Starting phenix.real_space_refine on Sat Aug 8 12:55:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fo6_50618/08_2026/9fo6_50618.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fo6_50618/08_2026/9fo6_50618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fo6_50618/08_2026/9fo6_50618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fo6_50618/08_2026/9fo6_50618.map" model { file = "/net/cci-nas-00/data/ceres_data/9fo6_50618/08_2026/9fo6_50618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fo6_50618/08_2026/9fo6_50618.cif" } resolution = 2.76 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= 0.014 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 76 5.49 5 Mg 4 5.21 5 S 70 5.16 5 C 17158 2.51 5 N 4893 2.21 5 O 5286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27489 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1777 Classifications: {'peptide': 226} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 211} Chain: "B" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1786 Classifications: {'peptide': 227} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 212} Chain: "C" Number of atoms: 8668 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1093, 8623 Classifications: {'peptide': 1093} Link IDs: {'PCIS': 1, 'PTRANS': 69, 'TRANS': 1022} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1093, 8623 Classifications: {'peptide': 1093} Link IDs: {'PCIS': 1, 'PTRANS': 69, 'TRANS': 1022} Chain breaks: 2 bond proxies already assigned to first conformer: 8737 Chain: "D" Number of atoms: 10909 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1364, 10763 Classifications: {'peptide': 1364} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1295} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1371, 10817 Classifications: {'peptide': 1371} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1302} Chain breaks: 2 bond proxies already assigned to first conformer: 10851 Chain: "E" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 761 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 6, 'TRANS': 87} Chain: "F" Number of atoms: 2107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 2087 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 13, 'TRANS': 245} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 259, 2087 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 13, 'TRANS': 245} Chain breaks: 1 bond proxies already assigned to first conformer: 2101 Chain: "G" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 632 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain breaks: 1 Chain: "H" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 753 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 95 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 7, 66 Unusual residues: {' MG': 3, ' ZN': 2, '2TM': 1, 'GTP': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Conformer: "A" Number of residues, atoms: 6, 65 Unusual residues: {' MG': 2, ' ZN': 2, '2TM': 1, 'GTP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} bond proxies already assigned to first conformer: 34 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20116 SG CYS D1112 100.528 86.383 90.837 1.00 45.23 S ATOM 20760 SG CYS D1194 97.263 86.216 89.002 1.00 42.99 S ATOM 20816 SG CYS D1201 100.300 84.494 87.536 1.00 36.77 S ATOM 20840 SG CYS D1204 98.562 82.975 90.448 1.00 46.53 S ATOM 12709 SG CYS D 58 76.334 127.518 44.472 1.00 92.61 S ATOM 12720 SG CYS D 60 73.657 130.032 43.811 1.00 88.32 S ATOM 12831 SG CYS D 73 76.772 131.197 45.613 1.00 91.23 S ATOM 12857 SG CYS D 76 74.411 128.999 47.444 1.00 84.65 S Residues with excluded nonbonded symmetry interactions: 27 residue: pdb=" N AARG C 345 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 345 " occ=0.50 residue: pdb=" N AARG C 945 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 945 " occ=0.50 residue: pdb=" N AARG C 946 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 946 " occ=0.50 residue: pdb=" N ATYR C 998 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR C 998 " occ=0.50 residue: pdb=" N AARG D 586 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 586 " occ=0.50 residue: pdb=" N AARG D 674 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 674 " occ=0.50 residue: pdb=" N AALA D1085 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA D1085 " occ=0.50 residue: pdb=" N ALEU D1086 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU D1086 " occ=0.50 residue: pdb=" N AARG D1087 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D1087 " occ=0.50 residue: pdb=" N ATHR D1088 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR D1088 " occ=0.50 residue: pdb=" N ATHR D1234 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR D1234 " occ=0.50 residue: pdb=" N AGLN D1235 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN D1235 " occ=0.50 ... (remaining 15 not shown) Time building chain proxies: 7.09, per 1000 atoms: 0.26 Number of scatterers: 27489 At special positions: 0 Unit cell: (140.878, 179.224, 135.043, 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 76 15.00 Mg 4 11.99 O 5286 8.00 N 4893 7.00 C 17158 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: 1.58 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1201 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1194 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1204 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1112 " pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 73 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 76 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 58 " Number of angles added : 12 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6084 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 51 sheets defined 42.8% alpha, 19.0% beta 20 base pairs and 51 stacking pairs defined. Time for finding SS restraints: 3.04 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 removed outlier: 3.526A pdb=" N HIS B 156 " --> pdb=" O PRO B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 223 Processing helix chain 'B' and resid 224 through 226 No H-bonds generated for 'chain 'B' and resid 224 through 226' Processing helix chain 'C' and resid 19 through 31 removed outlier: 4.140A pdb=" N SER C 25 " --> pdb=" O ILE C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 52 Processing helix chain 'C' and resid 79 through 87 Processing helix chain 'C' and resid 193 through 201 Processing helix chain 'C' and resid 203 through 212 Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 222 Processing helix chain 'C' and resid 223 through 229 removed outlier: 3.546A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 4.028A 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 315 Processing helix chain 'C' and resid 335 through 362 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.671A pdb=" N LEU C 372 " --> pdb=" O THR C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 389 Processing helix chain 'C' and resid 399 through 408 removed outlier: 3.607A pdb=" N SER C 403 " --> pdb=" O ASN C 399 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 435 removed outlier: 3.553A pdb=" N TYR C 435 " --> pdb=" O ARG C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 525 through 529 Processing helix chain 'C' and resid 535 through 540 Processing helix chain 'C' and resid 543 through 547 removed outlier: 3.537A pdb=" N ILE C 547 " --> pdb=" O THR C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 554 through 566 removed outlier: 4.105A 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: 4.104A pdb=" N ASP C 686 " --> pdb=" O ASN C 683 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA C 687 " --> pdb=" O PHE C 684 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 683 through 687' Processing helix chain 'C' and resid 692 through 697 Processing helix chain 'C' and resid 730 through 735 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 Processing helix chain 'C' and resid 910 through 932 removed outlier: 4.199A pdb=" N ARG C 929 " --> pdb=" O TYR C 925 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU C 932 " --> pdb=" O LYS C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 951 Processing helix chain 'C' and resid 958 through 969 removed outlier: 3.512A pdb=" N GLN C 969 " --> pdb=" O GLU C 965 " (cutoff:3.500A) 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 1073 Processing helix chain 'C' and resid 1082 through 1095 removed outlier: 3.745A pdb=" N ARG C1086 " --> pdb=" O PRO C1082 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 22 Processing helix chain 'D' and resid 46 through 51 Processing helix chain 'D' and resid 82 through 88 removed outlier: 3.507A pdb=" N VAL D 85 " --> pdb=" O LYS D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 105 Processing helix chain 'D' and resid 110 through 117 Processing helix chain 'D' and resid 119 through 128 Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 372 through 376 Processing helix chain 'D' and resid 423 through 426 removed outlier: 3.501A pdb=" N LYS D 426 " --> pdb=" O ASP D 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 423 through 426' Processing helix chain 'D' and resid 456 through 468 removed outlier: 4.006A pdb=" N ALA D 460 " --> pdb=" O MET D 456 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 468 " --> pdb=" O LEU D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 481 Processing helix chain 'D' and resid 485 through 506 removed outlier: 3.614A pdb=" N VAL D 498 " --> pdb=" O LYS D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 511 Processing helix chain 'D' and resid 521 through 525 Processing helix chain 'D' and resid 538 through 560 removed outlier: 4.067A 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: 3.928A pdb=" N ARG D 679 " --> pdb=" O ARG D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 683 Processing helix chain 'D' and resid 685 through 695 removed outlier: 3.919A pdb=" N ASP D 689 " --> pdb=" O ASP D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 711 No H-bonds generated for 'chain 'D' and resid 709 through 711' Processing helix chain 'D' and resid 729 through 731 No H-bonds generated for 'chain 'D' and resid 729 through 731' Processing helix chain 'D' and resid 732 through 737 Processing helix chain 'D' and resid 752 through 762 Processing helix chain 'D' and resid 764 through 768 Processing helix chain 'D' and resid 783 through 794 Processing helix chain 'D' and resid 808 through 819 Processing helix chain 'D' and resid 835 through 841 removed outlier: 3.636A pdb=" N LEU D 839 " --> pdb=" O SER D 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 855 Processing helix chain 'D' and resid 876 through 891 Processing helix chain 'D' and resid 892 through 900 Processing helix chain 'D' and resid 907 through 923 Processing helix chain 'D' and resid 923 through 945 removed outlier: 3.588A pdb=" N THR D 944 " --> pdb=" O THR D 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 950 through 954 Processing helix chain 'D' and resid 958 through 980 removed outlier: 3.767A pdb=" N GLN D 962 " --> pdb=" O GLU D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 984 through 1015 Processing helix chain 'D' and resid 1018 through 1026 Processing helix chain 'D' and resid 1031 through 1040 Processing helix chain 'D' and resid 1066 through 1103 removed outlier: 4.019A pdb=" N HIS D1075 " --> pdb=" O PHE D1071 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY D1076 " --> pdb=" O ILE D1072 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA D1089 " --> pdb=" O AALA D1085 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASP D1090 " --> pdb=" O BLEU D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 1136 through 1145 Processing helix chain 'D' and resid 1167 through 1180 Processing helix chain 'D' and resid 1190 through 1194 Processing helix chain 'D' and resid 1202 through 1206 Processing helix chain 'D' and resid 1220 through 1236 removed outlier: 3.509A pdb=" N VAL D1224 " --> pdb=" O ALA D1220 " (cutoff:3.500A) Proline residue: D1232 - end of helix removed outlier: 4.399A pdb=" N AGLN D1235 " --> pdb=" O GLU D1231 " (cutoff:3.500A) Processing helix chain 'D' and resid 1255 through 1264 Processing helix chain 'D' and resid 1331 through 1339 Processing helix chain 'D' and resid 1340 through 1359 removed outlier: 3.805A pdb=" N VAL D1355 " --> pdb=" O GLU D1351 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR D1356 " --> pdb=" O ILE D1352 " (cutoff:3.500A) Processing helix chain 'D' and resid 1364 through 1376 removed outlier: 4.403A pdb=" N ILE D1368 " --> pdb=" O HIS D1364 " (cutoff:3.500A) Processing helix chain 'D' and resid 1397 through 1411 Processing helix chain 'D' and resid 1423 through 1430 Processing helix chain 'D' and resid 1433 through 1441 removed outlier: 3.562A pdb=" N ALA D1437 " --> pdb=" O SER D1433 " (cutoff:3.500A) Processing helix chain 'D' and resid 1442 through 1454 Processing helix chain 'D' and resid 1461 through 1468 removed outlier: 4.118A pdb=" N ASN D1465 " --> pdb=" O GLY D1461 " (cutoff:3.500A) Processing helix chain 'D' and resid 1474 through 1478 Processing helix chain 'D' and resid 1489 through 1502 Processing helix chain 'E' and resid 5 through 12 Processing helix chain 'E' and resid 15 through 33 removed outlier: 3.515A pdb=" N LEU E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 71 removed outlier: 3.508A pdb=" N TRP E 63 " --> pdb=" O ASN E 59 " (cutoff:3.500A) removed outlier: 3.524A 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 90 removed outlier: 3.519A pdb=" N AGLN F 83 " --> pdb=" O ASP F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 121 Processing helix chain 'F' and resid 123 through 137 Processing helix chain 'F' and resid 152 through 164 Processing helix chain 'F' and resid 170 through 200 removed outlier: 5.150A pdb=" N ARG F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LEU F 194 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL F 195 " --> pdb=" O ASN F 191 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL F 196 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 227 Processing helix chain 'F' and resid 228 through 232 removed outlier: 3.844A pdb=" N ARG F 231 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 255 removed outlier: 3.798A pdb=" N TYR F 238 " --> pdb=" O LYS F 234 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TRP F 241 " --> pdb=" O THR F 237 " (cutoff:3.500A) removed outlier: 3.839A 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 329 through 333 Processing helix chain 'F' and resid 340 through 345 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 16 removed outlier: 5.632A pdb=" N TYR A 20 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N THR A 201 " --> pdb=" O TYR A 20 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLU A 22 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ILE A 199 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL A 24 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU A 197 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLU A 26 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU A 195 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N THR A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 6.363A 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: 