Starting phenix.real_space_refine on Sat Feb 7 00:35:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uko_64251/02_2026/9uko_64251.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uko_64251/02_2026/9uko_64251.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uko_64251/02_2026/9uko_64251.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uko_64251/02_2026/9uko_64251.map" model { file = "/net/cci-nas-00/data/ceres_data/9uko_64251/02_2026/9uko_64251.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uko_64251/02_2026/9uko_64251.cif" } resolution = 2.89 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= 0.003 sd= 0.049 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 94 5.49 5 Mg 4 5.21 5 S 70 5.16 5 C 17830 2.51 5 N 5097 2.21 5 O 5544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 28641 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1795 Classifications: {'peptide': 228} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 213} Chain: "B" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1782 Classifications: {'peptide': 226} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 211} 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: 10776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1365, 10776 Classifications: {'peptide': 1365} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1296} Chain breaks: 2 Chain: "E" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 761 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 6, 'TRANS': 87} Chain: "F" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2755 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 13, 'TRANS': 326} Chain breaks: 1 Chain: "G" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 883 Classifications: {'DNA': 43} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 42} Chain breaks: 1 Chain: "H" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 987 Classifications: {'DNA': 48} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 47} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "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: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 24 Unusual residues: {' MG': 2, ' ZN': 2, 'C5P%rna3p': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'B4P': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20205 SG CYS D1112 23.254 60.915 119.568 1.00 29.77 S ATOM 20849 SG CYS D1194 27.242 60.795 118.668 1.00 18.35 S ATOM 20905 SG CYS D1201 25.797 62.398 121.596 1.00 21.16 S ATOM 20929 SG CYS D1204 26.162 59.422 121.997 1.00 30.03 S ATOM 12849 SG CYS D 58 55.944 105.128 82.698 1.00 56.83 S ATOM 12860 SG CYS D 60 57.311 105.961 79.902 1.00 61.17 S ATOM 12971 SG CYS D 73 53.811 105.828 79.354 1.00 55.00 S ATOM 12997 SG CYS D 76 55.393 102.375 80.126 1.00 50.58 S Time building chain proxies: 6.56, per 1000 atoms: 0.23 Number of scatterers: 28641 At special positions: 0 Unit cell: (133.625, 158.212, 207.386, 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 94 15.00 Mg 4 11.99 O 5544 8.00 N 5097 7.00 C 17830 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 1.5 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 D1194 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1204 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1201 " pdb=" ZN D1602 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 76 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 58 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 73 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 60 " Number of angles added : 12 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6236 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 52 sheets defined 43.4% alpha, 17.8% beta 23 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 4.37 Creating SS restraints... Processing helix chain 'A' and resid 31 through 47 removed outlier: 3.842A pdb=" N THR A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 74 through 83 Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 152 through 157 removed outlier: 3.532A pdb=" N HIS A 156 " --> pdb=" O PRO A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 223 Processing helix chain 'B' and resid 31 through 47 removed outlier: 3.620A pdb=" N THR B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) 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: 4.054A pdb=" N SER C 25 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR C 26 " --> pdb=" O GLN C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 39 removed outlier: 3.661A pdb=" N ARG C 39 " --> pdb=" O PRO C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 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: 3.940A pdb=" N LEU C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 222 Processing helix chain 'C' and resid 223 through 228 removed outlier: 3.648A pdb=" N PHE C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 4.029A 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 388 Processing helix chain 'C' and resid 399 through 408 Processing helix chain 'C' and resid 431 through 435 removed outlier: 3.698A 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 removed outlier: 3.566A pdb=" N VAL C 529 " --> pdb=" O PRO C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 547 removed outlier: 3.527A pdb=" N LEU C 546 " --> pdb=" O ASN C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 554 through 565 removed outlier: 3.816A pdb=" N MET C 560 " --> pdb=" O ASN C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 568 No H-bonds generated for 'chain 'C' and resid 566 through 568' Processing helix chain 'C' and resid 583 through 591 Processing helix chain 'C' and resid 683 through 687 removed outlier: 3.755A pdb=" N ASP C 686 " --> pdb=" O ASN C 683 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA C 687 " --> pdb=" O PHE C 684 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 683 through 687' 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: 4.659A pdb=" N SER C 878 " --> pdb=" O LEU C 874 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG C 879 " --> pdb=" O GLY C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 898 Processing helix chain 'C' and resid 910 through 933 removed outlier: 4.200A pdb=" N LYS C 928 " --> pdb=" O VAL C 924 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG C 929 " --> pdb=" O TYR C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 950 Processing helix chain 'C' and resid 958 through 969 Processing helix chain 'C' and resid 1000 through 1004 Processing helix chain 'C' and resid 1033 through 1044 Processing helix chain 