Starting phenix.real_space_refine on Sun Jul 5 13:02:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fp3_50634/07_2026/9fp3_50634.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fp3_50634/07_2026/9fp3_50634.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fp3_50634/07_2026/9fp3_50634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fp3_50634/07_2026/9fp3_50634.map" model { file = "/net/cci-nas-00/data/ceres_data/9fp3_50634/07_2026/9fp3_50634.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fp3_50634/07_2026/9fp3_50634.cif" } resolution = 2.42 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= 0.015 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 73 5.49 5 Mg 4 5.21 5 S 69 5.16 5 C 17045 2.51 5 N 4861 2.21 5 O 5240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27294 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1792 Classifications: {'peptide': 228} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 213} Chain: "B" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1797 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 214} Chain: "C" Number of atoms: 8638 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1091, 8605 Classifications: {'peptide': 1091} Link IDs: {'PCIS': 1, 'PTRANS': 69, 'TRANS': 1020} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 1091, 8605 Classifications: {'peptide': 1091} Link IDs: {'PCIS': 1, 'PTRANS': 69, 'TRANS': 1020} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 8732 Chain: "D" Number of atoms: 10762 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1361, 10740 Classifications: {'peptide': 1361} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1292} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1361, 10740 Classifications: {'peptide': 1361} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1292} Chain breaks: 2 bond proxies already assigned to first conformer: 10899 Chain: "E" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 754 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain: "F" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2094 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 13, 'TRANS': 246} Chain breaks: 1 Chain: "G" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 635 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain breaks: 1 Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 731 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {' MG': 1, 'B4P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 3, ' ZN': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20081 SG CYS D1112 91.781 100.361 96.336 1.00 34.62 S ATOM 20725 SG CYS D1194 89.619 97.607 94.937 1.00 26.64 S ATOM 20781 SG CYS D1201 89.070 98.888 98.528 1.00 26.20 S ATOM 20805 SG CYS D1204 88.014 100.978 95.630 1.00 34.45 S ATOM 12716 SG CYS D 58 99.862 34.327 96.157 1.00 80.71 S ATOM 12727 SG CYS D 60 100.596 31.398 93.851 1.00 80.40 S ATOM 12838 SG CYS D 73 103.413 33.386 95.018 1.00 81.54 S ATOM 12864 SG CYS D 76 101.016 35.012 92.549 1.00 71.41 S Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AARG C 409 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 409 " occ=0.50 residue: pdb=" N AARG C 460 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 460 " 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 D 35 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 35 " occ=0.50 residue: pdb=" N AARG D 674 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 674 " occ=0.50 Time building chain proxies: 8.90, per 1000 atoms: 0.33 Number of scatterers: 27294 At special positions: 0 Unit cell: (145.88, 139.211, 159.218, 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 69 16.00 P 73 15.00 Mg 4 11.99 O 5240 8.00 N 4861 7.00 C 17045 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.8 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 D1204 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1112 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1194 " pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 73 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 58 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 76 " Number of angles added : 12 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6048 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 49 sheets defined 42.9% alpha, 18.7% beta 20 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 3.65 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 224 removed outlier: 3.714A pdb=" N TYR A 224 " --> pdb=" O GLU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'B' and resid 31 through 47 removed outlier: 3.515A pdb=" N THR B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Proline residue: B 39 - end of helix Processing helix chain 'B' and resid 74 through 