7.222A pdb=" N ASN A 139 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE A 58 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU A 141 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL A 56 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.579A 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 removed outlier: 6.670A pdb=" N LYS A 107 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N THR A 131 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL A 109 " --> pdb=" O ILE A 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 150 through 151 Processing sheet with id=AA6, first strand: chain 'A' and resid 229 through 230 removed outlier: 5.848A pdb=" N GLN A 229 " --> pdb=" O VAL B 13 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N THR B 15 " --> pdb=" O GLN A 229 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TYR B 20 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR B 201 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N GLU B 22 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ILE B 199 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N VAL B 24 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LEU B 197 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLU B 26 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU B 195 " --> pdb=" O GLU B 26 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N THR B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU B 186 " --> pdb=" O THR B 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 104 removed outlier: 7.700A pdb=" N ASN B 139 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE B 58 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLU B 141 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL B 56 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ARG B 143 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 89 Processing sheet with id=AA9, first strand: chain 'B' and resid 107 through 110 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 removed outlier: 6.198A pdb=" N GLU C 2 " --> pdb=" O ARG C 900 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE C 902 " --> pdb=" O GLU C 2 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LYS C 4 " --> pdb=" O ILE C 902 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 54 through 55 removed outlier: 5.546A pdb=" N LEU C 66 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ILE C 101 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N PHE C 68 " --> pdb=" O GLN C 99 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLN C 99 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU C 70 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA C 92 " --> pdb=" O HIS C 117 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N HIS C 117 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU C 94 " --> pdb=" O LEU C 115 " (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: 6.554A 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: 6.783A pdb=" N TYR C 158 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 4.686A 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: 5.444A pdb=" N GLU C 482 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL C 475 " --> pdb=" O THR C 480 " (cutoff:3.500A) removed outlier: 6.550A 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: 6.511A 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: 6.933A pdb=" N ARG C 610 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL C 606 " --> pdb=" O ARG C 610 " (cutoff:3.500A) removed outlier: 6.428A 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: 6.708A pdb=" N ILE C 688 " --> pdb=" O LYS C 851 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEU C 853 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE C 690 " --> pdb=" O LEU C 853 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C 689 " --> pdb=" O ILE C 870 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N VAL C 869 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU C 673 " --> pdb=" O VAL C 869 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU C 871 " --> pdb=" O LEU C 673 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA C 675 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 4.531A 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: 6.359A pdb=" N SER C 702 " --> pdb=" O LYS C 830 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS C 830 " --> pdb=" O SER C 702 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N HIS C 704 " --> pdb=" O ALA C 828 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ALA C 828 " --> pdb=" O HIS C 704 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLU C 706 " --> pdb=" O TYR C 826 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N TYR C 826 " --> pdb=" O GLU C 706 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR C 708 " --> pdb=" O ARG C 824 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG C 824 " --> pdb=" O TYR C 708 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE C 710 " --> pdb=" O VAL C 822 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL C 822 " --> pdb=" O ILE C 710 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA C 712 " --> pdb=" O ARG C 820 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ARG C 820 " --> pdb=" O ARG C 807 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ARG C 807 " --> pdb=" O ARG C 820 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL C 822 " --> pdb=" O ARG C 805 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG C 805 " --> pdb=" O VAL C 822 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG C 824 " --> pdb=" O THR C 803 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR C 803 " --> pdb=" O ARG C 824 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR C 826 " --> pdb=" O VAL C 801 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 721 through 722 removed outlier: 3.526A pdb=" N ARG C 721 " --> pdb=" O THR C 759 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 754 through 756 removed outlier: 6.796A 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: 6.448A pdb=" N CYS D 642 " --> pdb=" O VAL D 719 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL D 721 " --> pdb=" O CYS D 642 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU D 644 " --> pdb=" O VAL D 721 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1030 through 1032 removed outlier: 3.878A pdb=" N GLN C1030 " --> pdb=" O VAL D 623 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1097 through 1102 Processing sheet with id=AD4, first strand: chain 'D' and resid 71 through 72 removed outlier: 4.686A pdb=" N LYS D 71 " --> pdb=" O VAL D 80 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 91 through 100 removed outlier: 10.253A pdb=" N LEU D 95 " --> pdb=" O PRO D 518 " (cutoff:3.500A) removed outlier: 11.017A pdb=" N THR D 97 " --> pdb=" O ALA D 516 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ALA D 516 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 152 through 153 Processing sheet with id=AD7, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AD8, first strand: chain 'D' and resid 166 through 170 removed outlier: 7.126A pdb=" N VAL D 385 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL D 213 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU D 387 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL D 211 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLU D 389 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N PHE D 207 " --> pdb=" O ALA D 391 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE D 393 " --> pdb=" O TYR D 205 