'C' and resid 1045 through 1054 Processing helix chain 'C' and resid 1059 through 1072 Processing helix chain 'C' and resid 1082 through 1094 removed outlier: 3.616A pdb=" N ARG C1086 " --> pdb=" O PRO C1082 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 22 Processing helix chain 'D' and resid 46 through 51 Processing helix chain 'D' and resid 65 through 69 removed outlier: 3.567A 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 removed outlier: 3.724A pdb=" N ASP D 107 " --> pdb=" O TRP D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 117 Processing helix chain 'D' and resid 119 through 128 Processing helix chain 'D' and resid 154 through 164 Processing helix chain 'D' and resid 372 through 376 Processing helix chain 'D' and resid 423 through 426 Processing helix chain 'D' and resid 457 through 468 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 539 through 560 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: 3.969A pdb=" N ARG D 679 " --> pdb=" O ARG D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 683 Processing helix chain 'D' and resid 685 through 695 removed outlier: 3.954A pdb=" N ASP D 689 " --> pdb=" O ASP D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 711 No H-bonds generated for 'chain 'D' and resid 709 through 711' Processing helix chain 'D' and resid 729 through 731 No H-bonds generated for 'chain 'D' and resid 729 through 731' Processing helix chain 'D' and resid 732 through 737 Processing helix chain 'D' and resid 752 through 762 Processing helix chain 'D' and resid 764 through 768 Processing helix chain 'D' and resid 782 through 794 removed outlier: 3.579A pdb=" N ILE D 792 " --> pdb=" O GLY D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 808 through 818 removed outlier: 3.557A pdb=" N ALA D 812 " --> pdb=" O THR D 808 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 841 removed outlier: 3.657A 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 Processing helix chain 'D' and resid 907 through 923 Processing helix chain 'D' and resid 923 through 946 removed outlier: 3.549A pdb=" N THR D 944 " --> pdb=" O THR D 940 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLY D 946 " --> pdb=" O SER D 942 " (cutoff:3.500A) Processing helix chain 'D' and resid 950 through 954 removed outlier: 3.546A pdb=" N ALA D 954 " --> pdb=" O ILE D 951 " (cutoff:3.500A) Processing helix chain 'D' and resid 958 through 980 removed outlier: 4.225A 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 1102 removed outlier: 3.714A pdb=" N HIS D1075 " --> pdb=" O PHE D1071 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY D1076 " --> pdb=" O ILE D1072 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR D1088 " --> pdb=" O THR D1084 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ALA D1089 " --> pdb=" O ALA D1085 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP D1090 " --> pdb=" O LEU D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 1136 through 1145 Processing helix chain 'D' and resid 1167 through 1180 Processing helix chain 'D' and resid 1190 through 1194 Processing helix chain 'D' and resid 1202 through 1206 Processing helix chain 'D' and resid 1220 through 1231 Processing helix chain 'D' and resid 1232 through 1236 Processing helix chain 'D' and resid 1255 through 1264 Processing helix chain 'D' and resid 1331 through 1339 Processing helix chain 'D' and resid 1340 through 1359 removed outlier: 3.852A pdb=" N VAL D1355 " --> pdb=" O GLU D1351 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR D1356 " --> pdb=" O ILE D1352 " (cutoff:3.500A) Processing helix chain 'D' and resid 1364 through 1376 removed outlier: 4.334A pdb=" N ILE D1368 " --> pdb=" O HIS D1364 " (cutoff:3.500A) Processing helix chain 'D' and resid 1397 through 1410 Processing helix chain 'D' and resid 1423 through 1430 Processing helix chain 'D' and resid 1433 through 1441 removed outlier: 3.590A pdb=" N ALA D1437 " --> pdb=" O SER D1433 " (cutoff:3.500A) Processing helix chain 'D' and resid 1442 through 1454 Processing helix chain 'D' and resid 1462 through 1469 Processing helix chain 'D' and resid 1474 through 1478 Processing helix chain 'D' and resid 1489 through 1501 removed outlier: 3.607A pdb=" N ARG D1499 " --> pdb=" O ILE D1495 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 12 Processing helix chain 'E' and resid 15 through 33 Processing helix chain 'E' and resid 59 through 71 removed outlier: 3.597A pdb=" N TRP E 63 " --> pdb=" O ASN E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 93 Processing helix chain 'F' and resid 79 through 89 Processing helix chain 'F' and resid 95 through 121 Processing helix chain 'F' and resid 123 through 137 Processing helix chain 'F' and resid 152 through 165 Processing helix chain 'F' and resid 167 through 190 removed outlier: 4.418A pdb=" N TYR F 173 " --> pdb=" O GLU F 169 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU F 174 " --> pdb=" O HIS F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 200 removed outlier: 3.531A pdb=" N VAL F 195 " --> pdb=" O ASN F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 227 Processing helix chain 'F' and resid 234 through 255 removed outlier: 3.877A pdb=" N TYR F 238 " --> pdb=" O LYS F 234 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TRP F 241 " --> pdb=" O THR F 237 " (cutoff:3.500A) removed outlier: 3.838A 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 removed outlier: 3.532A pdb=" N GLY F 296 " --> pdb=" O ALA F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 311 Processing helix chain 'F' and resid 328 through 333 removed outlier: 3.811A pdb=" N ILE F 333 " --> pdb=" O GLY F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 359 Processing helix chain 'F' and resid 362 through 373 removed outlier: 3.699A pdb=" N MET F 367 " --> pdb=" O GLU F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 391 removed outlier: 3.534A pdb=" N PHE F 389 " --> pdb=" O GLU F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 416 removed outlier: 3.853A pdb=" N ILE F 397 " --> pdb=" O THR F 393 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG F 398 " --> pdb=" O ARG F 394 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN F 399 " --> pdb=" O GLU F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 423 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 16 removed outlier: 5.402A pdb=" N TYR A 20 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N THR A 201 " --> pdb=" O TYR A 20 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N GLU A 22 