimal weight: 2.9990 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 ASN B 229 GLN C 390 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 = 0.3216 r_free = 0.3216 target = 0.071426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.049246 restraints weight = 65996.432| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 2.39 r_work: 0.2585 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2473 r_free = 0.2473 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2473 r_free = 0.2473 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29141 Z= 0.133 Angle : 0.502 9.758 39801 Z= 0.263 Chirality : 0.041 0.147 4484 Planarity : 0.004 0.044 4890 Dihedral : 15.023 74.995 4791 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.42 % Allowed : 10.25 % Favored : 89.33 % 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: 1.73 (0.15), residues: 3333 helix: 1.92 (0.14), residues: 1315 sheet: 0.62 (0.26), residues: 399 loop : 0.80 (0.16), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 137 TYR 0.015 0.001 TYR D 128 PHE 0.023 0.001 PHE F 389 TRP 0.008 0.001 TRP B 200 HIS 0.005 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00309 (29133) covalent geometry : angle 0.50023 (39789) hydrogen bonds : bond 0.03528 ( 1321) hydrogen bonds : angle 4.27813 ( 3620) metal coordination : bond 0.00480 ( 8) metal coordination : angle 2.18633 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.9016 (ttpp) cc_final: 0.8501 (ttpp) REVERT: A 191 ASP cc_start: 0.8491 (p0) cc_final: 0.7768 (t0) REVERT: A 220 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8900 (tm-30) REVERT: B 93 SER cc_start: 0.9552 (t) cc_final: 0.9295 (p) REVERT: B 107 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8917 (pttm) REVERT: C 227 PHE cc_start: 0.8584 (m-80) cc_final: 0.8052 (m-80) REVERT: C 251 ASP cc_start: 0.8696 (p0) cc_final: 0.8424 (p0) REVERT: C 361 MET cc_start: 0.8793 (ptm) cc_final: 0.8494 (ppp) REVERT: C 771 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8273 (tm-30) REVERT: D 66 GLN cc_start: 0.8201 (tm-30) cc_final: 0.7907 (tm-30) REVERT: D 351 MET cc_start: 0.9454 (mtp) cc_final: 0.9018 (ptp) REVERT: D 480 GLU cc_start: 0.8955 (tt0) cc_final: 0.8622 (tm-30) REVERT: D 530 VAL cc_start: 0.8386 (t) cc_final: 0.8097 (m) REVERT: E 44 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8887 (mt-10) REVERT: E 86 GLN cc_start: 0.8670 (tp-100) cc_final: 0.8258 (tm-30) REVERT: E 90 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7005 (mp0) REVERT: F 367 MET cc_start: 0.9583 (tpp) cc_final: 0.9377 (tpp) REVERT: F 390 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.7679 (m-80) REVERT: F 419 ARG cc_start: 0.8418 (ttm110) cc_final: 0.7792 (ptp-110) outliers start: 12 outliers final: 6 residues processed: 157 average time/residue: 0.8633 time to fit residues: 154.1769 Evaluate side-chains 156 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain D residue 1281 VAL Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 390 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 330 optimal weight: 4.9990 chunk 128 optimal weight: 0.0060 chunk 275 optimal weight: 0.4980 chunk 219 optimal weight: 3.9990 chunk 331 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 262 optimal weight: 0.8980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 ASN B 229 GLN C 390 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 = 0.3235 r_free = 0.3235 target = 0.072226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.049973 restraints weight = 70887.956| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 2.49 r_work: 0.2564 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2445 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2445 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2500 r_free = 0.2500 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2500 r_free = 0.2500 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29141 Z= 0.109 Angle : 0.492 9.623 39801 Z= 0.258 Chirality : 0.041 0.147 4484 Planarity : 0.004 0.045 4890 Dihedral : 14.972 73.112 4791 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.49 % Allowed : 10.25 % Favored : 89.26 % 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: 1.76 (0.15), residues: 3333 helix: 1.97 (0.14), residues: 1311 sheet: 0.66 (0.26), residues: 390 loop : 0.79 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 230 TYR 0.013 0.001 TYR D 128 PHE 0.018 0.001 PHE D 68 TRP 0.009 0.001 TRP B 200 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00251 (29133) covalent geometry : angle 0.49093 (39789) hydrogen bonds : bond 0.03323 ( 1321) hydrogen bonds : angle 4.21618 ( 3620) metal coordination : bond 0.00378 ( 8) metal coordination : angle 2.09008 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13117.81 seconds wall clock time: 223 minutes 15.34 seconds (13395.34 seconds total)