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TYR D 205 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL D 395 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA D 203 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 184 through 185 removed outlier: 6.735A pdb=" N ALA D 203 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL D 395 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TYR D 205 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE D 393 " --> pdb=" O TYR D 205 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N PHE D 207 " --> pdb=" O ALA D 391 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLU D 389 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL D 211 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU D 387 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL D 213 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL D 385 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY D 383 " --> pdb=" O VAL D 361 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 190 through 192 Processing sheet with id=AE2, first strand: chain 'D' and resid 352 through 353 removed outlier: 6.621A pdb=" N VAL D 377 " --> pdb=" O ILE D 367 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 398 through 402 removed outlier: 4.015A pdb=" N ASP D 413 " --> pdb=" O VAL D 435 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 420 through 422 removed outlier: 3.721A pdb=" N LEU D 421 " --> pdb=" O VAL D 427 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N VAL D 427 " --> pdb=" O LEU D 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 527 through 529 removed outlier: 6.610A pdb=" N PHE D 535 " --> pdb=" O VAL F 315 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 805 through 806 Processing sheet with id=AE7, first strand: chain 'D' and resid 842 through 843 Processing sheet with id=AE8, first strand: chain 'D' and resid 1106 through 1109 Processing sheet with id=AE9, first strand: chain 'D' and resid 1118 through 1121 Processing sheet with id=AF1, first strand: chain 'D' and resid 1123 through 1125 Processing sheet with id=AF2, first strand: chain 'D' and resid 1153 through 1155 Processing sheet with id=AF3, first strand: chain 'D' and resid 1300 through 1304 Processing sheet with id=AF4, first strand: chain 'D' and resid 1394 through 1396 removed outlier: 6.649A pdb=" N ALA D1416 " --> pdb=" O THR D1382 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 1484 through 1488 Processing sheet with id=AF6, first strand: chain 'E' and resid 47 through 49 1207 hydrogen bonds defined for protein. 3352 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 51 stacking parallelities Total time for adding SS restraints: 6.98 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8849 1.34 - 1.46: 4144 1.46 - 1.58: 14861 1.58 - 1.70: 142 1.70 - 1.82: 131 Bond restraints: 28127 Sorted by residual: bond pdb=" C ALA D1082 " pdb=" N ASP D1083 " ideal model delta sigma weight residual 1.335 1.434 -0.099 1.31e-02 5.83e+03 5.73e+01 bond pdb=" C3' DC H 42 " pdb=" C2' DC H 42 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.40e+01 bond pdb=" O3BA2TM D2008 " pdb=" PG A2TM D2008 " ideal model delta sigma weight residual 1.700 1.628 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" O3BB2TM D2007 " pdb=" PG B2TM D2007 " ideal model delta sigma weight residual 1.700 1.628 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C3' DT H 27 " pdb=" C2' DT H 27 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.18e+01 ... (remaining 28122 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.27: 38292 4.27 - 8.53: 63 8.53 - 12.80: 9 12.80 - 17.07: 2 17.07 - 21.34: 1 Bond angle restraints: 38367 Sorted by residual: angle pdb=" PB GTP D2006 " pdb=" O3B GTP D2006 " pdb=" PG GTP D2006 " ideal model delta sigma weight residual 120.50 141.84 -21.34 3.00e+00 1.11e-01 5.06e+01 angle pdb=" O4' DC G 15 " pdb=" C4' DC G 15 " pdb=" C3' DC G 15 " ideal model delta sigma weight residual 106.00 102.87 3.13 6.00e-01 2.78e+00 2.72e+01 angle pdb=" PB A2TM D2008 " pdb=" O3BA2TM D2008 " pdb=" PG A2TM D2008 " ideal model delta sigma weight residual 132.18 147.37 -15.19 3.00e+00 1.11e-01 2.56e+01 angle pdb=" PB B2TM D2007 " pdb=" O3BB2TM D2007 " pdb=" PG B2TM D2007 " ideal model delta sigma weight residual 132.18 146.31 -14.13 3.00e+00 1.11e-01 2.22e+01 angle pdb=" O4' DG G 14 " pdb=" C4' DG G 14 " pdb=" C3' DG G 14 " ideal model delta sigma weight residual 106.00 103.38 2.62 6.00e-01 2.78e+00 1.91e+01 ... (remaining 38362 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 16269 35.52 - 71.05: 799 71.05 - 106.57: 62 106.57 - 142.10: 4 142.10 - 177.62: 4 Dihedral angle restraints: 17138 sinusoidal: 7675 harmonic: 9463 Sorted by residual: dihedral pdb=" C5' GTP D2006 " pdb=" O5' GTP D2006 " pdb=" PA GTP D2006 " pdb=" O3A GTP D2006 " ideal model delta sinusoidal sigma weight residual 69.27 -108.35 177.62 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2G GTP D2006 " pdb=" O3B GTP D2006 " pdb=" PG GTP D2006 " pdb=" PB GTP D2006 " ideal model delta sinusoidal sigma weight residual 177.30 15.43 161.87 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" C8 GTP D2006 " pdb=" C1' GTP D2006 " pdb=" N9 GTP D2006 " pdb=" O4' GTP D2006 " ideal model delta sinusoidal sigma weight residual 104.59 -47.41 152.00 1 2.00e+01 2.50e-03 4.52e+01 ... (remaining 17135 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2945 0.044 - 0.087: 1008 0.087 - 0.131: 341 0.131 - 0.174: 20 0.174 - 0.218: 2 Chirality restraints: 4316 Sorted by residual: chirality pdb=" C2' GTP D2006 " pdb=" C1' GTP D2006 " pdb=" C3' GTP D2006 " pdb=" O2' GTP D2006 " both_signs ideal model delta sigma weight residual False -2.47 -2.69 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB BTHR D1243 " pdb=" CA BTHR D1243 " pdb=" OG1BTHR D1243 " pdb=" CG2BTHR D1243 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ASP A 191 " pdb=" N ASP A 191 " pdb=" C ASP A 191 " pdb=" CB ASP A 191 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.83e-01 ... (remaining 4313 not shown) Planarity restraints: 4780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA BTHR D1088 " -0.021 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C BTHR D1088 " 0.074 2.00e-02 2.50e+03 pdb=" O BTHR D1088 " -0.027 2.00e-02 2.50e+03 pdb=" N ALA D1089 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1'A2TM D2008 " 0.030 2.00e-02 2.50e+03 1.55e-02 5.42e+00 pdb=" C2 A2TM D2008 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A2TM D2008 " -0.004 2.00e-02 2.50e+03 pdb=" C5 A2TM D2008 " -0.013 2.00e-02 2.50e+03 pdb=" C6 A2TM D2008 " -0.015 2.00e-02 2.50e+03 pdb=" N1 A2TM D2008 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A2TM D2008 " -0.003 2.00e-02 2.50e+03 pdb=" N4 A2TM D2008 " 0.025 2.00e-02 2.50e+03 pdb=" O2 A2TM D2008 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 420 " 0.172 9.50e-02 1.11e+02 7.75e-02 4.25e+00 pdb=" NE ARG C 420 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG C 420 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C 420 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG C 420 " 0.002 2.00e-02 2.50e+03 ... (remaining 4777 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 136 2.55 - 3.14: 19922 3.14 - 3.73: 41936 3.73 - 4.31: 61894 4.31 - 4.90: 101515 Nonbonded interactions: 225403 Sorted by model distance: nonbonded pdb="MG B MG D2004 " pdb=" O1BB2TM D2007 " model vdw 1.963 2.170 nonbonded pdb="MG MG D2003 " pdb=" O3' GTP D2006 " model vdw 2.138 2.170 nonbonded pdb=" OD2 ASP D 739 " pdb="MG B MG D2004 " model vdw 2.207 2.170 nonbonded pdb=" OD2 ASP C 680 " pdb=" NH1 ARG C 978 " model vdw 2.222 3.120 nonbonded pdb=" NZ LYS F 226 " pdb=" OP2 DG H 26 " model vdw 2.222 3.120 ... (remaining 225398 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' selection = (chain 'B' and resid 6 through 231) } 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=0.50 max=1.00 mean=0.99 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: 12.920 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: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 30.080 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:8.