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ILE A 199 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N VAL A 24 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LEU A 197 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N GLU A 26 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LEU A 195 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N THR A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 6.447A 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: 7.376A pdb=" N ASN A 139 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ILE A 58 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLU A 141 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL A 56 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ARG A 143 " --> pdb=" O THR A 54 " (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 15 removed outlier: 5.119A pdb=" N TYR B 20 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR B 201 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N GLU B 22 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ILE B 199 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL B 24 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU B 197 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N GLU B 26 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU B 195 " --> pdb=" O GLU B 26 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 6.508A 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: 7.462A pdb=" N ASN B 139 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE B 58 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLU B 141 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL B 56 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG B 143 " --> pdb=" O THR B 54 " (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: 6.900A pdb=" N VAL B 109 " --> pdb=" O ILE B 129 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 150 through 151 Processing sheet with id=AB2, first strand: chain 'C' and resid 2 through 5 Processing sheet with id=AB3, first strand: chain 'C' and resid 54 through 55 removed outlier: 5.588A pdb=" N LEU C 66 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE C 101 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N PHE C 68 " --> pdb=" O GLN C 99 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN C 99 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU C 70 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA C 96 " --> pdb=" O PHE C 114 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N PHE C 114 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU C 98 " --> pdb=" O GLU C 112 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLU C 112 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU C 100 " --> pdb=" O GLU C 110 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N GLU C 110 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N HIS C 102 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 6.587A 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: 6.318A 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: 6.675A pdb=" N TYR C 158 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 4.420A 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: 7.006A pdb=" N ILE C 467 " --> pdb=" O MET C 486 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N MET C 486 " --> pdb=" O ILE C 467 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N THR C 469 " --> pdb=" O VAL C 484 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL C 484 " --> pdb=" O THR C 469 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TYR C 471 " --> pdb=" O GLU C 482 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLU C 482 " --> pdb=" O TYR C 471 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ARG C 473 " --> pdb=" O THR C 480 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C 478 " --> 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 495 through 497 Processing sheet with id=AC2, first strand: chain 'C' and resid 503 through 504 removed outlier: 3.701A pdb=" N ARG C 507 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 595 through 596 removed outlier: 6.504A pdb=" N LEU C 595 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 620 through 624 removed outlier: 6.884A pdb=" N ARG C 610 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL C 606 " --> pdb=" O ARG C 610 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL C 612 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 629 through 630 Processing sheet with id=AC6, first strand: chain 'C' and resid 661 through 662 Processing sheet with id=AC7, first strand: chain 'C' and resid 971 through 972 removed outlier: 7.078A pdb=" N ILE C 688 " --> pdb=" O ALA C 850 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE C 852 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE C 690 " --> pdb=" O ILE C 852 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 689 " --> pdb=" O ILE C 870 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N VAL C 869 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU C 673 " --> pdb=" O VAL C 869 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N LEU C 871 " --> pdb=" O LEU C 673 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA C 675 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL C 988 " --> pdb=" O ILE C 676 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 702 through 713 removed outlier: 3.643A pdb=" N GLU C 821 " --> pdb=" O ALA C 712 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG C 802 " --> pdb=" O TYR C 826 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA C 828 " --> pdb=" O VAL C 800 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N VAL C 800 " --> pdb=" O ALA C 828 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N LYS C 830 " --> pdb=" O GLY C 798 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N GLY C 798 " --> pdb=" O LYS C 830 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 721 through 722 Processing sheet with id=AD1, first strand: chain 'C' and resid 754 through 756 removed outlier: 6.945A pdb=" N LEU C 790 " --> pdb=" O LEU C 755 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1006 through 1008 Processing sheet with id=AD3, first strand: chain 'C' and resid 1030 through 1032 removed outlier: 3.656A pdb=" N GLN C1030 " --> pdb=" O VAL D 623 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1097 through 1102 Processing sheet with id=AD5, first strand: chain 'D' and resid 71 through 72 removed outlier: 4.193A pdb=" N LYS D 71 " --> pdb=" O VAL D 80 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 