84 removed outlier: 3.597A pdb=" N GLU B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) 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: 3.626A 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 'C' and resid 19 through 31 removed outlier: 4.067A pdb=" N SER C 25 " --> pdb=" O ILE C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 39 Processing helix chain 'C' and resid 43 through 52 Processing helix chain 'C' and resid 79 through 87 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 203 through 212 Processing helix chain 'C' and resid 216 through 222 Processing helix chain 'C' and resid 223 through 229 removed outlier: 3.557A pdb=" N PHE C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 4.048A 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 Processing helix chain 'C' and resid 375 through 389 removed outlier: 3.543A pdb=" N SER C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 408 Processing helix chain 'C' and resid 431 through 435 Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 525 through 529 Processing helix chain 'C' and resid 535 through 540 Processing helix chain 'C' and resid 543 through 547 removed outlier: 3.505A 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 565 Processing helix chain 'C' and resid 583 through 591 Processing helix chain 'C' and resid 683 through 687 removed outlier: 4.080A pdb=" N ASP C 686 " --> pdb=" O ASN C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 697 Processing helix chain 'C' and resid 854 through 858 Processing helix chain 'C' and resid 874 through 880 removed outlier: 4.846A pdb=" N SER C 878 " --> pdb=" O LEU C 874 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG C 879 " --> pdb=" O GLY C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 898 Processing helix chain 'C' and resid 910 through 933 removed outlier: 4.141A pdb=" N ARG C 929 " --> pdb=" O TYR C 925 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY C 933 " --> pdb=" O ARG C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 951 Processing helix chain 'C' and resid 958 through 969 Processing helix chain 'C' and resid 1000 through 1004 Processing helix chain 'C' and resid 1033 through 1044 Processing helix chain 'C' and resid 1045 through 1054 Processing helix chain 'C' and resid 1059 through 1073 Processing helix chain 'C' and resid 1082 through 1095 removed outlier: 3.617A pdb=" N ARG C1086 " --> pdb=" O PRO C1082 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C1095 " --> pdb=" O GLU C1091 " (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: 3.525A pdb=" N VAL D 85 " --> pdb=" O LYS D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.553A pdb=" N ASP D 107 " --> pdb=" O TRP D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 117 Processing helix chain 'D' and resid 119 through 128 Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 372 through 376 Processing helix chain 'D' and resid 422 through 426 Processing helix chain 'D' and resid 456 through 468 removed outlier: 3.944A pdb=" N ALA D 460 " --> pdb=" O MET D 456 " (cutoff:3.500A) removed outlier: 3.565A 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: 3.697A 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: 3.944A pdb=" N ASP D 542 " --> pdb=" O SER D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 583 Processing helix chain 'D' and resid 602 through 608 Processing helix chain 'D' and resid 612 through 618 Processing helix chain 'D' and resid 646 through 653 Processing helix chain 'D' and resid 653 through 664 Processing helix chain 'D' and resid 669 through 679 removed outlier: 4.010A 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: 3.652A 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 Processing helix chain 'D' and resid 845 through 855 Processing helix chain 'D' and resid 876 through 891 Processing helix chain 'D' and resid 892 through 900 Processing helix chain 'D' and resid 907 through 923 Processing helix chain 'D' and resid 923 through 946 removed outlier: 3.571A pdb=" N THR D 944 " --> pdb=" O THR D 940 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLY D 946 " --> pdb=" O SER D 942 " (cutoff:3.500A) Processing helix chain 'D' and resid 950 through 954 Processing helix chain 'D' and resid 958 through 980 removed outlier: 3.798A pdb=" N GLN D 962 " --> pdb=" O GLU D 958 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU D 972 " --> pdb=" O ASP D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 984 through 1015 Processing helix chain 'D' and resid 1018 through 1026 Processing helix chain 'D' and resid 1031 through 1040 Processing helix chain 'D' and resid 1066 through 1103 removed outlier: 3.778A pdb=" N HIS D1075 " --> pdb=" O PHE D1071 