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9095 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 : 0.006 0.099 28135 Z= 0.282 Angle : 0.676 21.336 38379 Z= 0.380 Chirality : 0.047 0.218 4316 Planarity : 0.005 0.078 4780 Dihedral : 18.830 177.622 11054 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.61 % Allowed : 20.07 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.14), residues: 3281 helix: 1.33 (0.15), residues: 1225 sheet: 0.15 (0.23), residues: 489 loop : 0.21 (0.16), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 420 TYR 0.017 0.002 TYR C 158 PHE 0.018 0.002 PHE A 179 TRP 0.011 0.002 TRP A 200 HIS 0.009 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.28 (28127) covalent geometry : angle 0.67430 / 0.38 (38367) hydrogen bonds : bond 0.13867 / 9.51 ( 1255) hydrogen bonds : angle 5.77706 / 4.01 ( 3456) metal coordination : bond 0.00460 / 0.20 ( 8) metal coordination : angle 2.91355 / 1.38 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 16 GLN cc_start: 0.7355 (tm-30) cc_final: 0.7136 (tm-30) REVERT: C 102 HIS cc_start: 0.8023 (t-90) cc_final: 0.7788 (t-90) REVERT: D 442 ASN cc_start: 0.9144 (m110) cc_final: 0.8870 (t0) REVERT: D 1286 THR cc_start: 0.8752 (p) cc_final: 0.8447 (p) REVERT: D 1318 TYR cc_start: 0.7759 (t80) cc_final: 0.7310 (t80) outliers start: 14 outliers final: 4 residues processed: 204 average time/residue: 0.8875 time to fit residues: 201.9210 Evaluate side-chains 127 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 123 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 972 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 229 GLN C 670 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.059967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.039089 restraints weight = 274891.262| |-----------------------------------------------------------------------------| r_work (start): 0.2612 rms_B_bonded: 4.29 r_work: 0.2421 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2421 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2424 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2424 r_free = 0.2424 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2422 r_free = 0.2422 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (14 function evaluations) r_final: 0.2422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9327 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28135 Z= 0.178 Angle : 0.602 10.420 38379 Z= 0.317 Chirality : 0.044 0.157 4316 Planarity : 0.005 0.056 4780 Dihedral : 15.018 165.739 4476 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.97 % Allowed : 19.57 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % 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: 1.17 (0.15), residues: 3281 helix: 1.69 (0.15), residues: 1240 sheet: 0.24 (0.23), residues: 469 loop : 0.33 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D1310 TYR 0.016 0.001 TYR D 128 PHE 0.024 0.001 PHE C 227 TRP 0.012 0.001 TRP D1434 HIS 0.008 0.001 HIS D 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (28127) covalent geometry : angle 0.60033 / 0.32 (38367) hydrogen bonds : bond 0.05106 / 3.40 ( 1255) hydrogen bonds : angle 4.78850 / 3.33 ( 3456) metal coordination : bond 0.00385 / 0.18 ( 8) metal coordination : angle 2.29307 / 1.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 131 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 GLN cc_start: 0.7731 (tm-30) cc_final: 0.7292 (tm-30) REVERT: C 102 HIS cc_start: 0.8459 (t-90) cc_final: 0.8046 (t-90) REVERT: D 434 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8895 (ttp80) REVERT: D 442 ASN cc_start: 0.9273 (m110) cc_final: 0.8918 (t0) REVERT: D 1412 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8977 (mptm) REVERT: E 41 GLU cc_start: 0.9337 (mm-30) cc_final: 0.9123 (mm-30) REVERT: E 44 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8438 (mt-10) REVERT: E 77 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8758 (mt-10) REVERT: E 88 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8712 (mt-10) outliers start: 52 outliers final: 15 residues processed: 173 average time/residue: 0.7556 time to fit residues: 149.0620 Evaluate side-chains 136 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 564 MET Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain C residue 1117 SER Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 434 ARG Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 676 MET Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 1185 GLU Chi-restraints excluded: chain D residue 1304 LYS Chi-restraints excluded: chain D residue 1412 LYS Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 88 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 7 optimal weight: 0.9980 chunk 186 optimal weight: 3.9990 chunk 156 optimal weight: 0.0870 chunk 117 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 267 optimal weight: 8.9990 chunk 216 optimal weight: 0.7980 chunk 277 optimal weight: 3.9990 chunk 222 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.060375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.039798 restraints weight = 232592.000| |-----------------------------------------------------------------------------| r_work (start): 0.2639 rms_B_bonded: 4.01 r_work: 0.2457 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2460 r_free = 0.2460 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2460 r_free = 0.2460 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9307 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28135 Z= 0.124 Angle : 0.548 9.377 38379 Z= 0.287 Chirality : 0.043 0.154 4316 Planarity : 0.004 0.046 4780 Dihedral : 14.750 153.636 4474 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.32 % Allowed : 20.18 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % 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 (0.15), residues: 3281 helix: 1.92 (0.15), residues: 1243 sheet: 0.34 (0.24), residues: 453 loop : 0.40 (0.16), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 422 TYR 0.023 0.001 TYR D1318 PHE 0.019 0.001 PHE D 982 TRP 0.011 0.001 TRP B 200 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (28127) covalent geometry : angle 0.54728 / 0.29 (38367) hydrogen bonds : bond 0.04321 / 2.86 ( 1255) hydrogen bonds : angle 4.50782 / 3.14 ( 3456) metal coordination : bond 0.00274 / 0.12 ( 8) metal coordination : angle 1.85023 / 0.94 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8507 (mm-30) REVERT: B 16 GLN cc_start: 0.7736 (tm-30) cc_final: 0.7306 (tm-30) REVERT: C 102 HIS cc_start: 0.8546 (t-90) cc_final: 0.8055 (t-90) REVERT: D 351 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8457 (pmt) REVERT: D 1412 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8969 (mptm) REVERT: E 41 GLU cc_start: 0.9283 (mm-30) cc_final: 0.9031 (mm-30) REVERT: E 44 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8463 (mt-10) REVERT: E 77 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8682 (mt-10) REVERT: E 87 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8755 (pttm) REVERT: E 88 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8726 (mt-10) REVERT: E 89 