91 through 100 removed outlier: 10.171A pdb=" N LEU D 95 " --> pdb=" O PRO D 518 " (cutoff:3.500A) removed outlier: 10.941A pdb=" N THR D 97 " --> pdb=" O ALA D 516 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ALA D 516 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 152 through 153 removed outlier: 6.918A pdb=" N ASP D 453 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AD9, first strand: chain 'D' and resid 166 through 170 removed outlier: 3.643A pdb=" N GLU D 183 " --> pdb=" O ALA D 203 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 342 through 346 removed outlier: 3.693A pdb=" N ALA D 359 " --> pdb=" O VAL D 385 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 342 through 346 removed outlier: 6.869A pdb=" N GLU D 389 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL D 211 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU D 387 " --> pdb=" O VAL D 211 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 352 through 353 Processing sheet with id=AE4, first strand: chain 'D' and resid 398 through 402 Processing sheet with id=AE5, first strand: chain 'D' and resid 420 through 422 removed outlier: 7.151A pdb=" N VAL D 427 " --> pdb=" O LEU D 421 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 527 through 529 removed outlier: 6.589A pdb=" N PHE D 535 " --> pdb=" O VAL F 315 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 827 through 828 Processing sheet with id=AE8, first strand: chain 'D' and resid 842 through 843 Processing sheet with id=AE9, first strand: chain 'D' and resid 1106 through 1109 Processing sheet with id=AF1, first strand: chain 'D' and resid 1118 through 1121 Processing sheet with id=AF2, first strand: chain 'D' and resid 1123 through 1126 Processing sheet with id=AF3, first strand: chain 'D' and resid 1153 through 1155 Processing sheet with id=AF4, first strand: chain 'D' and resid 1300 through 1305 removed outlier: 4.091A pdb=" N LEU D1290 " --> pdb=" O LEU D1305 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 1394 through 1396 removed outlier: 6.781A pdb=" N ALA D1416 " --> pdb=" O THR D1382 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 1485 through 1488 Processing sheet with id=AF7, first strand: chain 'E' and resid 47 through 49 1248 hydrogen bonds defined for protein. 3480 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 58 hydrogen bonds 116 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 8.91 Time building geometry restraints manager: 3.56 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: 4708 1.31 - 1.43: 7445 1.43 - 1.56: 16874 1.56 - 1.68: 189 1.68 - 1.81: 127 Bond restraints: 29343 Sorted by residual: bond pdb=" O5' C5P D1605 " pdb=" P C5P D1605 " ideal model delta sigma weight residual 1.709 1.594 0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" O3' DA G 15 " pdb=" P DG G 16 " ideal model delta sigma weight residual 1.607 1.549 0.058 1.50e-02 4.44e+03 1.51e+01 bond pdb=" O3' DC H 36 " pdb=" P DC H 37 " ideal model delta sigma weight residual 1.607 1.549 0.058 1.50e-02 4.44e+03 1.47e+01 bond pdb=" O5E B4P G 101 " pdb=" PA B4P G 101 " ideal model delta sigma weight residual 1.656 1.589 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" O5F B4P G 101 " pdb=" PD B4P G 101 " ideal model delta sigma weight residual 1.650 1.590 0.060 2.00e-02 2.50e+03 9.12e+00 ... (remaining 29338 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 39850 2.78 - 5.57: 220 5.57 - 8.35: 15 8.35 - 11.13: 2 11.13 - 13.91: 2 Bond angle restraints: 40089 Sorted by residual: angle pdb=" O3B B4P G 101 " pdb=" PG B4P G 101 " pdb=" O3G B4P G 101 " ideal model delta sigma weight residual 95.27 109.18 -13.91 3.00e+00 1.11e-01 2.15e+01 angle pdb=" C4' DG G 16 " pdb=" C3' DG G 16 " pdb=" O3' DG G 16 " ideal model delta sigma weight residual 110.00 103.45 6.55 1.50e+00 4.44e-01 1.90e+01 angle pdb=" O3A B4P G 101 " pdb=" PA B4P G 101 " pdb=" O5E B4P G 101 " ideal model delta sigma weight residual 92.61 104.25 -11.64 3.00e+00 1.11e-01 1.51e+01 angle pdb=" PD B4P G 101 " pdb=" O3G B4P G 101 " pdb=" PG B4P G 101 " ideal model delta sigma weight residual 122.47 132.96 -10.49 3.00e+00 1.11e-01 1.22e+01 angle pdb=" O3' DA G 15 " pdb=" C3' DA G 15 " pdb=" C2' DA G 15 " ideal model delta sigma weight residual 111.50 106.46 5.04 1.50e+00 4.44e-01 1.13e+01 ... (remaining 40084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.25: 16914 27.25 - 54.51: 814 54.51 - 81.76: 170 81.76 - 109.02: 12 109.02 - 136.27: 3 Dihedral angle restraints: 17913 sinusoidal: 8225 harmonic: 9688 Sorted by residual: dihedral pdb=" C22 1N7 B 401 " pdb=" C23 1N7 B 401 " pdb=" C24 1N7 B 401 " pdb=" N1 1N7 B 401 " ideal model delta sinusoidal sigma weight residual -132.70 3.57 -136.27 1 3.00e+01 1.11e-03 1.84e+01 dihedral pdb=" C4' DG H 38 " pdb=" C3' DG H 38 " pdb=" O3' DG H 38 " pdb=" P DT H 39 " ideal model delta sinusoidal sigma weight residual 220.00 85.24 134.76 1 3.50e+01 8.16e-04 1.34e+01 dihedral pdb=" C4' DA H 5 " pdb=" C3' DA H 5 " pdb=" O3' DA H 5 " pdb=" P DC H 6 " ideal model delta sinusoidal sigma weight residual 220.00 88.73 131.27 1 3.50e+01 8.16e-04 1.30e+01 ... (remaining 17910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 3406 0.044 - 0.089: 807 0.089 - 0.133: 279 0.133 - 0.178: 25 0.178 - 0.222: 1 Chirality restraints: 4518 Sorted by residual: chirality pdb=" C1F B4P G 101 " pdb=" C2F B4P G 101 " pdb=" N9B B4P G 101 " pdb=" O4F B4P G 101 " both_signs ideal model delta sigma weight residual False 2.32 2.55 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C3' DG G 16 " pdb=" C4' DG G 16 " pdb=" O3' DG G 16 " pdb=" C2' DG G 16 " both_signs ideal model delta sigma weight residual False -2.66 -2.83 0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CB VAL D 354 " pdb=" CA VAL D 354 " pdb=" CG1 VAL D 354 " pdb=" CG2 VAL D 354 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.35e-01 ... (remaining 4515 not shown) Planarity restraints: 4911 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA G 15 " -0.037 2.00e-02 2.50e+03 1.80e-02 8.87e+00 pdb=" N9 DA G 15 " 0.041 2.00e-02 2.50e+03 pdb=" C8 DA G 15 " -0.009 2.00e-02 2.50e+03 pdb=" N7 DA G 15 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DA G 15 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DA G 15 " -0.005 2.00e-02 2.50e+03 pdb=" N6 DA G 15 " -0.011 2.00e-02 2.50e+03 pdb=" N1 DA G 15 " -0.006 2.00e-02 2.50e+03 pdb=" C2 DA G 15 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DA G 15 " 0.011 2.00e-02 2.50e+03 pdb=" C4 DA G 15 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 145 " -0.046 5.00e-02 4.00e+02 7.08e-02 8.02e+00 pdb=" N PRO D 146 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO D 146 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 146 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 247 " 0.031 5.00e-02 4.00e+02 4.63e-02 3.42e+00 pdb=" N PRO C 248 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 248 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 248 " 0.026 5.00e-02 4.00e+02 ... (remaining 4908 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 121 2.51 - 3.11: 20281 3.11 - 3.71: 42730 3.71 - 4.30: 64177 4.30 - 4.90: 107883 Nonbonded interactions: 235192 Sorted by model distance: nonbonded pdb=" OD1 ASP D 739 " pdb="MG MG D1603 " model vdw 1.916 2.170 nonbonded pdb="MG MG D1603 " pdb=" O3' C5P D1605 " model vdw 2.068 2.170 nonbonded pdb=" O GLU C 720 " pdb=" NH2 ARG C 820 " model vdw 2.196 3.120 nonbonded pdb=" NH1 ARG D 65 " pdb=" O GLY F 378 " model vdw 2.204 3.120 nonbonded pdb=" NH1 ARG D1108 " pdb=" O TYR D1198 " model vdw 2.208 3.120 ... (remaining 235187 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 4 through 229) selection = (chain 'B' and resid 4 through 229) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.05 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.400 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 37.970 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 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 0.115 29352 Z= 0.152 Angle : 0.592 27.822 40101 Z= 0.282 Chirality : 0.043 0.222 4518 Planarity : 0.004 0.071 4911 Dihedral : 15.542 136.273 11677 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: 1.10 (0.15), residues: 3347 helix: 1.71 (0.15), residues: 1280 sheet: 0.25 (0.25), residues: 427 loop : 0.17 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1282 TYR 0.014 0.001 TYR D 989 PHE 0.017 0.002 PHE C 148 TRP 0.016 0.001 TRP D1398 HIS 0.007 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00320 (29343) covalent geometry : angle 0.54405 (40089) hydrogen bonds : bond 0.14158 ( 1300) hydrogen bonds : angle 5.81125 ( 3596) metal coordination : bond 0.01476 ( 8) metal coordination : angle 13.46375 ( 12) Misc. bond : bond 0.03603 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 1.0722 time to fit residues: 192.6776 Evaluate side-chains 91 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 0.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 538 GLN D 593 ASN D 762 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.051313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.035656 restraints weight = 102715.362| |-----------------------------------------------------------------------------| r_work (start): 0.2533 rms_B_bonded: 3.00 r_work: 0.2379 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2416 r_free = 0.2416 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2416 r_free = 0.2416 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29352 Z= 0.183 Angle : 0.543 8.239 40101 Z= 0.283 Chirality : 0.042 0.171 4518 Planarity : 0.004 0.056 4911 Dihedral : 15.818 131.676 4902 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.56 % Allowed : 4.32 % Favored : 95.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.15), residues: 3347 helix: 1.85 (0.15), residues: 1309 sheet: 0.23 (0.25), residues: 437 loop : 0.29 (0.16), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 137 TYR 0.013 0.001 TYR D 989 PHE 0.011 0.001 PHE D1008 TRP 0.008 0.001 TRP D1434 HIS 0.008 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00429 (29343) covalent geometry : angle 0.53685 (40089) hydrogen bonds : bond 0.04313 ( 1300) hydrogen bonds : angle 4.74142 ( 3596) metal coordination : bond 0.00879 ( 8) metal coordination : angle 4.61592 ( 12) Misc. bond : bond 0.00088 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 LYS cc_start: 0.9161 (mtmm) cc_final: 0.8857 (pttp) REVERT: C 359 MET cc_start: 0.9117 (ptm) cc_final: 0.8905 (ptm) REVERT: C 1091 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8503 (mt-10) REVERT: D 351 MET cc_start: 0.9354 (mtp) cc_final: 0.8931 (ptm) REVERT: D 924 MET cc_start: 0.8850 (mtt) cc_final: 0.8611 (mtp) REVERT: E 87 LYS cc_start: 0.9058 (ttpp) cc_final: 0.8837 (ttpp) REVERT: F 290 GLU cc_start: 0.9213 (OUTLIER) cc_final: 0.8922 (mt-10) REVERT: F 410 TYR cc_start: 0.8880 (t80) cc_final: 0.8561 (t80) outliers start: 16 outliers final: 4 residues processed: 105 average time/residue: 0.8688 time to fit residues: 104.0216 Evaluate side-chains 95 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain C residue 995 MET Chi-restraints excluded: chain D residue 648 MET Chi-restraints excluded: chain D residue 980 MET Chi-restraints excluded: chain F residue 290 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 26 optimal weight: 7.9990 chunk 150 optimal weight: 0.9980 chunk 225 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 319 optimal weight: 8.9990 chunk 114 optimal weight: 0.9990 chunk 214 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.050452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.034842 restraints weight = 103057.808| |-----------------------------------------------------------------------------| r_work (start): 0.2494 rms_B_bonded: 2.99 r_work: 0.2336 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 29352 Z= 0.178 Angle : 0.507 6.622 40101 Z= 0.267 Chirality : 0.042 0.162 4518 Planarity : 0.004 0.046 4911 Dihedral : 15.504 131.003 4902 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.52 % Allowed : 5.54 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.15), residues: 3347 helix: 1.94 (0.15), residues: 1310 sheet: 0.26 (0.25), residues: 445 loop : 0.36 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 360 TYR 0.013 0.001 TYR D 989 PHE 0.011 0.001 PHE D1008 TRP 0.009 0.001 TRP B 200 HIS 0.008 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00417 (29343) covalent geometry : angle 0.50405 (40089) hydrogen bonds : bond 0.04021 ( 1300) hydrogen bonds : angle 4.43782 ( 3596) metal coordination : bond 0.00872 ( 8) metal coordination : angle 3.29498 ( 12) Misc. bond : bond 0.00120 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 7 LYS cc_start: 0.9130 (mtmm) cc_final: 0.8788 (ptpp) REVERT: C 229 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8149 (ppp) REVERT: C 1091 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8546 (mt-10) REVERT: D 481 MET cc_start: 0.9462 (tpp) cc_final: 0.9005 (tpt) REVERT: D 924 MET cc_start: 0.8870 (mtt) cc_final: 0.8652 (mtp) REVERT: E 83 ASP cc_start: 0.9604 (p0) cc_final: 0.9234 (p0) REVERT: F 290 