Starting phenix.real_space_refine on Sat Feb 7 00:22:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uks_64253/02_2026/9uks_64253.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uks_64253/02_2026/9uks_64253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uks_64253/02_2026/9uks_64253.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uks_64253/02_2026/9uks_64253.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uks_64253/02_2026/9uks_64253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uks_64253/02_2026/9uks_64253.map" } resolution = 2.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 88 5.49 5 Mg 3 5.21 5 S 70 5.16 5 C 17760 2.51 5 N 5072 2.21 5 O 5606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28601 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 1776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1776 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 210} Chain: "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: 2 Conformer: "A" Number of residues, atoms: 1113, 8783 Classifications: {'peptide': 1113} Link IDs: {'PCIS': 1, 'PTRANS': 71, 'TRANS': 1040} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 1113, 8783 Classifications: {'peptide': 1113} Link IDs: {'PCIS': 1, 'PTRANS': 71, 'TRANS': 1040} Chain breaks: 1 bond proxies already assigned to first conformer: 8938 Chain: "D" Number of atoms: 10751 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1362, 10743 Classifications: {'peptide': 1362} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1293} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 1362, 10743 Classifications: {'peptide': 1362} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1293} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 10917 Chain: "E" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 761 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 6, 'TRANS': 87} Chain: "G" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 861 Classifications: {'DNA': 42} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 41} Chain breaks: 1 Chain: "H" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 987 Classifications: {'DNA': 48} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 47} Chain: "F" Number of atoms: 2748 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 338, 2740 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 13, 'TRANS': 324} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 338, 2740 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 13, 'TRANS': 324} Chain breaks: 1 bond proxies already assigned to first conformer: 2773 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20172 SG CYS D1112 21.651 58.934 115.264 1.00 11.15 S ATOM 20816 SG CYS D1194 25.350 59.156 114.534 1.00 3.38 S ATOM 20872 SG CYS D1201 23.925 60.676 117.824 1.00 6.31 S ATOM 20896 SG CYS D1204 24.293 57.255 117.622 1.00 16.28 S ATOM 12821 SG CYS D 58 53.057 103.376 79.086 1.00 35.91 S ATOM 12832 SG CYS D 60 54.440 103.545 75.986 1.00 47.91 S ATOM 12943 SG CYS D 73 50.886 103.668 75.326 1.00 45.67 S ATOM 12969 SG CYS D 76 52.186 100.667 76.517 1.00 50.96 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG C 945 " occ=0.59 ... (20 atoms not shown) pdb=" NH2BARG C 945 " occ=0.41 Time building chain proxies: 9.96, per 1000 atoms: 0.35 Number of scatterers: 28601 At special positions: 0 Unit cell: (129.525, 156.75, 200.475, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 70 16.00 P 88 15.00 Mg 3 11.99 O 5606 8.00 N 5072 7.00 C 17760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1601 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1204 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1194 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1112 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1201 " pdb=" ZN D1602 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 73 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 60 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 58 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 76 " Number of angles added : 12 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6224 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 48 sheets defined 44.9% alpha, 17.6% beta 28 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 4.22 Creating SS restraints... Processing helix chain 'A' and resid 31 through 47 Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 74 through 83 Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 206 through 223 Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'B' and resid 31 through 47 Proline residue: B 39 - end of helix Processing helix chain 'B' and resid 74 through 83 Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 206 through 223 Processing helix chain 'C' and resid 19 through 31 removed outlier: 4.292A pdb=" N SER C 25 " --> pdb=" O ILE C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 39 Processing helix chain 'C' and resid 42 through 52 Processing helix chain 'C' and resid 79 through 86 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 203 through 212 Processing helix chain 'C' and resid 216 through 221 removed outlier: 4.007A pdb=" N GLY C 220 " --> pdb=" O GLU C 216 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 216 through 221' Processing helix chain 'C' and resid 223 through 229 removed outlier: 3.550A pdb=" N MET C 229 " --> pdb=" O SER C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 243 Processing helix chain 'C' and resid 249 through 262 Processing helix chain 'C' and resid 270 through 282 Processing helix chain 'C' and resid 302 through 316 Processing helix chain 'C' and resid 335 through 362 removed outlier: 3.707A pdb=" N GLY C 362 " --> pdb=" O ARG C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 367 removed outlier: 3.716A pdb=" N LEU C 367 " --> pdb=" O GLU C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 375 through 389 removed outlier: 3.719A pdb=" N SER C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 408 Processing helix chain 'C' and resid 424 through 429 removed outlier: 3.605A pdb=" N ARG C 428 " --> pdb=" O GLY C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 435 Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 525 through 529 Processing helix chain 'C' and resid 535 through 540 removed outlier: 3.507A pdb=" N GLN C 538 " --> pdb=" O SER C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 554 through 566 removed outlier: 3.603A pdb=" N MET C 560 " --> pdb=" O ASN C 556 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR C 566 " --> pdb=" O SER C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 591 Processing helix chain 'C' and resid 683 through 687 removed outlier: 3.686A pdb=" N ASP C 686 " --> pdb=" O ASN C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 697 Processing helix chain 'C' and resid 768 through 779 Processing helix chain 'C' and resid 854 through 858 Processing helix chain 'C' and resid 872 through 876 Processing helix chain 'C' and resid 882 through 898 removed outlier: 3.564A pdb=" N PHE C 896 " --> pdb=" O LEU C 892 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 926 removed outlier: 3.663A pdb=" N VAL C 924 " --> pdb=" O GLN C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 932 Processing helix chain 'C' and resid 937 through 950 removed outlier: 3.583A pdb=" N LYS C 949 " --> pdb=" O AARG C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 969 Processing helix chain 'C' and resid 1000 through 1005 Processing helix chain 'C' and resid 1033 through 1044 Processing helix chain 'C' and resid 1045 through 1054 Processing helix chain 'C' and resid 1059 through 1072 Processing helix chain 'C' and resid 1082 through 1095 