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8634 (ttp) outliers start: 34 outliers final: 9 residues processed: 143 average time/residue: 0.7769 time to fit residues: 127.1062 Evaluate side-chains 130 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 1117 SER Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 351 MET Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 1185 GLU Chi-restraints excluded: chain D residue 1304 LYS Chi-restraints excluded: chain D residue 1412 LYS Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 89 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 329 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 326 optimal weight: 20.0000 chunk 209 optimal weight: 0.8980 chunk 83 optimal weight: 0.0050 chunk 230 optimal weight: 1.9990 chunk 316 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 257 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 320 optimal weight: 0.5980 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.060013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.039323 restraints weight = 268867.292| |-----------------------------------------------------------------------------| r_work (start): 0.2628 rms_B_bonded: 4.27 r_work: 0.2439 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2443 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2443 r_free = 0.2443 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2443 r_free = 0.2443 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2443 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9318 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28135 Z= 0.138 Angle : 0.537 9.789 38379 Z= 0.281 Chirality : 0.042 0.156 4316 Planarity : 0.004 0.045 4780 Dihedral : 14.505 147.652 4470 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.29 % Allowed : 20.14 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.15), residues: 3281 helix: 1.96 (0.15), residues: 1255 sheet: 0.35 (0.24), residues: 453 loop : 0.49 (0.16), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 284 TYR 0.013 0.001 TYR D 128 PHE 0.018 0.001 PHE C 227 TRP 0.011 0.001 TRP B 200 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (28127) covalent geometry : angle 0.53586 / 0.28 (38367) hydrogen bonds : bond 0.04213 / 2.78 ( 1255) hydrogen bonds : angle 4.40563 / 3.07 ( 3456) metal coordination : bond 0.00384 / 0.16 ( 8) metal coordination : angle 1.96550 / 0.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8546 (mm-30) REVERT: B 16 GLN cc_start: 0.7788 (tm-30) cc_final: 0.7356 (tm-30) REVERT: C 102 HIS cc_start: 0.8566 (t-90) cc_final: 0.8041 (t-90) REVERT: C 252 LYS cc_start: 0.9391 (mtpt) cc_final: 0.8947 (ptmt) REVERT: D 351 MET cc_start: 0.8968 (pmm) cc_final: 0.8376 (pmt) REVERT: D 1412 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8963 (mptm) REVERT: E 41 GLU cc_start: 0.9271 (mm-30) cc_final: 0.9017 (mm-30) REVERT: E 44 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8492 (mt-10) REVERT: E 77 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8713 (mt-10) REVERT: E 87 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8826 (ptpp) REVERT: F 241 TRP cc_start: 0.8939 (m100) cc_final: 0.8569 (m100) outliers start: 33 outliers final: 9 residues processed: 145 average time/residue: 0.7455 time to fit residues: 124.0298 Evaluate side-chains 129 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 676 MET Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 1412 LYS Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain F residue 176 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 244 optimal weight: 0.5980 chunk 177 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 chunk 86 optimal weight: 0.3980 chunk 178 optimal weight: 0.8980 chunk 263 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 670 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.059788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.039345 restraints weight = 224872.963| |-----------------------------------------------------------------------------| r_work (start): 0.2632 rms_B_bonded: 3.94 r_work: 0.2449 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2453 r_free = 0.2453 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2453 r_free = 0.2453 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9317 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28135 Z= 0.139 Angle : 0.526 10.480 38379 Z= 0.274 Chirality : 0.042 0.158 4316 Planarity : 0.004 0.052 4780 Dihedral : 14.299 143.436 4470 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.29 % Allowed : 20.25 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.15), residues: 3281 helix: 2.04 (0.15), residues: 1255 sheet: 0.40 (0.23), residues: 460 loop : 0.52 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 91 TYR 0.018 0.001 TYR D1318 PHE 0.020 0.001 PHE D 982 TRP 0.011 0.001 TRP B 200 HIS 0.006 0.001 HIS D1445 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (28127) covalent geometry : angle 0.52538 / 0.27 (38367) hydrogen bonds : bond 0.04145 / 2.74 ( 1255) hydrogen bonds : angle 4.33225 / 3.02 ( 3456) metal coordination : bond 0.00400 / 0.17 ( 8) metal coordination : angle 1.98009 / 0.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 84 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8531 (mm-30) REVERT: B 16 GLN cc_start: 0.7775 (tm-30) cc_final: 0.7351 (tm-30) REVERT: C 102 HIS cc_start: 0.8563 (t-90) cc_final: 0.8040 (t-90) REVERT: C 252 LYS cc_start: 0.9417 (mtpt) cc_final: 0.8980 (ptmt) REVERT: D 65 ARG cc_start: 0.7905 (ttp-110) cc_final: 0.7641 (tmt170) REVERT: D 351 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8343 (pmt) REVERT: D 442 ASN cc_start: 0.9552 (m-40) cc_final: 0.9236 (t0) REVERT: D 980 MET cc_start: 0.8378 (ttp) cc_final: 0.7939 (OUTLIER) REVERT: E 44 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8541 (mt-10) REVERT: E 77 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8670 (mt-10) REVERT: E 87 LYS cc_start: 0.9183 (ptpp) cc_final: 0.8822 (ptpp) REVERT: F 241 TRP cc_start: 0.8938 (m100) cc_final: 0.8558 (m100) outliers start: 33 outliers final: 11 residues processed: 149 average time/residue: 0.8117 time to fit residues: 137.8907 Evaluate side-chains 130 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 351 MET Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 1185 GLU Chi-restraints excluded: chain E residue 77 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 72 optimal weight: 3.9990 chunk 306 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 199 optimal weight: 4.9990 chunk 307 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 294 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 286 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 83 optimal weight: 0.0980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.059139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.038527 restraints weight = 253980.814| |-----------------------------------------------------------------------------| r_work (start): 0.2606 rms_B_bonded: 4.15 r_work: 0.2420 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2423 r_free = 0.2423 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2423 r_free = 0.2423 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9336 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28135 Z= 0.191 Angle : 0.558 10.918 38379 Z= 0.289 Chirality : 0.043 0.159 4316 Planarity : 0.004 0.045 4780 Dihedral : 14.238 138.573 4470 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.43 % Allowed : 20.25 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % 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: 1.57 (0.15), residues: 3281 helix: 2.08 (0.15), residues: 1250 sheet: 0.39 (0.24), residues: 462 loop : 0.52 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 91 TYR 0.014 0.001 TYR D 128 PHE 0.014 0.001 PHE A 179 TRP 0.011 0.001 TRP B 200 HIS 0.007 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (28127) covalent geometry : angle 0.55626 / 0.29 (38367) hydrogen bonds : bond 0.04435 / 2.93 ( 1255) hydrogen bonds : angle 4.35835 / 3.04 ( 3456) metal coordination : bond 0.00593 / 0.26 ( 8) metal coordination : angle 2.23102 / 1.12 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 84 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8563 (mm-30) REVERT: B 16 GLN cc_start: 0.7772 (tm-30) cc_final: 0.7342 (tm-30) REVERT: C 102 HIS cc_start: 0.8385 (t-90) cc_final: 0.7816 (t-90) REVERT: C 252 LYS cc_start: 0.9418 (mtpt) cc_final: 0.8990 (ptmt) REVERT: D 351 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8322 (pmt) REVERT: D 442 ASN cc_start: 0.9542 (m-40) cc_final: 0.9228 (t0) REVERT: E 44 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8582 (mt-10) REVERT: E 77 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8738 (mt-10) outliers start: 37 outliers final: 13 residues processed: 141 average time/residue: 0.8035 time to fit residues: 129.4784 Evaluate side-chains 129 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 351 MET Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 1185 GLU Chi-restraints excluded: chain D residue 1243 THR Chi-restraints excluded: chain D residue 1299 PHE Chi-restraints excluded: chain E residue 77 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 241 optimal weight: 0.6980 chunk 208 optimal weight: 3.9990 chunk 205 optimal weight: 0.4980 chunk 119 optimal weight: 4.9990 chunk 171 optimal weight: 6.9990 chunk 313 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 125 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 284 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.059287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.038866 restraints weight = 226965.239| |-----------------------------------------------------------------------------| r_work (start): 0.2619 rms_B_bonded: 3.92 r_work: 0.2436 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2439 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2439 r_free = 0.2439 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2439 r_free = 0.2439 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2439 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9326 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28135 Z= 0.155 Angle : 0.540 11.414 38379 Z= 0.279 Chirality : 0.043 0.160 4316 Planarity : 0.004 0.049 4780 Dihedral : 14.091 134.010 4470 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.14 % Allowed : 20.39 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % 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: 1.61 (0.15), residues: 3281 helix: 2.11 (0.15), residues: 1250 sheet: 0.37 (0.24), residues: 461 loop : 0.55 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 91 TYR 0.014 0.001 TYR D1318 PHE 0.028 0.001 PHE D 982 TRP 0.011 0.001 TRP F 299 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (28127) covalent geometry : angle 0.53851 / 0.28 (38367) hydrogen bonds : bond 0.04247 / 2.80 ( 1255) hydrogen bonds : angle 4.31709 / 3.01 ( 3456) metal coordination : bond 0.00473 / 0.21 ( 8) metal coordination : angle 2.03049 / 1.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 1.042 Fit side-chains REVERT: A 84 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8545 (mm-30) REVERT: B 16 GLN cc_start: 0.7754 (tm-30) cc_final: 0.7316 (tm-30) REVERT: C 102 HIS cc_start: 0.8402 (t-90) cc_final: 0.7830 (t-90) REVERT: C 252 LYS cc_start: 0.9424 (mtpt) cc_final: 0.9025 (ptmt) REVERT: D 351 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8330 (pmt) REVERT: D 442 ASN cc_start: 0.9528 (m-40) cc_final: 0.9218 (t0) REVERT: E 44 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8544 (mt-10) REVERT: E 77 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8676 (mt-10) REVERT: F 241 TRP cc_start: 0.8963 (m100) cc_final: 0.8564 (m100) outliers start: 28 outliers final: 12 residues processed: 136 average time/residue: 0.7102 time to fit residues: 110.5211 Evaluate side-chains 132 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 351 MET Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 1185 GLU Chi-restraints excluded: chain D residue 1243 THR Chi-restraints excluded: chain D residue 1299 PHE Chi-restraints excluded: chain E residue 77 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 286 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 266 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 267 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 219 GLN C 670 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.059441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.038853 restraints weight = 260728.246| |-----------------------------------------------------------------------------| r_work (start): 0.2619 rms_B_bonded: 4.20 r_work: 0.2431 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2434 r_free = 0.2434 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2434 r_free = 0.2434 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9330 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28135 Z= 0.139 Angle : 0.542 11.733 38379 Z= 0.280 Chirality : 0.042 0.163 4316 Planarity : 0.004 0.044 4780 Dihedral : 14.031 133.763 4470 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.04 % Allowed : 20.61 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.15), residues: 3281 helix: 2.13 (0.15), residues: 1250 sheet: 0.40 (0.24), residues: 459 loop : 0.57 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG D1499 TYR 0.013 0.001 TYR D 128 PHE 0.013 0.001 PHE A 179 TRP 0.011 0.001 TRP B 200 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (28127) covalent geometry : angle 0.54067 / 0.28 (38367) hydrogen bonds : bond 0.04125 / 2.72 ( 1255) hydrogen bonds : angle 4.28235 / 2.99 ( 3456) metal coordination : bond 0.00407 / 0.18 ( 8) metal coordination : angle 1.98674 / 0.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: A 84 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8558 (mm-30) REVERT: B 16 GLN cc_start: 0.7774 (tm-30) cc_final: 0.7341 (tm-30) REVERT: C 102 HIS cc_start: 0.8372 (t-90) cc_final: 0.7896 (t-90) REVERT: C 252 LYS cc_start: 0.9414 (mtpt) cc_final: 0.9019 (ptmt) REVERT: D 65 ARG cc_start: 0.7875 (ttp-110) cc_final: 0.7461 (ttp80) REVERT: D 351 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8337 (pmt) REVERT: D 442 ASN cc_start: 0.9537 (m-40) cc_final: 0.8956 (t0) REVERT: E 44 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8584 (mt-10) REVERT: E 77 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8682 (mt-10) REVERT: F 241 TRP cc_start: 0.8960 (m100) cc_final: 0.8579 (m100) outliers start: 25 outliers final: 12 residues processed: 141 average time/residue: 0.7713 time to fit residues: 123.8436 Evaluate side-chains 130 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 351 MET Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 1185 GLU Chi-restraints excluded: chain D residue 1243 THR Chi-restraints excluded: chain D residue 1299 PHE Chi-restraints excluded: chain E residue 77 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 48 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 299 optimal weight: 0.7980 chunk 218 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 320 optimal weight: 0.0040 chunk 40 optimal weight: 3.