GLU cc_start: 0.9218 (OUTLIER) cc_final: 0.8992 (mt-10) REVERT: F 402 ASN cc_start: 0.8944 (t0) cc_final: 0.8650 (t0) REVERT: F 410 TYR cc_start: 0.8928 (t80) cc_final: 0.8599 (t80) outliers start: 15 outliers final: 1 residues processed: 104 average time/residue: 0.8281 time to fit residues: 98.1527 Evaluate side-chains 92 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 995 MET Chi-restraints excluded: chain F residue 290 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 113 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 254 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 223 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 330 optimal weight: 8.9990 chunk 183 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1367 HIS D1441 GLN ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.048094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.032919 restraints weight = 101284.348| |-----------------------------------------------------------------------------| r_work (start): 0.2456 rms_B_bonded: 2.93 r_work: 0.2295 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 29352 Z= 0.305 Angle : 0.587 8.253 40101 Z= 0.305 Chirality : 0.044 0.156 4518 Planarity : 0.004 0.046 4911 Dihedral : 15.560 131.894 4902 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.73 % Allowed : 6.41 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.15), residues: 3347 helix: 1.85 (0.15), residues: 1315 sheet: -0.04 (0.24), residues: 452 loop : 0.34 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 237 TYR 0.016 0.001 TYR D 158 PHE 0.014 0.002 PHE C 896 TRP 0.010 0.001 TRP B 200 HIS 0.007 0.001 HIS C 434 Details of bonding type rmsd covalent geometry : bond 0.00719 (29343) covalent geometry : angle 0.58445 (40089) hydrogen bonds : bond 0.04729 ( 1300) hydrogen bonds : angle 4.55064 ( 3596) metal coordination : bond 0.01400 ( 8) metal coordination : angle 3.36278 ( 12) Misc. bond : bond 0.00186 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: B 7 LYS cc_start: 0.9161 (mtmm) cc_final: 0.8800 (ptpp) REVERT: C 442 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8553 (tt0) REVERT: C 1091 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8579 (mt-10) REVERT: D 351 MET cc_start: 0.9585 (mtp) cc_final: 0.9211 (ptm) REVERT: F 402 ASN cc_start: 0.9013 (t0) cc_final: 0.8696 (t0) REVERT: F 410 TYR cc_start: 0.8955 (t80) cc_final: 0.8656 (t80) outliers start: 21 outliers final: 3 residues processed: 97 average time/residue: 0.8017 time to fit residues: 89.3820 Evaluate side-chains 91 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain C residue 995 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 76 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 190 optimal weight: 8.9990 chunk 136 optimal weight: 0.7980 chunk 291 optimal weight: 5.9990 chunk 116 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 260 optimal weight: 3.9990 chunk 289 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1047 HIS ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.050164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.034637 restraints weight = 102191.932| |-----------------------------------------------------------------------------| r_work (start): 0.2507 rms_B_bonded: 3.00 r_work: 0.2344 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29352 Z= 0.102 Angle : 0.479 7.762 40101 Z= 0.253 Chirality : 0.041 0.149 4518 Planarity : 0.004 0.045 4911 Dihedral : 15.379 133.691 4902 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.35 % Allowed : 7.14 % 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: 1.48 (0.15), residues: 3347 helix: 2.03 (0.15), residues: 1311 sheet: 0.29 (0.24), residues: 450 loop : 0.41 (0.16), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 84 TYR 0.013 0.001 TYR D 989 PHE 0.010 0.001 PHE A 179 TRP 0.009 0.001 TRP B 200 HIS 0.004 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00228 (29343) covalent geometry : angle 0.47753 (40089) hydrogen bonds : bond 0.03429 ( 1300) hydrogen bonds : angle 4.21651 ( 3596) metal coordination : bond 0.00350 ( 8) metal coordination : angle 2.25570 ( 12) Misc. bond : bond 0.00067 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 7 LYS cc_start: 0.9175 (mtmm) cc_final: 0.8836 (ptpp) REVERT: C 1091 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8529 (mt-10) REVERT: D 351 MET cc_start: 0.9551 (mtp) cc_final: 0.9126 (ptm) REVERT: D 481 MET cc_start: 0.9409 (tpp) cc_final: 0.9057 (tpt) REVERT: F 402 ASN cc_start: 0.8988 (t0) cc_final: 0.8607 (t0) REVERT: F 410 TYR cc_start: 0.8970 (t80) cc_final: 0.8629 (t80) outliers start: 10 outliers final: 6 residues processed: 101 average time/residue: 0.8275 time to fit residues: 96.6368 Evaluate side-chains 92 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain C residue 781 LYS Chi-restraints excluded: chain C residue 995 MET Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 1422 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 131 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 206 optimal weight: 0.0870 chunk 46 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 322 optimal weight: 0.9980 chunk 191 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.049611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.034105 restraints weight = 103218.308| |-----------------------------------------------------------------------------| r_work (start): 0.2485 rms_B_bonded: 2.99 r_work: 0.2321 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 29352 Z= 0.158 Angle : 0.492 8.664 40101 Z= 0.257 Chirality : 0.041 0.145 4518 Planarity : 0.004 0.043 4911 Dihedral : 15.366 135.253 4902 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.66 % Allowed : 7.46 % Favored : 91.88 % 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: 1.53 (0.15), residues: 3347 helix: 2.05 (0.15), residues: 1317 sheet: 0.31 (0.24), residues: 453 loop : 0.45 (0.16), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 172 TYR 0.011 0.001 TYR D 989 PHE 0.010 0.001 PHE C 896 TRP 0.008 0.001 TRP B 200 HIS 0.004 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00372 (29343) covalent geometry : angle 0.49003 (40089) hydrogen bonds : bond 0.03656 ( 1300) hydrogen bonds : angle 4.19909 ( 3596) metal coordination : bond 0.00650 ( 8) metal coordination : angle 2.42147 ( 12) Misc. bond : bond 0.00077 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 THR cc_start: 0.9391 (OUTLIER) cc_final: 0.9086 (t) REVERT: B 7 LYS cc_start: 0.9194 (mtmm) cc_final: 0.8873 (ptpp) REVERT: C 122 THR cc_start: 0.9300 (OUTLIER) cc_final: 