removed outlier: 3.528A pdb=" N ARG C1086 " --> pdb=" O PRO C1082 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 46 through 51 Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 102 through 107 Processing helix chain 'D' and resid 110 through 117 Processing helix chain 'D' and resid 119 through 128 Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 372 through 376 Processing helix chain 'D' and resid 456 through 467 removed outlier: 3.675A pdb=" N ALA D 460 " --> pdb=" O MET D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 481 Processing helix chain 'D' and resid 485 through 506 Processing helix chain 'D' and resid 508 through 511 Processing helix chain 'D' and resid 521 through 525 Processing helix chain 'D' and resid 538 through 560 removed outlier: 4.187A pdb=" N ASP D 542 " --> pdb=" O SER D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 583 Processing helix chain 'D' and resid 602 through 608 Processing helix chain 'D' and resid 612 through 618 Processing helix chain 'D' and resid 646 through 653 Processing helix chain 'D' and resid 653 through 664 Processing helix chain 'D' and resid 669 through 679 removed outlier: 4.087A pdb=" N ARG D 679 " --> pdb=" O ARG D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 683 Processing helix chain 'D' and resid 684 through 695 removed outlier: 4.194A pdb=" N TRP D 688 " --> pdb=" O LYS D 684 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP D 689 " --> pdb=" O ASP D 685 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU D 693 " --> pdb=" O ASP D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 711 No H-bonds generated for 'chain 'D' and resid 709 through 711' Processing helix chain 'D' and resid 729 through 731 No H-bonds generated for 'chain 'D' and resid 729 through 731' Processing helix chain 'D' and resid 732 through 737 Processing helix chain 'D' and resid 752 through 762 Processing helix chain 'D' and resid 764 through 768 Processing helix chain 'D' and resid 783 through 794 Processing helix chain 'D' and resid 808 through 818 Processing helix chain 'D' and resid 835 through 841 Processing helix chain 'D' and resid 845 through 855 Processing helix chain 'D' and resid 876 through 891 Processing helix chain 'D' and resid 892 through 900 Processing helix chain 'D' and resid 907 through 946 removed outlier: 7.752A pdb=" N MET D 924 " --> pdb=" O LEU D 920 " (cutoff:3.500A) removed outlier: 9.672A pdb=" N GLU D 925 " --> pdb=" O ARG D 921 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYS D 926 " --> pdb=" O LEU D 922 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLY D 946 " --> pdb=" O SER D 942 " (cutoff:3.500A) Processing helix chain 'D' and resid 950 through 954 Processing helix chain 'D' and resid 958 through 980 removed outlier: 3.959A pdb=" N GLN D 962 " --> pdb=" O GLU D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 984 through 1015 Processing helix chain 'D' and resid 1018 through 1027 Processing helix chain 'D' and resid 1031 through 1040 Processing helix chain 'D' and resid 1066 through 1103 removed outlier: 3.821A pdb=" N HIS D1075 " --> pdb=" O PHE D1071 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY D1076 " --> pdb=" O ILE D1072 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA D1089 " --> pdb=" O ALA D1085 " (cutoff:3.500A) Processing helix chain 'D' and resid 1136 through 1145 Processing helix chain 'D' and resid 1167 through 1180 Processing helix chain 'D' and resid 1190 through 1194 Processing helix chain 'D' and resid 1202 through 1206 Processing helix chain 'D' and resid 1208 through 1212 Processing helix chain 'D' and resid 1220 through 1231 Processing helix chain 'D' and resid 1232 through 1236 Processing helix chain 'D' and resid 1254 through 1264 removed outlier: 3.666A pdb=" N ARG D1258 " --> pdb=" O GLN D1254 " (cutoff:3.500A) Processing helix chain 'D' and resid 1331 through 1340 Processing helix chain 'D' and resid 1340 through 1359 removed outlier: 3.572A pdb=" N VAL D1355 " --> pdb=" O GLU D1351 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN D1359 " --> pdb=" O VAL D1355 " (cutoff:3.500A) Processing helix chain 'D' and resid 1364 through 1376 removed outlier: 4.047A pdb=" N ILE D1368 " --> pdb=" O HIS D1364 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL D1371 " --> pdb=" O HIS D1367 " (cutoff:3.500A) Processing helix chain 'D' and resid 1397 through 1409 Processing helix chain 'D' and resid 1423 through 1430 Processing helix chain 'D' and resid 1433 through 1439 Processing helix chain 'D' and resid 1442 through 1454 Processing helix chain 'D' and resid 1461 through 1468 removed outlier: 4.021A pdb=" N ASN D1465 " --> pdb=" O GLY D1461 " (cutoff:3.500A) Processing helix chain 'D' and resid 1474 through 1477 Processing helix chain 'D' and resid 1478 through 1483 removed outlier: 4.572A pdb=" N PHE D1483 " --> pdb=" O ASP D1479 " (cutoff:3.500A) Processing helix chain 'D' and resid 1489 through 1502 Processing helix chain 'E' and resid 5 through 12 Processing helix chain 'E' and resid 15 through 33 removed outlier: 3.620A pdb=" N LEU E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 45 Processing helix chain 'E' and resid 59 through 71 removed outlier: 3.672A pdb=" N GLY E 71 " --> pdb=" O GLU E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 93 Processing helix chain 'F' and resid 79 through 89 Processing helix chain 'F' and resid 95 through 121 Processing helix chain 'F' and resid 123 through 137 Processing helix chain 'F' and resid 153 through 165 Processing helix chain 'F' and resid 167 through 190 removed outlier: 3.936A pdb=" N TYR F 173 " --> pdb=" O GLU F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 200 removed outlier: 3.655A pdb=" N VAL F 195 " --> pdb=" O ASN F 191 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL F 196 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 203 No H-bonds generated for 'chain 'F' and resid 201 through 203' Processing helix chain 'F' and resid 208 through 227 Processing helix chain 'F' and resid 228 through 232 removed outlier: 3.677A pdb=" N ARG F 231 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 255 removed outlier: 3.613A pdb=" N TYR F 238 " --> pdb=" O LYS F 234 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TRP F 241 " --> pdb=" O THR F 237 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TRP F 242 " --> pdb=" O TYR F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 283 Processing helix chain 'F' and resid 287 through 296 Processing helix chain 'F' and resid 300 through 311 Processing helix chain 'F' and resid 328 through 333 removed outlier: 3.624A pdb=" N ILE F 333 " --> pdb=" O GLY F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 360 removed outlier: 3.728A pdb=" N LYS F 360 " --> pdb=" O LYS F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 373 removed outlier: 3.552A pdb=" N LEU F 369 " --> pdb=" O GLU F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 391 Processing helix chain 'F' and resid 393 through 416 removed outlier: 3.675A pdb=" N ILE F 397 " --> pdb=" O THR F 393 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG F 398 " --> pdb=" O ARG F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 16 removed outlier: 6.351A pdb=" N ASP A 193 " --> pdb=" O PRO A 27 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N THR A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 6.867A 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: 7.176A pdb=" N ASN A 139 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE A 58 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU A 141 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL A 56 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 