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 670 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.059514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.038997 restraints weight = 255090.775| |-----------------------------------------------------------------------------| r_work (start): 0.2624 rms_B_bonded: 4.15 r_work: 0.2437 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2440 r_free = 0.2440 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2440 r_free = 0.2440 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9327 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28135 Z= 0.135 Angle : 0.540 12.336 38379 Z= 0.279 Chirality : 0.042 0.155 4316 Planarity : 0.004 0.057 4780 Dihedral : 13.970 133.587 4470 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.97 % Allowed : 20.64 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.15), residues: 3281 helix: 2.15 (0.15), residues: 1251 sheet: 0.43 (0.24), residues: 459 loop : 0.61 (0.16), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 284 TYR 0.014 0.001 TYR D1318 PHE 0.033 0.001 PHE D 982 TRP 0.011 0.001 TRP B 200 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (28127) covalent geometry : angle 0.53912 / 0.28 (38367) hydrogen bonds : bond 0.04051 / 2.67 ( 1255) hydrogen bonds : angle 4.25067 / 2.97 ( 3456) metal coordination : bond 0.00390 / 0.17 ( 8) metal coordination : angle 1.96462 / 0.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: A 84 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8571 (mm-30) REVERT: B 16 GLN cc_start: 0.7770 (tm-30) cc_final: 0.7336 (tm-30) REVERT: C 102 HIS cc_start: 0.8499 (t-90) cc_final: 0.7930 (t-90) REVERT: C 252 LYS cc_start: 0.9419 (mtpt) cc_final: 0.9034 (ptmt) REVERT: D 65 ARG cc_start: 0.7879 (ttp-110) cc_final: 0.7652 (ppt170) REVERT: D 351 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8339 (pmt) REVERT: D 442 ASN cc_start: 0.9526 (m-40) cc_final: 0.8956 (t0) REVERT: E 44 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8627 (mt-10) REVERT: E 83 ASP cc_start: 0.9088 (p0) cc_final: 0.8877 (p0) REVERT: F 241 TRP cc_start: 0.8967 (m100) cc_final: 0.8589 (m100) outliers start: 23 outliers final: 15 residues processed: 133 average time/residue: 0.7257 time to fit residues: 110.4752 Evaluate side-chains 133 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 351 MET Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 676 MET Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 1185 GLU Chi-restraints excluded: chain D residue 1243 THR Chi-restraints excluded: chain D residue 1299 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 234 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 291 optimal weight: 1.9990 chunk 237 optimal weight: 0.7980 chunk 171 optimal weight: 0.7980 chunk 240 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 272 optimal weight: 4.9990 chunk 277 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 219 GLN C 670 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.059192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.038492 restraints weight = 294037.306| |-----------------------------------------------------------------------------| r_work (start): 0.2610 rms_B_bonded: 4.42 r_work: 0.2417 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2420 r_free = 0.2420 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2420 r_free = 0.2420 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9338 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28135 Z= 0.151 Angle : 0.550 12.902 38379 Z= 0.283 Chirality : 0.042 0.159 4316 Planarity : 0.004 0.045 4780 Dihedral : 13.936 133.829 4470 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.89 % Allowed : 20.75 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.15), residues: 3281 helix: 2.15 (0.15), residues: 1251 sheet: 0.41 (0.23), residues: 469 loop : 0.61 (0.16), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 284 TYR 0.013 0.001 TYR D 128 PHE 0.014 0.001 PHE D 982 TRP 0.011 0.001 TRP F 299 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (28127) covalent geometry : angle 0.54910 / 0.28 (38367) hydrogen bonds : bond 0.04177 / 2.76 ( 1255) hydrogen bonds : angle 4.26004 / 2.97 ( 3456) metal coordination : bond 0.00475 / 0.21 ( 8) metal coordination : angle 2.09507 / 1.05 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6562 Ramachandran restraints generated. 3281 Oldfield, 0 Emsley, 3281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.860 Fit side-chains REVERT: A 84 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8599 (mm-30) REVERT: A 229 GLN cc_start: 0.8049 (mm110) cc_final: 0.7679 (mm110) REVERT: B 16 GLN cc_start: 0.7778 (tm-30) cc_final: 0.7346 (tm-30) REVERT: C 102 HIS cc_start: 0.8539 (t-90) cc_final: 0.8010 (t-90) REVERT: C 252 LYS cc_start: 0.9441 (mtpt) cc_final: 0.9059 (ptmt) REVERT: D 351 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8337 (pmt) REVERT: D 442 ASN cc_start: 0.9512 (m-40) cc_final: 0.8939 (t0) REVERT: E 44 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8604 (mt-10) REVERT: E 87 LYS cc_start: 0.9107 (pptt) cc_final: 0.8890 (pttm) REVERT: E 88 GLU cc_start: 0.8971 (tp30) cc_final: 0.8645 (tp30) REVERT: F 241 TRP cc_start: 0.8990 (m100) cc_final: 0.8603 (m100) outliers start: 21 outliers final: 16 residues processed: 133 average time/residue: 0.7301 time to fit residues: 110.8970 Evaluate side-chains 134 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 351 MET Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain D residue 676 MET Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 1185 GLU Chi-restraints excluded: chain D residue 1243 THR Chi-restraints excluded: chain D residue 1299 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 135 optimal weight: 0.6980 chunk 213 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 185 optimal weight: 0.0040 chunk 323 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 269 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 45 optimal weight: 0.0070 chunk 99 optimal weight: 1.9990 overall best weight: 0.5010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 670 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.059691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.039094 restraints weight = 274065.175| |-----------------------------------------------------------------------------| r_work (start): 0.2630 rms_B_bonded: 4.30 r_work: 0.2439 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2443 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2443 r_free = 0.2443 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2443 r_free = 0.2443 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2443 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9324 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 28135 Z= 0.111 Angle : 0.539 13.140 38379 Z= 0.278 Chirality : 0.042 0.154 4316 Planarity : 0.004 0.052 4780 Dihedral : 13.894 133.273 4470 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.82 % Allowed : 20.79 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.15), residues: 3281 helix: 2.19 (0.15), residues: 1251 sheet: 0.43 (0.23), residues: 468 loop : 0.65 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 284 TYR 0.014 0.001 TYR D1318 PHE 0.030 0.001 PHE D 982 TRP 0.011 0.001 TRP B 200 HIS 0.005 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (28127) covalent geometry : angle 0.53814 / 0.28 (38367) hydrogen bonds : bond 0.03901 / 2.57 ( 1255) hydrogen bonds : angle 4.21202 / 2.94 ( 3456) metal coordination : bond 0.00272 / 0.12 ( 8) metal coordination : angle 1.86453 / 0.92 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8298.56 seconds wall clock time: 141 minutes 48.20 seconds (8508.20 seconds total)