0.8862 (p) REVERT: C 788 THR cc_start: 0.9284 (OUTLIER) cc_final: 0.8826 (p) REVERT: C 1091 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8530 (mt-10) REVERT: D 351 MET cc_start: 0.9564 (mtp) cc_final: 0.9165 (ptm) REVERT: D 481 MET cc_start: 0.9430 (tpp) cc_final: 0.9156 (tpt) REVERT: F 402 ASN cc_start: 0.9001 (t0) cc_final: 0.8604 (t0) REVERT: F 410 TYR cc_start: 0.8989 (t80) cc_final: 0.8690 (t80) outliers start: 19 outliers final: 7 residues processed: 102 average time/residue: 0.8012 time to fit residues: 95.4027 Evaluate side-chains 97 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 995 MET Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 1422 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 126 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 100 optimal weight: 0.0980 chunk 199 optimal weight: 3.9990 chunk 333 optimal weight: 10.0000 chunk 296 optimal weight: 6.9990 chunk 240 optimal weight: 5.9990 chunk 220 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.048380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.033251 restraints weight = 100497.904| |-----------------------------------------------------------------------------| r_work (start): 0.2471 rms_B_bonded: 2.93 r_work: 0.2309 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 29352 Z= 0.226 Angle : 0.529 8.909 40101 Z= 0.275 Chirality : 0.042 0.145 4518 Planarity : 0.004 0.045 4911 Dihedral : 15.430 134.520 4902 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.80 % Allowed : 7.35 % Favored : 91.85 % 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: 1.50 (0.15), residues: 3347 helix: 2.05 (0.15), residues: 1316 sheet: 0.15 (0.24), residues: 450 loop : 0.47 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 172 TYR 0.011 0.001 TYR D 128 PHE 0.012 0.001 PHE C 896 TRP 0.008 0.001 TRP B 200 HIS 0.006 0.001 HIS C 434 Details of bonding type rmsd covalent geometry : bond 0.00535 (29343) covalent geometry : angle 0.52699 (40089) hydrogen bonds : bond 0.04089 ( 1300) hydrogen bonds : angle 4.28507 ( 3596) metal coordination : bond 0.01008 ( 8) metal coordination : angle 2.54303 ( 12) Misc. bond : bond 0.00114 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 1.187 Fit side-chains revert: symmetry clash REVERT: A 201 THR cc_start: 0.9407 (OUTLIER) cc_final: 0.9061 (t) REVERT: A 220 GLU cc_start: 0.9314 (OUTLIER) cc_final: 0.8431 (tm-30) REVERT: C 1 MET cc_start: 0.8297 (ptt) cc_final: 0.7960 (ttt) REVERT: C 122 THR cc_start: 0.9320 (OUTLIER) cc_final: 0.8896 (p) REVERT: C 781 LYS cc_start: 0.9388 (OUTLIER) cc_final: 0.9107 (pptt) REVERT: C 788 THR cc_start: 0.9334 (OUTLIER) cc_final: 0.8883 (p) REVERT: C 1091 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8530 (mt-10) REVERT: D 351 MET cc_start: 0.9586 (mtp) cc_final: 0.9216 (ptm) REVERT: F 410 TYR cc_start: 0.8988 (t80) cc_final: 0.8693 (t80) outliers start: 23 outliers final: 7 residues processed: 101 average time/residue: 0.8151 time to fit residues: 95.5722 Evaluate side-chains 97 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 781 LYS Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 995 MET Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 1238 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 204 optimal weight: 2.9990 chunk 203 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 297 optimal weight: 0.9980 chunk 310 optimal weight: 2.9990 chunk 300 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 329 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.049235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.034117 restraints weight = 100731.008| |-----------------------------------------------------------------------------| r_work (start): 0.2483 rms_B_bonded: 2.95 r_work: 0.2324 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29352 Z= 0.132 Angle : 0.484 9.949 40101 Z= 0.253 Chirality : 0.041 0.143 4518 Planarity : 0.004 0.044 4911 Dihedral : 15.358 135.403 4902 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.59 % Allowed : 7.87 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.15), residues: 3347 helix: 2.09 (0.15), residues: 1317 sheet: 0.32 (0.24), residues: 455 loop : 0.52 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 360 TYR 0.012 0.001 TYR D 989 PHE 0.009 0.001 PHE A 179 TRP 0.009 0.001 TRP B 200 HIS 0.005 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00310 (29343) covalent geometry : angle 0.48242 (40089) hydrogen bonds : bond 0.03514 ( 1300) hydrogen bonds : angle 4.14142 ( 3596) metal coordination : bond 0.00523 ( 8) metal coordination : angle 2.04453 ( 12) Misc. bond : bond 0.00075 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 1.227 Fit side-chains revert: symmetry clash REVERT: A 201 THR cc_start: 0.9382 (OUTLIER) cc_final: 0.9092 (t) REVERT: B 7 LYS cc_start: 0.9123 (mtmm) cc_final: 0.8795 (ptpp) REVERT: C 1 MET cc_start: 0.8269 (ptt) cc_final: 0.7985 (ttt) REVERT: C 122 THR cc_start: 0.9286 (OUTLIER) cc_final: 0.8841 (p) REVERT: C 222 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8619 (mtm) REVERT: C 781 LYS cc_start: 0.9394 (OUTLIER) cc_final: 0.9115 (pptt) REVERT: C 788 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.8818 (p) REVERT: D 351 MET cc_start: 0.9569 (mtp) cc_final: 0.9200 (ptm) REVERT: D 817 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8646 (mm-30) REVERT: F 410 TYR cc_start: 0.9010 (t80) cc_final: 0.8692 (t80) outliers start: 17 outliers final: 6 residues processed: 102 average time/residue: 0.8374 time to fit residues: 99.2707 Evaluate side-chains 97 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 781 LYS Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 817 GLU Chi-restraints excluded: chain D residue 1422 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 205 optimal weight: 5.9990 chunk 340 optimal weight: 6.9990 chunk 255 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 304 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 172 optimal weight: 0.6980 chunk 199 optimal weight: 3.9990 chunk 141 optimal weight: 0.0040 chunk 145 optimal weight: 6.9990 overall best weight: 2.