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY D1076 " --> pdb=" O ILE D1072 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA D1089 " --> pdb=" O ALA D1085 " (cutoff:3.500A) Processing helix chain 'D' and resid 1136 through 1145 Processing helix chain 'D' and resid 1167 through 1180 Processing helix chain 'D' and resid 1190 through 1194 Processing helix chain 'D' and resid 1202 through 1206 Processing helix chain 'D' and resid 1220 through 1234 Proline residue: D1232 - end of helix 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 1360 removed outlier: 3.506A pdb=" N VAL D1344 " --> pdb=" O GLY D1340 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL D1355 " --> pdb=" O GLU D1351 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR D1356 " --> pdb=" O ILE D1352 " (cutoff:3.500A) Processing helix chain 'D' and resid 1364 through 1376 removed outlier: 4.363A 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 Processing helix chain 'D' and resid 1442 through 1454 Processing helix chain 'D' and resid 1461 through 1468 removed outlier: 4.058A 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 1498 Processing helix chain 'E' and resid 5 through 12 Processing helix chain 'E' and resid 15 through 33 Processing helix chain 'E' and resid 59 through 71 removed outlier: 3.563A pdb=" N TRP E 63 " --> pdb=" O ASN E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 93 Processing helix chain 'F' and resid 79 through 90 removed outlier: 3.514A pdb=" N GLN 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 removed outlier: 3.563A pdb=" N ILE F 127 " --> pdb=" O ASP F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 165 removed outlier: 3.573A pdb=" N SER F 165 " --> pdb=" O GLN F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 200 removed outlier: 3.853A pdb=" N HIS F 175 " --> pdb=" O LYS F 171 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ARG F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU F 194 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL F 195 " --> pdb=" O ASN F 191 " (cutoff:3.500A) removed outlier: 3.538A 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: 3.764A pdb=" N ARG F 231 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 255 removed outlier: 3.817A pdb=" N TYR F 238 " --> pdb=" O LYS F 234 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TRP F 241 " --> pdb=" O THR F 237 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TRP F 242 " --> pdb=" O TYR F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 283 Processing helix chain 'F' and resid 287 through 296 removed outlier: 3.679A pdb=" N GLY F 296 " --> pdb=" O ALA F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 311 Processing helix chain 'F' and resid 328 through 333 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: 5.684A pdb=" N TYR A 20 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N THR A 201 " --> pdb=" O TYR A 20 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLU A 22 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ILE A 199 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL A 24 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU A 197 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N GLU A 26 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU A 195 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N THR A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 6.919A 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: 7.279A pdb=" N ASN A 139 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE A 58 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLU A 141 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL A 56 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG A 143 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 107 through 110 Processing sheet with id=AA5, first strand: chain 'A' and resid 150 through 151 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 16 removed outlier: 6.245A pdb=" N ASP B 193 " --> pdb=" O PRO B 27 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N THR B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 6.767A 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: 7.710A pdb=" N ASN B 139 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ILE B 58 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLU B 141 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL B 56 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.511A 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 removed outlier: 6.390A pdb=" N LYS B 107 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR B 131 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 109 " --> pdb=" O ILE B 129 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 150 through 151 Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AB3, first strand: chain 'C' and resid 54 through 55 removed outlier: 5.653A pdb=" N LEU C 66 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ILE C 101 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N PHE C 68 " --> pdb=" O GLN C 99 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN C 99 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU C 70 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ALA C 92 " --> pdb=" O HIS C 117 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N HIS C 117 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 6.452A 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: 6.416A 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: 6.570A pdb=" N TYR C 158 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 4.516A 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: 5.528A pdb=" N GLU C 482 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N VAL C 475 " --> pdb=" O THR C 480 " (cutoff:3.500A) removed outlier: 6.726A 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: 6.596A 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: 6.650A pdb=" N ARG C 610 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL C 606 " --> pdb=" O ARG C 610 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL C 612 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 629 through 630 Processing sheet with id=AC5, first strand: chain 'C' and resid 661 through 662 Processing sheet with id=AC6, first strand: chain 'C' and resid 971 through 972 removed outlier: 7.174A pdb=" N ILE C 688 " --> pdb=" O ALA C 850 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE C 852 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE C 690 " --> pdb=" O ILE C 852 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 689 " --> pdb=" O ILE C 870 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N VAL C 869 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU C 673 " --> pdb=" O VAL C 869 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU C 871 " --> pdb=" O LEU C 673 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA C 675 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 4.504A 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: 8.126A pdb=" N ARG C 820 " --> pdb=" O ARG C 807 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ARG C 807 " --> pdb=" O ARG C 820 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL C 822 " --> pdb=" O ARG C 805 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ARG C 805 " --> pdb=" O VAL C 822 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG C 824 " --> pdb=" O THR C 803 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N THR C 803 " --> pdb=" O ARG C 824 " (cutoff:3.500A) removed outlier: 6.544A 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: 3.550A 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: 6.810A 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: 6.300A pdb=" N CYS D 642 " --> pdb=" O VAL D 719 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL D 721 " --> pdb=" O CYS D 642 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU D 644 " --> pdb=" O VAL D 721 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1031 through 1032 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 91 through 100 removed outlier: 10.229A pdb=" N LEU D 95 " --> pdb=" O PRO D 518 " (cutoff:3.500A) removed outlier: 10.834A pdb=" N THR D 97 " --> pdb=" O ALA D 516 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ALA D 516 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 152 through 153 Processing sheet with id=AD6, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AD7, first strand: chain 'D' and resid 166 through 170 removed outlier: 6.917A pdb=" N VAL D 385 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL D 213 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU D 387 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL D 211 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLU D 389 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N PHE D 207 " --> pdb=" O ALA D 391 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE D 393 " --> pdb=" O TYR D 205 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR D 205 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL D 395 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA D 203 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 166 through 170 removed outlier: 6.917A pdb=" N VAL D 385 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL D 213 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU D 387 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL D 211 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLU D 389 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N PHE D 207 " --> pdb=" O ALA D 391 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE D 393 " --> pdb=" O TYR D 205 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR D 205 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL D 395 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA D 203 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 190 through 192 Processing sheet with id=AE1, first strand: chain 'D' and resid 352 through 353 removed outlier: 6.760A pdb=" N VAL D 377 " --> pdb=" O ILE D 367 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 398 through 402 removed outlier: 3.817A pdb=" N ASP D 413 " --> pdb=" O VAL D 435 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 527 through 529 Processing sheet with id=AE4, first strand: chain 'D' and resid 805 through 806 Processing sheet with id=AE5, first strand: chain 'D' and resid 842 through 843 Processing sheet with id=AE6, first strand: chain 'D' and resid 1106 through 1109 Processing sheet with id=AE7, first strand: chain 'D' and resid 1118 through 1121 Processing sheet with id=AE8, first strand: chain 'D' and resid 1123 through 1125 Processing sheet with id=AE9, first strand: chain 'D' and resid 1153 through 1155 Processing sheet with id=AF1, first strand: chain 'D' and resid 1300 through 1305 removed outlier: 3.701A pdb=" N LEU D1305 " --> pdb=" O LEU D1290 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU D1290 " --> pdb=" O LEU D1305 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1394 through 1396 removed outlier: 5.550A pdb=" N VAL D1381 " --> pdb=" O LYS D1418 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LYS D1418 " --> pdb=" O VAL D1381 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 1485 through 1488 Processing sheet with id=AF4, first strand: chain 'E' and resid 47 through 49 1217 hydrogen bonds defined for protein. 3360 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 7.08 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5029 1.33 - 1.45: 6743 1.45 - 1.57: 15888 1.57 - 1.69: 140 1.69 - 1.82: 127 Bond restraints: 27927 Sorted by residual: bond pdb=" O3B G2P G2201 " pdb=" PG G2P G2201 " ideal model delta sigma weight residual 1.716 1.629 0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" C3' DT H 19 " pdb=" C2' DT H 19 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.60e+01 bond pdb=" C3' DG G 19 " pdb=" C2' DG G 19 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.44e+01 bond pdb=" C3' DT H 27 " pdb=" C2' DT H 27 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.37e+01 bond pdb=" O5E B4P C1202 " pdb=" PA B4P C1202 " ideal model delta sigma weight residual 1.656 1.597 0.059 2.00e-02 2.50e+03 8.74e+00 ... (remaining 27922 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 37804 2.76 - 5.52: 265 5.52 - 8.28: 14 8.28 - 11.04: 1 11.04 - 13.80: 4 Bond angle restraints: 38088 Sorted by residual: angle pdb=" N3 DT G 3 " pdb=" C4 DT G 3 " pdb=" O4 DT G 3 " ideal model delta sigma weight residual 119.90 122.83 -2.93 6.00e-01 2.78e+00 2.39e+01 angle pdb=" N3 DT H 27 " pdb=" C4 DT H 27 " pdb=" O4 DT H 27 " ideal model delta sigma weight residual 119.90 122.72 -2.82 6.00e-01 2.78e+00 2.21e+01 angle pdb=" PB G2P G2201 " pdb=" O3B G2P G2201 " pdb=" PG G2P G2201 " ideal model delta sigma weight residual 126.39 140.19 -13.80 3.00e+00 1.11e-01 2.12e+01 angle pdb=" N3 DT G 7 " pdb=" C4 DT G 7 " pdb=" O4 DT G 7 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+00 2.04e+01 angle pdb=" O4 DT G 3 " pdb=" C4 DT G 3 " pdb=" C5 DT G 3 " ideal model delta sigma weight residual 124.90 121.80 3.10 7.00e-01 2.04e+00 1.97e+01 ... (remaining 38083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.45: 15781 29.45 - 58.90: 1115 58.90 - 88.35: 122 88.35 - 117.80: 7 117.80 - 147.25: 2 Dihedral angle restraints: 17027 sinusoidal: 7624 harmonic: 9403 Sorted by residual: dihedral pdb=" CA ASP C 268 " pdb=" C ASP C 268 " pdb=" N LEU C 269 " pdb=" CA LEU C 269 " ideal model delta harmonic sigma weight residual 180.00 156.92 23.08 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA TYR D1207 " pdb=" C TYR D1207 " pdb=" N ASP D1208 " pdb=" CA ASP D1208 " ideal model delta harmonic sigma weight residual 180.00 157.16 22.84 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA SER A 46 " pdb=" C SER A 46 " pdb=" N SER A 47 " pdb=" CA SER A 47 " ideal model delta harmonic sigma weight residual -180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 17024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3487 0.056 - 0.111: 699 0.111 - 0.167: 96 0.167 - 0.222: 3 0.222 - 0.278: 2 Chirality restraints: 4287 Sorted by residual: chirality pdb=" CG LEU E 92 " pdb=" CB LEU E 92 " pdb=" CD1 