7.013A 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 16 removed outlier: 3.769A pdb=" N TYR B 20 " --> pdb=" O GLN B 16 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASP B 193 " --> pdb=" O PRO B 27 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N THR B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU B 186 " --> pdb=" O THR B 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 104 removed outlier: 3.512A pdb=" N SER B 55 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASP B 145 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL B 53 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLY B 147 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR B 51 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 89 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 110 removed outlier: 6.695A 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: 5.497A pdb=" N LEU C 66 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE C 101 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N PHE C 68 " --> pdb=" O GLN C 99 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN C 99 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU C 70 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY C 116 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA C 96 " --> pdb=" O PHE C 114 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N PHE C 114 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU C 98 " --> pdb=" O GLU C 112 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N GLU C 112 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU C 100 " --> pdb=" O GLU C 110 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N GLU C 110 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N HIS C 102 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 6.285A 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: 6.514A 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: 6.663A pdb=" N TYR C 158 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL C 176 " --> pdb=" O TYR C 158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 291 through 294 Processing sheet with id=AB8, first strand: chain 'C' and resid 460 through 461 removed outlier: 5.513A pdb=" N GLU C 482 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL C 475 " --> pdb=" O THR C 480 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR C 480 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 460 through 461 Processing sheet with id=AC1, first strand: chain 'C' and resid 503 through 504 Processing sheet with id=AC2, first strand: chain 'C' and resid 595 through 596 removed outlier: 6.507A pdb=" N LEU C 595 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 620 through 624 removed outlier: 6.869A pdb=" N ARG C 610 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N VAL C 606 " --> pdb=" O ARG C 610 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL C 612 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 629 through 630 Processing sheet with id=AC5, first strand: chain 'C' and resid 661 through 662 Processing sheet with id=AC6, first strand: chain 'C' and resid 971 through 972 removed outlier: 6.812A pdb=" N ILE C 688 " --> pdb=" O LYS C 851 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N LEU C 853 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE C 690 " --> pdb=" O LEU C 853 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL C 988 " --> pdb=" O ILE C 676 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 702 through 713 removed outlier: 3.558A pdb=" N GLU C 821 " --> pdb=" O ALA C 712 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG C 802 " --> pdb=" O TYR C 826 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ALA C 828 " --> pdb=" O VAL C 800 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N VAL C 800 " --> pdb=" O ALA C 828 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N LYS C 830 " --> pdb=" O GLY C 798 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N GLY C 798 " --> pdb=" O LYS C 830 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 721 through 722 Processing sheet with id=AC9, first strand: chain 'C' and resid 754 through 756 removed outlier: 6.912A pdb=" N LEU C 790 " --> pdb=" O LEU C 755 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1006 through 1008 removed outlier: 6.366A pdb=" N CYS D 642 " --> pdb=" O VAL D 719 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL D 721 " --> pdb=" O CYS D 642 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU D 644 " --> pdb=" O VAL D 721 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE D 726 " --> pdb=" O ARG D 628 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL D 630 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU D 728 " --> pdb=" O VAL D 630 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL D 632 " --> pdb=" O LEU D 728 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1030 through 1032 removed outlier: 3.658A pdb=" N GLN C1030 " --> pdb=" O VAL D 623 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1108 through 1109 removed outlier: 4.485A pdb=" N THR C1101 " --> pdb=" O VAL C1109 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 22 through 25 removed outlier: 7.710A pdb=" N HIS D 92 " --> pdb=" O TYR D 23 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU D 25 " --> pdb=" O HIS D 92 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLU D 94 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N LEU D 95 " --> pdb=" O PRO D 518 " (cutoff:3.500A) removed outlier: 10.732A pdb=" N THR D 97 " --> pdb=" O ALA D 516 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ALA D 516 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 152 through 153 removed outlier: 6.773A pdb=" N ASP D 453 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AD7, first strand: chain 'D' and resid 166 through 170 Processing sheet with id=AD8, first strand: chain 'D' and resid 342 through 344 removed outlier: 6.939A pdb=" N GLU D 389 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL D 211 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU D 387 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL D 213 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL D 385 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR D 215 " --> pdb=" O GLY D 383 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLY D 383 " --> pdb=" O TYR D 215 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 352 through 353 removed outlier: 6.900A pdb=" N VAL D 377 " --> pdb=" O ILE D 367 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 398 through 402 Processing sheet with id=AE2, first strand: chain 'D' and resid 527 through 529 removed outlier: 6.572A pdb=" N PHE D 535 " --> pdb=" O VAL F 315 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 827 through 828 Processing sheet with id=AE4, first strand: chain 'D' and resid 842 through 843 Processing sheet with id=AE5, first strand: chain 'D' and resid 1106 through 1109 Processing sheet with id=AE6, first strand: chain 'D' and resid 1118 through 1121 Processing sheet with id=AE7, first strand: chain 'D' and resid 1123 through 1126 Processing sheet with id=AE8, first strand: chain 'D' and resid 1153 through 1155 Processing sheet with id=AE9, first strand: chain 'D' and resid 1300 through 1303 removed outlier: 3.598A pdb=" N LYS D1301 " --> pdb=" O VAL D1294 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER D1291 " --> pdb=" O GLU D1284 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1394 through 1396 removed outlier: 5.498A pdb=" N VAL D1381 " --> pdb=" O LYS D1418 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LYS D1418 " --> pdb=" O VAL D1381 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1485 through 1488 Processing sheet with id=AF3, first strand: chain 'E' and resid 47 through 50 1271 hydrogen bonds defined for protein. 