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN ** C 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.048869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.033377 restraints weight = 103412.626| |-----------------------------------------------------------------------------| r_work (start): 0.2482 rms_B_bonded: 3.00 r_work: 0.2319 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 29352 Z= 0.186 Angle : 0.508 10.224 40101 Z= 0.264 Chirality : 0.041 0.143 4518 Planarity : 0.004 0.045 4911 Dihedral : 15.384 135.962 4902 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.70 % Allowed : 8.01 % Favored : 91.29 % 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: 1.56 (0.15), residues: 3347 helix: 2.07 (0.15), residues: 1317 sheet: 0.20 (0.24), residues: 450 loop : 0.52 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 360 TYR 0.011 0.001 TYR D 989 PHE 0.011 0.001 PHE C 896 TRP 0.008 0.001 TRP B 200 HIS 0.004 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00439 (29343) covalent geometry : angle 0.50668 (40089) hydrogen bonds : bond 0.03772 ( 1300) hydrogen bonds : angle 4.18220 ( 3596) metal coordination : bond 0.00781 ( 8) metal coordination : angle 2.25926 ( 12) Misc. bond : bond 0.00100 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 1.175 Fit side-chains revert: symmetry clash REVERT: A 201 THR cc_start: 0.9413 (OUTLIER) cc_final: 0.9097 (t) REVERT: A 220 GLU cc_start: 0.9264 (OUTLIER) cc_final: 0.8424 (tm-30) REVERT: B 139 ASN cc_start: 0.8900 (OUTLIER) cc_final: 0.8488 (t0) REVERT: C 122 THR cc_start: 0.9341 (OUTLIER) cc_final: 0.8908 (p) REVERT: C 222 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8625 (mtm) REVERT: C 781 LYS cc_start: 0.9414 (OUTLIER) cc_final: 0.9107 (pptt) REVERT: C 788 THR cc_start: 0.9327 (OUTLIER) cc_final: 0.8870 (p) REVERT: D 351 MET cc_start: 0.9578 (mtp) cc_final: 0.9203 (ptm) REVERT: D 481 MET cc_start: 0.9514 (tpp) cc_final: 0.9313 (mmp) REVERT: D 817 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8674 (mm-30) REVERT: F 110 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8908 (mtp) REVERT: F 410 TYR cc_start: 0.9015 (t80) cc_final: 0.8701 (t80) outliers start: 20 outliers final: 7 residues processed: 98 average time/residue: 0.8060 time to fit residues: 91.5142 Evaluate side-chains 100 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 781 LYS Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 995 MET Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 607 LEU Chi-restraints excluded: chain D residue 817 GLU Chi-restraints excluded: chain F residue 110 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 28 optimal weight: 0.8980 chunk 269 optimal weight: 8.9990 chunk 161 optimal weight: 0.0980 chunk 78 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 211 optimal weight: 0.8980 chunk 312 optimal weight: 1.9990 chunk 243 optimal weight: 0.6980 chunk 257 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN ** C 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.049952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.034513 restraints weight = 102593.440| |-----------------------------------------------------------------------------| r_work (start): 0.2515 rms_B_bonded: 2.99 r_work: 0.2353 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 29352 Z= 0.104 Angle : 0.482 11.000 40101 Z= 0.252 Chirality : 0.040 0.143 4518 Planarity : 0.004 0.042 4911 Dihedral : 15.335 136.065 4902 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.56 % Allowed : 8.22 % Favored : 91.22 % 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: 1.65 (0.15), residues: 3347 helix: 2.14 (0.15), residues: 1311 sheet: 0.35 (0.25), residues: 441 loop : 0.55 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 360 TYR 0.012 0.001 TYR D 989 PHE 0.009 0.001 PHE A 179 TRP 0.010 0.001 TRP B 200 HIS 0.005 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00237 (29343) covalent geometry : angle 0.48115 (40089) hydrogen bonds : bond 0.03333 ( 1300) hydrogen bonds : angle 4.08105 ( 3596) metal coordination : bond 0.00342 ( 8) metal coordination : angle 1.90506 ( 12) Misc. bond : bond 0.00029 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6694 Ramachandran restraints generated. 3347 Oldfield, 0 Emsley, 3347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: A 201 THR cc_start: 0.9359 (OUTLIER) cc_final: 0.9100 (t) REVERT: A 220 GLU cc_start: 0.9252 (OUTLIER) cc_final: 0.8346 (tm-30) REVERT: B 7 LYS cc_start: 0.9150 (mtmm) cc_final: 0.8751 (pttp) REVERT: B 139 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8456 (t0) REVERT: C 122 THR cc_start: 0.9314 (OUTLIER) cc_final: 0.8882 (p) REVERT: C 222 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8607 (mtm) REVERT: C 781 LYS cc_start: 0.9408 (OUTLIER) cc_final: 0.9101 (pptt) REVERT: C 788 THR cc_start: 0.9320 (OUTLIER) cc_final: 0.8868 (p) REVERT: D 351 MET cc_start: 0.9566 (mtp) cc_final: 0.9201 (ptm) REVERT: D 817 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8638 (mm-30) REVERT: F 410 TYR cc_start: 0.9011 (t80) cc_final: 0.8697 (t80) outliers start: 16 outliers final: 7 residues processed: 98 average time/residue: 0.7955 time to fit residues: 89.8754 Evaluate side-chains 100 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 781 LYS Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 995 MET Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 817 GLU Chi-restraints excluded: chain D residue 1422 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 19 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 8 optimal weight: 0.0570 chunk 227 optimal weight: 0.6980 chunk 318 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 overall best weight: 2.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.048878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.033402 restraints weight = 104186.148| |-----------------------------------------------------------------------------| r_work (start): 0.2477 rms_B_bonded: 3.00 r_work: 0.2314 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 29352 Z= 0.215 Angle : 0.524 10.625 40101 Z= 0.271 Chirality : 0.042 0.143 4518 Planarity : 0.004 0.045 4911 Dihedral : 15.382 136.342 4902 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.49 % Allowed : 8.26 % Favored : 91.25 % 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: 1.60 (0.15), residues: 3347 helix: 2.12 (0.15), residues: 1317 sheet: 0.21 (0.24), residues: 450 loop : 0.54 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 137 TYR 0.011 0.001 TYR D 989 PHE 0.012 0.001 PHE C 896 TRP 0.007 0.001 TRP B 200 HIS 0.005 0.001 HIS C 434 Details of bonding type rmsd covalent geometry : bond 0.00510 (29343) covalent geometry : angle 0.52259 (40089) hydrogen bonds : bond 0.03830 ( 1300) hydrogen bonds : angle 4.17695 ( 3596) metal coordination : bond 0.00911 ( 8) metal coordination : angle 2.31114 ( 12) Misc. bond : bond 0.00114 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6490.06 seconds wall clock time: 111 minutes 46.43 seconds (6706.43 seconds total)