3510 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 64 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 8.04 Time building geometry restraints manager: 2.98 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: 4694 1.31 - 1.43: 7434 1.43 - 1.56: 16757 1.56 - 1.68: 179 1.68 - 1.81: 127 Bond restraints: 29191 Sorted by residual: bond pdb=" C23 1N7 B 401 " pdb=" C24 1N7 B 401 " ideal model delta sigma weight residual 1.512 1.574 -0.062 2.00e-02 2.50e+03 9.57e+00 bond pdb=" C24 1N7 B 401 " pdb=" O1 1N7 B 401 " ideal model delta sigma weight residual 1.224 1.183 0.041 2.00e-02 2.50e+03 4.24e+00 bond pdb=" N HIS D 709 " pdb=" CA HIS D 709 " ideal model delta sigma weight residual 1.455 1.482 -0.027 1.41e-02 5.03e+03 3.72e+00 bond pdb=" CA TYR D1207 " pdb=" C TYR D1207 " ideal model delta sigma weight residual 1.524 1.499 0.025 1.33e-02 5.65e+03 3.48e+00 bond pdb=" C20 1N7 B 401 " pdb=" C21 1N7 B 401 " ideal model delta sigma weight residual 1.528 1.565 -0.037 2.00e-02 2.50e+03 3.45e+00 ... (remaining 29186 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 39026 1.39 - 2.78: 690 2.78 - 4.16: 128 4.16 - 5.55: 18 5.55 - 6.94: 8 Bond angle restraints: 39870 Sorted by residual: angle pdb=" N TYR D1207 " pdb=" CA TYR D1207 " pdb=" C TYR D1207 " ideal model delta sigma weight residual 110.32 116.54 -6.22 1.59e+00 3.96e-01 1.53e+01 angle pdb=" N ASP D1208 " pdb=" CA ASP D1208 " pdb=" C ASP D1208 " ideal model delta sigma weight residual 107.99 101.32 6.67 1.76e+00 3.23e-01 1.43e+01 angle pdb=" C THR C 443 " pdb=" N PRO C 444 " pdb=" CA PRO C 444 " ideal model delta sigma weight residual 120.13 115.93 4.20 1.13e+00 7.83e-01 1.38e+01 angle pdb=" N GLY D1206 " pdb=" CA GLY D1206 " pdb=" C GLY D1206 " ideal model delta sigma weight residual 111.35 115.60 -4.25 1.20e+00 6.94e-01 1.26e+01 angle pdb=" CA HIS D 709 " pdb=" C HIS D 709 " pdb=" O HIS D 709 " ideal model delta sigma weight residual 121.40 117.64 3.76 1.11e+00 8.12e-01 1.14e+01 ... (remaining 39865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 16122 17.36 - 34.72: 1192 34.72 - 52.07: 322 52.07 - 69.43: 127 69.43 - 86.79: 26 Dihedral angle restraints: 17789 sinusoidal: 8116 harmonic: 9673 Sorted by residual: dihedral pdb=" CA ASP C 698 " pdb=" C ASP C 698 " pdb=" N PHE C 699 " pdb=" CA PHE C 699 " ideal model delta harmonic sigma weight residual 180.00 162.77 17.23 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA SER A 46 " pdb=" C SER A 46 " pdb=" N SER A 47 " pdb=" CA SER A 47 " ideal model delta harmonic sigma weight residual 180.00 -162.85 -17.15 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA ASP D1488 " pdb=" CB ASP D1488 " pdb=" CG ASP D1488 " pdb=" OD1 ASP D1488 " ideal model delta sinusoidal sigma weight residual -30.00 -88.87 58.87 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 17786 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2829 0.029 - 0.059: 1052 0.059 - 0.088: 335 0.088 - 0.117: 243 0.117 - 0.147: 35 Chirality restraints: 4494 Sorted by residual: chirality pdb=" C20 1N7 B 401 " pdb=" C21 1N7 B 401 " pdb=" C22 1N7 B 401 " pdb=" C9 1N7 B 401 " both_signs ideal model delta sigma weight residual False 2.59 2.73 -0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA ILE C 118 " pdb=" N ILE C 118 " pdb=" C ILE C 118 " pdb=" CB ILE C 118 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" C9 1N7 B 401 " pdb=" C20 1N7 B 401 " pdb=" C5 1N7 B 401 " pdb=" C8 1N7 B 401 " both_signs ideal model delta sigma weight residual False 2.62 2.48 0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 4491 not shown) Planarity restraints: 4901 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 192 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.98e+00 pdb=" N PRO D 193 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 193 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 193 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 443 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO C 444 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 444 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 444 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 260 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO F 261 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO F 261 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 261 " -0.022 5.00e-02 4.00e+02 ... (remaining 4898 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 207 2.57 - 3.15: 22203 3.15 - 3.73: 46839 3.73 - 4.32: 68488 4.32 - 4.90: 109029 Nonbonded interactions: 246766 Sorted by model distance: nonbonded pdb=" OD1 ASP D 739 " pdb="MG MG D1603 " model vdw 1.982 2.170 nonbonded pdb=" OD1 ASP D 743 " pdb="MG MG D1603 " model vdw 2.008 2.170 nonbonded pdb="MG MG D1603 " pdb=" O HOH D1717 " model vdw 2.049 2.170 nonbonded pdb="MG MG A 401 " pdb=" O HOH A 504 " model vdw 2.091 2.170 nonbonded pdb="MG MG A 401 " pdb=" O HOH A 507 " model vdw 2.093 2.170 ... (remaining 246761 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 5 through 229) selection = (chain 'B' and resid 5 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: 5.910 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: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 40.290 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 : 0.002 0.062 29199 Z= 0.111 Angle : 0.526 30.844 39882 Z= 0.263 Chirality : 0.040 0.147 4494 Planarity : 0.004 0.053 4901 Dihedral : 14.242 86.787 11565 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.14), residues: 3343 helix: 1.00 (0.14), residues: 1301 sheet: 0.43 (0.25), residues: 427 loop : 0.73 (0.16), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 674 TYR 0.017 0.001 TYR D 34 PHE 0.026 0.002 PHE C 699 TRP 0.016 0.001 TRP A 200 HIS 0.010 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00235 (29191) covalent geometry : angle 0.48625 (39870) hydrogen bonds : bond 0.21565 ( 1333) hydrogen bonds : angle 7.31423 ( 3638) metal coordination : bond 0.01473 ( 8) metal coordination : angle 11.63003 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 332 average time/residue: 0.9819 time to fit residues: 363.2130 Evaluate side-chains 167 residues out of total 2859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN B 163 ASN C 320 HIS C 390 GLN C 538 GLN C 633 GLN F 83 GLN F 381 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.074328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.048511 restraints weight = 95868.435| |-----------------------------------------------------------------------------| r_work (start): 0.2611 rms_B_bonded: 2.69 r_work: 0.2452 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2327 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2371 r_free = 0.2371 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2371 r_free = 0.2371 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9084 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29199 Z= 0.173 Angle : 0.594 8.009 39882 Z= 0.316 Chirality : 0.044 0.174 4494 Planarity : 0.005 0.072 4901 Dihedral : 14.885 72.808 4807 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.77 % Allowed : 5.73 % Favored : 93.51 % 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: 1.38 (0.14), residues: 3343 helix: 1.52 (0.14), residues: 1315 sheet: 0.41 (0.25), residues: 418 loop : 0.72 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 414 TYR 0.020 0.001 TYR D 345 PHE 0.023 0.002 PHE C 699 TRP 0.012 0.001 TRP A 200 HIS 0.010 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00396 (29191) covalent geometry : angle 0.59110 (39870) hydrogen bonds : bond 0.05087 ( 1333) hydrogen bonds : angle 5.11955 ( 3638) metal coordination : bond 0.00620 ( 8) metal coordination : angle 3.14922 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 1.164 Fit side-chains REVERT: A 155 LYS cc_start: 0.9409 (mtpp) cc_final: 0.9164 (ttpp) REVERT: B 91 ASN cc_start: 0.9350 (t0) cc_final: 0.9131 (t0) REVERT: B 163 ASN cc_start: 0.8946 (m110) cc_final: 0.8711 (p0) REVERT: C 1000 MET cc_start: 0.8947 (mtm) cc_final: 0.8719 (mtt) REVERT: D 67 ARG cc_start: 0.8543 (ttp-170) cc_final: 0.8286 (OUTLIER) REVERT: D 198 ARG cc_start: 0.9040 (mtp-110) cc_final: 0.8201 (mtm-85) REVERT: D 212 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8292 (tpp80) REVERT: D 351 MET cc_start: 0.9260 (mtp) cc_final: 0.8998 (mtm) REVERT: D 380 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8258 (pm20) REVERT: E 44 GLU cc_start: 0.9362 (mt-10) cc_final: 0.9053 (mt-10) REVERT: E 50 THR cc_start: 0.8752 (m) cc_final: 0.8476 (p) REVERT: E 88 GLU cc_start: 0.9201 (tp30) cc_final: 0.8987 (tp30) REVERT: F 367 MET cc_start: 0.9261 (tpt) cc_final: 0.9036 (tpp) outliers start: 22 outliers final: 4 residues processed: 186 average time/residue: 0.9009 time to fit residues: 191.1496 Evaluate side-chains 155 residues out of total 2859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 150 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 380 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 70 optimal weight: 0.9980 chunk 192 optimal weight: 3.9990 chunk 302 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 234 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 218 optimal weight: 3.9990 chunk 224 optimal weight: 7.9990 chunk 320 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN B 16 GLN C 187 ASN C 390 GLN D 994 GLN D1124 GLN ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.072408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.046427 restraints weight = 102741.043| |-----------------------------------------------------------------------------| r_work (start): 0.2607 rms_B_bonded: 2.77 r_work: 0.2449 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2328 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2321 r_free = 0.2321 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2321 r_free = 0.2321 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9151 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 29199 Z= 0.205 Angle : 0.568 9.167 39882 Z= 0.299 Chirality : 0.044 0.160 4494 Planarity : 0.005 0.047 4901 Dihedral : 15.081 74.778 4803 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.63 % Allowed : 6.22 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.14), residues: 3343 helix: 1.68 (0.14), residues: 1327 sheet: 0.29 (0.25), residues: 425 loop : 0.69 (0.16), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 414 TYR 0.016 0.001 TYR C 615 PHE 0.025 0.002 PHE C 699 TRP 0.011 0.001 TRP A 200 HIS 0.011 0.001 HIS C 434 Details of bonding type rmsd covalent geometry : bond 0.00479 (29191) covalent geometry : angle 0.56660 (39870) hydrogen bonds : bond 0.04739 ( 1333) hydrogen bonds : angle 4.79274 ( 3638) metal coordination : bond 0.00812 ( 8) metal coordination : angle 2.64213 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 LYS cc_start: 0.9406 (mtpp) cc_final: 0.9160 (ttpp) REVERT: B 91 ASN cc_start: 0.9401 (t0) cc_final: 0.9163 (t0) REVERT: B 102 LYS cc_start: 0.9210 (ttmm) cc_final: 0.9008 (mptm) REVERT: B 163 ASN cc_start: 0.9003 (m110) cc_final: 0.8761 (p0) REVERT: C 781 LYS cc_start: 0.8712 (pptt) cc_final: 0.8460 (tmmt) REVERT: C 814 GLU cc_start: 0.8516 (mp0) cc_final: 0.8304 (mp0) REVERT: D 67 ARG cc_start: 0.8500 (ttp-170) cc_final: 0.8243 (tpm170) REVERT: D 167 GLU cc_start: 0.8540 (tp30) cc_final: 0.8206 (tm-30) REVERT: D 191 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9107 (OUTLIER) REVERT: D 351 MET cc_start: 0.9276 (mtp) cc_final: 0.8962 (mtm) REVERT: E 44 GLU cc_start: 0.9397 (mt-10) cc_final: 0.9163 (mt-10) REVERT: E 50 THR cc_start: 0.8896 (m) cc_final: 0.8670 (p) REVERT: E 87 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.9101 (ptpp) REVERT: F 367 MET cc_start: 0.9319 (tpt) cc_final: 0.9095 (tpp) REVERT: F 390 PHE cc_start: 0.8708 (m-80) cc_final: 0.8493 (m-80) REVERT: F 402 ASN cc_start: 0.8873 (t160) cc_final: 0.8496 (p0) outliers start: 18 outliers final: 5 residues processed: 179 average time/residue: 0.8792 time to fit residues: 178.7465 Evaluate side-chains 154 residues out of total 2859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 148 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 380 GLU Chi-restraints excluded: chain D residue 1281 VAL Chi-restraints excluded: chain E residue 87 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 42 optimal weight: 0.9980 chunk 122 optimal weight: 7.9990 chunk 116 optimal weight: 0.7980 chunk 336 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 chunk 170 optimal weight: 0.5980 chunk 317 optimal weight: 8.9990 chunk 198 optimal weight: 1.9990 chunk 318 optimal weight: 0.6980 chunk 282 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN B 16 GLN C 390 GLN ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 HIS F 402 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.073375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.047502 restraints weight = 104150.183| |-----------------------------------------------------------------------------| r_work (start): 0.2595 rms_B_bonded: 2.80 r_work: 0.2434 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2311 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2353 r_free = 0.2353 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2353 r_free = 0.2353 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9115 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29199 Z= 0.135 Angle : 0.525 8.333 39882 Z= 0.277 Chirality : 0.042 0.151 4494 Planarity : 0.004 0.041 4901 Dihedral : 15.076 76.555 4803 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.73 % Allowed : 6.63 % Favored : 92.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.15), residues: 3343 helix: 1.84 (0.14), residues: 1323 sheet: 0.32 (0.25), residues: 437 loop : 0.69 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D1310 TYR 0.011 0.001 TYR C 615 PHE 0.013 0.001 PHE D1299 TRP 0.011 0.001 TRP B 200 HIS 0.008 0.001 HIS C 434 Details of bonding type rmsd covalent geometry : bond 0.00310 (29191) covalent geometry : angle 0.52408 (39870) hydrogen bonds : bond 0.03954 ( 1333) hydrogen bonds : angle 4.56824 ( 3638) metal coordination : bond 0.00473 ( 8) metal coordination : angle 2.25923 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 ASN cc_start: 0.9412 (t0) cc_final: 0.9040 (t0) REVERT: A 133 GLU cc_start: 0.8898 (tt0) cc_final: 0.8438 (pt0) REVERT: A 155 LYS cc_start: 0.9372 (mtpp) cc_final: 0.9147 (ttpp) REVERT: B 91 ASN cc_start: 0.9426 (t0) cc_final: 0.9179 (t0) REVERT: C 8 ARG cc_start: 0.8123 (mtm-85) cc_final: 0.7762 (mtm-85) REVERT: C 713 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8128 (mpp-170) REVERT: C 781 LYS cc_start: 0.8735 (pptt) cc_final: 0.8463 (tmmt) REVERT: C 814 GLU cc_start: 0.8540 (mp0) cc_final: 0.8323 (mp0) REVERT: C 1000 MET cc_start: 0.9181 (mtm) cc_final: 0.8875 (mtt) REVERT: C 1100 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8358 (pt0) REVERT: D 167 GLU cc_start: 0.8548 (tp30) cc_final: 0.8191 (tm-30) REVERT: D 351 MET cc_start: 0.9271 (mtp) cc_final: 0.8925 (mtm) REVERT: E 44 GLU cc_start: 0.9365 (mt-10) cc_final: 0.9114 (mt-10) REVERT: F 367 MET cc_start: 0.9335 (tpt) cc_final: 0.9083 (tpp) REVERT: F 402 ASN cc_start: 0.8899 (t0) cc_final: 0.8457 (p0) outliers start: 21 outliers final: 6 residues processed: 183 average time/residue: 0.8501 time to fit residues: 177.0671 Evaluate side-chains 157 residues out of total 2859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 713 ARG Chi-restraints excluded: chain C residue 1100 GLN Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 1281 VAL Chi-restraints excluded: chain F residue 248 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 221 optimal weight: 2.9990 chunk 320 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 333 optimal weight: 3.9990 chunk 276 optimal weight: 0.5980 chunk 233 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 286 optimal weight: 4.9990 chunk 327 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 139 ASN B 16 GLN C 390 GLN ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.071920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.046170 restraints weight = 88540.975| |-----------------------------------------------------------------------------| r_work (start): 0.2561 rms_B_bonded: 2.58 r_work: 0.2406 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2281 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2321 r_free = 0.2321 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2321 r_free = 0.2321 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9135 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 29199 Z= 0.199 Angle : 0.547 7.848 39882 Z= 0.287 Chirality : 0.043 0.149 4494 Planarity : 0.004 0.045 4901 Dihedral : 15.162 76.047 4803 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.63 % Allowed : 7.54 % Favored : 91.83 % 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: 3343 helix: 1.86 (0.14), residues: 1323 sheet: 0.30 (0.25), residues: 425 loop : 0.73 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D1310 TYR 0.016 0.001 TYR D 128 PHE 0.021 0.002 PHE F 389 TRP 0.010 0.001 TRP A 200 HIS 0.010 0.001 HIS C 434 Details of bonding type rmsd covalent geometry : bond 0.00467 (29191) covalent geometry : angle 0.54594 (39870) hydrogen bonds : bond 0.04313 ( 1333) hydrogen bonds : angle 4.55292 ( 3638) metal coordination : bond 0.00736 ( 8) metal coordination : angle 2.33784 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 ASN cc_start: 0.9407 (t0) cc_final: 0.9038 (t0) REVERT: A 155 LYS cc_start: 0.9392 (mtpp) cc_final: 0.9153 (ttpp) REVERT: A 194 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.8997 (tttt) REVERT: B 72 LYS cc_start: 0.9310 (mttt) cc_final: 0.9033 (mmtm) REVERT: B 91 ASN cc_start: 0.9424 (t0) cc_final: 0.9175 (t0) REVERT: C 8 ARG cc_start: 0.8117 (mtm-85) cc_final: 0.7777 (mtm-85) REVERT: C 713 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8413 (mpp80) REVERT: C 814 GLU cc_start: 0.8561 (mp0) cc_final: 0.8323 (mp0) REVERT: C 1100 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8514 (mm-40) REVERT: D 167 GLU cc_start: 0.8579 (tp30) cc_final: 0.8210 (tm-30) REVERT: D 351 MET cc_start: 0.9280 (mtp) cc_final: 0.9018 (mtm) REVERT: E 44 GLU cc_start: 0.9358 (mt-10) cc_final: 0.9074 (mt-10) REVERT: F 367 MET cc_start: 0.9353 (tpt) cc_final: 0.9060 (tpt) REVERT: F 402 ASN cc_start: 0.8910 (t0) cc_final: 0.8496 (p0) outliers start: 18 outliers final: 7 residues processed: 173 average time/residue: 0.8318 time to fit residues: 163.3481 Evaluate side-chains 158 residues out of total 2859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 713 ARG Chi-restraints excluded: chain C residue 1100 GLN Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 1281 VAL Chi-restraints excluded: chain F residue 248 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 58 optimal weight: 0.2980 chunk 97 optimal weight: 4.9990 chunk 331 optimal weight: 7.9990 chunk 259 optimal weight: 0.9990 chunk 187 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 251 optimal weight: 3.9990 chunk 291 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN B 16 GLN C 390 GLN D1172 HIS ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.072111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.046065 restraints weight = 108645.513| |-----------------------------------------------------------------------------| r_work (start): 0.2559 rms_B_bonded: 2.85 r_work: 0.2391 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2264 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2307 r_free = 0.2307 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2307 r_free = 0.2307 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9142 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29199 Z= 0.177 Angle : 0.536 8.483 39882 Z= 0.282 Chirality : 0.043 0.149 4494 Planarity : 0.004 0.046 4901 Dihedral : 15.161 75.837 4803 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.73 % Allowed : 7.68 % Favored : 91.59 % 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: 1.62 (0.15), residues: 3343 helix: 1.90 (0.14), residues: 1323 sheet: 0.33 (0.26), residues: 423 loop : 0.74 (0.16), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D1310 TYR 0.014 0.001 TYR C 615 PHE 0.016 0.002 PHE C 699 TRP 0.011 0.001 TRP A 200 HIS 0.008 0.001 HIS C 434 Details of bonding type rmsd covalent geometry : bond 0.00413 (29191) covalent geometry : angle 0.53492 (39870) hydrogen bonds : bond 0.04078 ( 1333) hydrogen bonds : angle 4.48671 ( 3638) metal coordination : bond 0.00624 ( 8) metal coordination : angle 2.15413 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 ASN cc_start: 0.9416 (t0) cc_final: 0.9048 (t0) REVERT: A 155 LYS cc_start: 0.9400 (mtpp) cc_final: 0.9167 (ttpp) REVERT: A 194 LYS cc_start: 0.9346 (OUTLIER) cc_final: 0.8993 (tttt) REVERT: B 5 LYS cc_start: 0.9128 (tttm) cc_final: 0.8869 (tptp) REVERT: B 72 LYS cc_start: 0.9323 (mttt) cc_final: 0.8996 (mmtm) REVERT: B 91 ASN cc_start: 0.9437 (t0) cc_final: 0.9192 (t0) REVERT: B 155 LYS cc_start: 0.9307 (tppp) cc_final: 0.9102 (mmmm) REVERT: C 8 ARG cc_start: 0.8154 (mtm-85) cc_final: 0.7823 (mtm-85) REVERT: C 781 LYS cc_start: 0.8773 (pptt) cc_final: 0.8569 (tmmt) REVERT: C 814 GLU cc_start: 0.8581 (mp0) cc_final: 0.8314 (mp0) REVERT: C 1100 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8548 (mm-40) REVERT: D 167 GLU cc_start: 0.8617 (tp30) cc_final: 0.8163 (tm-30) REVERT: D 351 MET cc_start: 0.9286 (mtp) cc_final: 0.8976 (mtm) REVERT: D 986 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8167 (tpp-160) REVERT: E 44 GLU cc_start: 0.9352 (mt-10) cc_final: 0.9102 (mt-10) REVERT: F 367 MET cc_start: 0.9305 (tpt) cc_final: 0.9048 (tpp) outliers start: 21 outliers final: 9 residues processed: 170 average time/residue: 0.8674 time to fit residues: 167.8582 Evaluate side-chains 161 residues out of total 2859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 1100 GLN Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 986 ARG Chi-restraints excluded: chain D residue 1281 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain F residue 248 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 112 optimal weight: 0.9990 chunk 181 optimal weight: 6.9990 chunk 237 optimal weight: 0.2980 chunk 205 optimal weight: 3.9990 chunk 238 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 325 optimal weight: 0.0970 chunk 152 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN B 16 GLN C 390 GLN D1359 GLN ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.075046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.049661 restraints weight = 115192.132| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 2.84 r_work: 0.2564 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2453 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2444 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2444 r_free = 0.2444 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2444 r_free = 0.2444 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2444 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9164 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29199 Z= 0.123 Angle : 0.509 9.212 39882 Z= 0.268 Chirality : 0.042 0.146 4494 Planarity : 0.004 0.050 4901 Dihedral : 15.078 76.993 4803 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.49 % Allowed : 8.07 % Favored : 91.45 % 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: 1.67 (0.15), residues: 3343 helix: 1.98 (0.14), residues: 1324 sheet: 0.27 (0.25), residues: 413 loop : 0.75 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D1310 TYR 0.010 0.001 TYR C 615 PHE 0.026 0.001 PHE F 389 TRP 0.012 0.001 TRP B 200 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00282 (29191) covalent geometry : angle 0.50786 (39870) hydrogen bonds : bond 0.03655 ( 1333) hydrogen bonds : angle 4.37134 ( 3638) metal coordination : bond 0.00386 ( 8) metal coordination : angle 1.86730 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 1.110 Fit side-chains REVERT: A 91 ASN cc_start: 0.9426 (t0) cc_final: 0.9062 (t0) REVERT: A 155 LYS cc_start: 0.9380 (mtpp) cc_final: 0.9142 (ttpp) REVERT: A 162 ILE cc_start: 0.9295 (mp) cc_final: 0.8969 (tp) REVERT: A 194 LYS cc_start: 0.9382 (OUTLIER) cc_final: 0.9024 (tttt) REVERT: B 5 LYS cc_start: 0.9114 (tttm) cc_final: 0.8872 (tptp) REVERT: B 72 LYS cc_start: 0.9284 (mttt) cc_final: 0.8994 (mmtm) REVERT: B 91 ASN cc_start: 0.9477 (t0) cc_final: 0.9262 (t0) REVERT: B 155 LYS cc_start: 0.9280 (tppp) cc_final: 0.9076 (mmmm) REVERT: B 163 ASN cc_start: 0.9039 (m110) cc_final: 0.8834 (p0) REVERT: C 422 ARG cc_start: 0.8129 (mtm110) cc_final: 0.7897 (mtt90) REVERT: C 781 LYS cc_start: 0.8754 (pptt) cc_final: 0.8490 (tmmt) REVERT: C 814 GLU cc_start: 0.8546 (mp0) cc_final: 0.8302 (mp0) REVERT: C 1100 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8626 (mm-40) REVERT: D 167 GLU cc_start: 0.8611 (tp30) cc_final: 0.8220 (tm-30) REVERT: D 198 ARG cc_start: 0.9064 (mtp-110) cc_final: 0.8408 (mtp-110) REVERT: D 351 MET cc_start: 0.9237 (mtp) cc_final: 0.8976 (mtm) REVERT: D 388 HIS cc_start: 0.9143 (m90) cc_final: 0.8899 (m90) REVERT: E 44 GLU cc_start: 0.9386 (mt-10) cc_final: 0.9127 (mt-10) REVERT: F 367 MET cc_start: 0.9403 (tpt) cc_final: 0.9114 (tpt) outliers start: 14 outliers final: 4 residues processed: 174 average time/residue: 0.8425 time to fit residues: 167.6063 Evaluate side-chains 154 residues out of total 2859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 148 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 1100 GLN Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 1281 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 170 optimal weight: 0.6980 chunk 158 optimal weight: 0.0980 chunk 187 optimal weight: 7.9990 chunk 199 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 chunk 329 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN B 16 GLN C 390 GLN ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.075488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.050234 restraints weight = 113923.965| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 2.82 r_work: 0.2577 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2465 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2459 r_free = 0.2459 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2459 r_free = 0.2459 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9156 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29199 Z= 0.115 Angle : 0.509 9.179 39882 Z= 0.267 Chirality : 0.041 0.145 4494 Planarity : 0.004 0.054 4901 Dihedral : 15.013 78.315 4803 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.45 % Allowed : 8.34 % Favored : 91.20 % 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: 1.70 (0.15), residues: 3343 helix: 2.02 (0.14), residues: 1325 sheet: 0.25 (0.25), residues: 424 loop : 0.76 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D1310 TYR 0.010 0.001 TYR D1198 PHE 0.026 0.001 PHE F 389 TRP 0.011 0.001 TRP B 200 HIS 0.005 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00261 (29191) covalent geometry : angle 0.50842 (39870) hydrogen bonds : bond 0.03527 ( 1333) hydrogen bonds : angle 4.29612 ( 3638) metal coordination : bond 0.00356 ( 8) metal coordination : angle 1.89814 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 1.202 Fit side-chains REVERT: A 91 ASN cc_start: 0.9421 (t0) cc_final: 0.9074 (t0) REVERT: A 155 LYS cc_start: 0.9366 (mtpp) cc_final: 0.9136 (ttpp) REVERT: A 162 ILE cc_start: 0.9292 (mp) cc_final: 0.8996 (tp) REVERT: A 194 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.9021 (tttt) REVERT: B 5 LYS cc_start: 0.9118 (tttm) cc_final: 0.8880 (tptp) REVERT: B 72 LYS cc_start: 0.9270 (mttt) cc_final: 0.8983 (mmtm) REVERT: B 91 ASN cc_start: 0.9489 (t0) cc_final: 0.9278 (t0) REVERT: B 155 LYS cc_start: 0.9270 (tppp) cc_final: 0.9056 (mmmm) REVERT: C 422 ARG cc_start: 0.8151 (mtm110) cc_final: 0.7923 (mtt90) REVERT: C 781 LYS cc_start: 0.8751 (pptt) cc_final: 0.8471 (tmmt) REVERT: C 814 GLU cc_start: 0.8535 (mp0) cc_final: 0.8273 (mp0) REVERT: C 1100 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8445 (pt0) REVERT: D 167 GLU cc_start: 0.8631 (tp30) cc_final: 0.8299 (tm-30) REVERT: D 351 MET cc_start: 0.9238 (mtp) cc_final: 0.8993 (mtm) REVERT: D 388 HIS cc_start: 0.9127 (m90) cc_final: 0.8881 (m90) REVERT: E 44 GLU cc_start: 0.9384 (mt-10) cc_final: 0.9160 (mt-10) REVERT: E 84 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8795 (mmp80) REVERT: F 367 MET cc_start: 0.9392 (tpt) cc_final: 0.9101 (tpt) outliers start: 13 outliers final: 5 residues processed: 166 average time/residue: 0.8859 time to fit residues: 166.4670 Evaluate side-chains 158 residues out of total 2859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 150 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 1100 GLN Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 1281 VAL Chi-restraints excluded: chain E residue 84 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 58 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 338 optimal weight: 0.9990 chunk 195 optimal weight: 4.9990 chunk 324 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 265 optimal weight: 2.9990 chunk 322 optimal weight: 3.9990 chunk 277 optimal weight: 1.9990 chunk 145 optimal weight: 0.0030 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN B 16 GLN C 390 GLN ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.075543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.050450 restraints weight = 99010.638| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 2.65 r_work: 0.2592 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2480 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2471 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2471 r_free = 0.2471 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2471 r_free = 0.2471 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2471 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9148 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29199 Z= 0.116 Angle : 0.509 9.561 39882 Z= 0.267 Chirality : 0.041 0.191 4494 Planarity : 0.004 0.045 4901 Dihedral : 14.986 78.775 4803 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.31 % Allowed : 8.55 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.15), residues: 3343 helix: 2.05 (0.14), residues: 1325 sheet: 0.32 (0.25), residues: 412 loop : 0.79 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 230 TYR 0.009 0.001 TYR D 128 PHE 0.010 0.001 PHE D 68 TRP 0.010 0.001 TRP B 200 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00265 (29191) covalent geometry : angle 0.50842 (39870) hydrogen bonds : bond 0.03493 ( 1333) hydrogen bonds : angle 4.26704 ( 3638) metal coordination : bond 0.00363 ( 8) metal coordination : angle 1.88191 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 1.298 Fit side-chains REVERT: A 91 ASN cc_start: 0.9420 (t0) cc_final: 0.9073 (t0) REVERT: A 155 LYS cc_start: 0.9355 (mtpp) cc_final: 0.9128 (ttpp) REVERT: A 162 ILE cc_start: 0.9283 (mp) cc_final: 0.8993 (tp) REVERT: A 194 LYS cc_start: 0.9382 (OUTLIER) cc_final: 0.9017 (tttt) REVERT: B 5 LYS cc_start: 0.9119 (tttm) cc_final: 0.8887 (tptp) REVERT: B 72 LYS cc_start: 0.9269 (mttt) cc_final: 0.9001 (mmtm) REVERT: B 91 ASN cc_start: 0.9491 (t0) cc_final: 0.9288 (t0) REVERT: B 155 LYS cc_start: 0.9258 (tppp) cc_final: 0.9042 (mmmm) REVERT: C 422 ARG cc_start: 0.8177 (mtm110) cc_final: 0.7941 (mtt90) REVERT: C 814 GLU cc_start: 0.8536 (mp0) cc_final: 0.8268 (mp0) REVERT: C 1100 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8434 (pt0) REVERT: D 167 GLU cc_start: 0.8580 (tp30) cc_final: 0.8361 (tm-30) REVERT: D 351 MET cc_start: 0.9213 (mtp) cc_final: 0.8986 (mtm) REVERT: D 388 HIS cc_start: 0.9128 (m90) cc_final: 0.8867 (m90) REVERT: E 44 GLU cc_start: 0.9382 (mt-10) cc_final: 0.9137 (mt-10) REVERT: F 323 ASP cc_start: 0.8917 (m-30) cc_final: 0.8665 (m-30) REVERT: F 367 MET cc_start: 0.9374 (tpt) cc_final: 0.9070 (tpt) outliers start: 9 outliers final: 5 residues processed: 161 average time/residue: 0.8781 time to fit residues: 160.7921 Evaluate side-chains 158 residues out of total 2859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 151 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 1100 GLN Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 1281 VAL Chi-restraints excluded: chain E residue 50 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 301 optimal weight: 5.9990 chunk 150 optimal weight: 0.0470 chunk 291 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 196 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 chunk 246 optimal weight: 3.9990 chunk 193 optimal weight: 0.9990 chunk 250 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 220 optimal weight: 0.0070 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN B 16 GLN C 390 GLN ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.075166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.049880 restraints weight = 107817.528| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 2.75 r_work: 0.2575 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2463 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2451 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2451 r_free = 0.2451 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2451 r_free = 0.2451 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2451 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9161 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29199 Z= 0.132 Angle : 0.520 9.202 39882 Z= 0.272 Chirality : 0.042 0.203 4494 Planarity : 0.004 0.082 4901 Dihedral : 15.002 78.652 4803 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.31 % Allowed : 8.66 % Favored : 91.03 % 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: 1.77 (0.15), residues: 3343 helix: 2.04 (0.14), residues: 1325 sheet: 0.37 (0.25), residues: 412 loop : 0.80 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D1310 TYR 0.011 0.001 TYR D1198 PHE 0.031 0.001 PHE F 389 TRP 0.009 0.001 TRP A 200 HIS 0.006 0.001 HIS C 434 Details of bonding type rmsd covalent geometry : bond 0.00306 (29191) covalent geometry : angle 0.51880 (39870) hydrogen bonds : bond 0.03615 ( 1333) hydrogen bonds : angle 4.27897 ( 3638) metal coordination : bond 0.00430 ( 8) metal coordination : angle 1.91501 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 153 time to evaluate : 1.185 Fit side-chains REVERT: A 91 ASN cc_start: 0.9423 (t0) cc_final: 0.9077 (t0) REVERT: A 155 LYS cc_start: 0.9358 (mtpp) cc_final: 0.9131 (ttpp) REVERT: A 162 ILE cc_start: 0.9289 (mp) cc_final: 0.8990 (tp) REVERT: A 194 LYS cc_start: 0.9395 (OUTLIER) cc_final: 0.9037 (tttt) REVERT: B 5 LYS cc_start: 0.9112 (tttm) cc_final: 0.8890 (tptp) REVERT: B 72 LYS cc_start: 0.9265 (mttt) cc_final: 0.9002 (mmtm) REVERT: B 91 ASN cc_start: 0.9494 (t0) cc_final: 0.9287 (t0) REVERT: B 155 LYS cc_start: 0.9257 (tppp) cc_final: 0.9046 (mmmm) REVERT: C 422 ARG cc_start: 0.8192 (mtm110) cc_final: 0.7962 (mtt90) REVERT: C 814 GLU cc_start: 0.8528 (mp0) cc_final: 0.8277 (mp0) REVERT: C 1100 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8428 (pt0) REVERT: D 167 GLU cc_start: 0.8646 (tp30) cc_final: 0.8381 (tm-30) REVERT: D 351 MET cc_start: 0.9224 (mtp) cc_final: 0.8988 (mtm) REVERT: D 388 HIS cc_start: 0.9112 (m90) cc_final: 0.8803 (m90) REVERT: D 980 MET cc_start: 0.8310 (mtp) cc_final: 0.8062 (ttp) REVERT: D 982 PHE cc_start: 0.9243 (m-80) cc_final: 0.7968 (m-80) REVERT: D 1310 ARG cc_start: 0.8679 (ttp-110) cc_final: 0.8394 (mtp-110) REVERT: E 44 GLU cc_start: 0.9402 (mt-10) cc_final: 0.9150 (mt-10) REVERT: E 84 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8759 (mmp80) REVERT: F 323 ASP cc_start: 0.8928 (m-30) cc_final: 0.8692 (m-30) REVERT: F 367 MET cc_start: 0.9378 (tpt) cc_final: 0.9066 (tpt) outliers start: 9 outliers final: 6 residues processed: 159 average time/residue: 0.8648 time to fit residues: 156.7217 Evaluate side-chains 159 residues out of total 2859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 1100 GLN Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 1281 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 84 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 255 optimal weight: 10.0000 chunk 326 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 187 optimal weight: 7.9990 chunk 224 optimal weight: 7.9990 chunk 233 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 330 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 230 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN B 16 GLN C 390 GLN ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.074033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.049005 restraints weight = 87266.009| |-----------------------------------------------------------------------------| r_work (start): 0.2689 rms_B_bonded: 2.47 r_work: 0.2550 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2439 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2428 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2428 r_free = 0.2428 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2428 r_free = 0.2428 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2428 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9181 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 29199 Z= 0.186 Angle : 0.548 11.906 39882 Z= 0.286 Chirality : 0.043 0.198 4494 Planarity : 0.004 0.063 4901 Dihedral : 15.081 77.306 4803 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.38 % Allowed : 8.69 % Favored : 90.92 % 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: 1.71 (0.15), residues: 3343 helix: 1.97 (0.14), residues: 1325 sheet: 0.35 (0.25), residues: 414 loop : 0.80 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 230 TYR 0.014 0.001 TYR D 128 PHE 0.015 0.002 PHE C 699 TRP 0.009 0.001 TRP A 200 HIS 0.008 0.001 HIS C 434 Details of bonding type rmsd covalent geometry : bond 0.00436 (29191) covalent geometry : angle 0.54657 (39870) hydrogen bonds : bond 0.04015 ( 1333) hydrogen bonds : angle 4.36819 ( 3638) metal coordination : bond 0.00623 ( 8) metal coordination : angle 2.07509 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14634.76 seconds wall clock time: 248 minutes 20.67 seconds (14900.67 seconds total)