LEU E 92 " pdb=" CD2 LEU E 92 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C1' DA G 18 " pdb=" O4' DA G 18 " pdb=" C2' DA G 18 " pdb=" N9 DA G 18 " both_signs ideal model delta sigma weight residual False 2.43 2.17 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" P DA G 18 " pdb=" OP1 DA G 18 " pdb=" OP2 DA G 18 " pdb=" O5' DA G 18 " both_signs ideal model delta sigma weight residual True 2.34 -2.56 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 4284 not shown) Planarity restraints: 4744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 832 " -0.234 9.50e-02 1.11e+02 1.05e-01 8.60e+00 pdb=" NE ARG D 832 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG D 832 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG D 832 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG D 832 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1E B4P C1202 " 0.014 2.00e-02 2.50e+03 1.67e-02 7.70e+00 pdb=" C2A B4P C1202 " -0.015 2.00e-02 2.50e+03 pdb=" C4A B4P C1202 " 0.018 2.00e-02 2.50e+03 pdb=" C5A B4P C1202 " 0.012 2.00e-02 2.50e+03 pdb=" C6A B4P C1202 " -0.006 2.00e-02 2.50e+03 pdb=" C8A B4P C1202 " -0.022 2.00e-02 2.50e+03 pdb=" N1A B4P C1202 " -0.022 2.00e-02 2.50e+03 pdb=" N3A B4P C1202 " 0.007 2.00e-02 2.50e+03 pdb=" N6A B4P C1202 " 0.030 2.00e-02 2.50e+03 pdb=" N7A B4P C1202 " -0.016 2.00e-02 2.50e+03 pdb=" N9A B4P C1202 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD BARG C 460 " 0.215 9.50e-02 1.11e+02 9.71e-02 7.56e+00 pdb=" NE BARG C 460 " -0.021 2.00e-02 2.50e+03 pdb=" CZ BARG C 460 " 0.021 2.00e-02 2.50e+03 pdb=" NH1BARG C 460 " -0.010 2.00e-02 2.50e+03 pdb=" NH2BARG C 460 " -0.000 2.00e-02 2.50e+03 ... (remaining 4741 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 188 2.60 - 3.17: 21535 3.17 - 3.75: 42580 3.75 - 4.32: 60880 4.32 - 4.90: 98666 Nonbonded interactions: 223849 Sorted by model distance: nonbonded pdb=" OD1 ASP D 739 " pdb="MG MG D2003 " model vdw 2.022 2.170 nonbonded pdb=" O3E B4P C1202 " pdb="MG MG D2003 " model vdw 2.042 2.170 nonbonded pdb=" OD1 ASP D 741 " pdb="MG MG D2003 " model vdw 2.085 2.170 nonbonded pdb=" O LYS D 840 " pdb="MG MG D2005 " model vdw 2.137 2.170 nonbonded pdb=" O VAL F 265 " pdb=" ND2 ASN F 269 " model vdw 2.239 3.120 ... (remaining 223844 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 4 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 37.990 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 27935 Z= 0.214 Angle : 0.610 13.804 38100 Z= 0.362 Chirality : 0.045 0.278 4287 Planarity : 0.007 0.105 4744 Dihedral : 18.613 147.248 10979 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.29 % Allowed : 19.83 % Favored : 79.88 % 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: 0.78 (0.15), residues: 3255 helix: 1.31 (0.15), residues: 1234 sheet: 0.05 (0.23), residues: 459 loop : 0.15 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG D 360 TYR 0.024 0.001 TYR D1198 PHE 0.017 0.001 PHE C 227 TRP 0.014 0.001 TRP E 63 HIS 0.004 0.001 HIS C 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.21 (27927) covalent geometry : angle 0.60833 / 0.36 (38088) hydrogen bonds : bond 0.13537 / 8.89 ( 1258) hydrogen bonds : angle 5.74371 / 3.96 ( 3462) metal coordination : bond 0.00303 / 0.17 ( 8) metal coordination : angle 2.64712 / 1.45 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 248 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 222 MET cc_start: 0.7680 (mmm) cc_final: 0.7422 (mmt) REVERT: E 88 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7837 (mm-30) outliers start: 8 outliers final: 1 residues processed: 255 average time/residue: 0.9759 time to fit residues: 279.1490 Evaluate side-chains 154 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 338 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.2980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 920 GLN D 166 GLN D 350 HIS D1172 HIS D1323 GLN E 78 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.067869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.045911 restraints weight = 205469.309| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 3.37 r_work: 0.2697 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9198 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27935 Z= 0.168 Angle : 0.605 10.386 38100 Z= 0.323 Chirality : 0.044 0.238 4287 Planarity : 0.005 0.052 4744 Dihedral : 14.496 132.061 4439 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.73 % Allowed : 20.34 % Favored : 77.93 % 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: 1.21 (0.15), residues: 3255 helix: 1.76 (0.15), residues: 1236 sheet: 0.34 (0.24), residues: 449 loop : 0.28 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 900 TYR 0.020 0.001 TYR D1198 PHE 0.017 0.002 PHE C 684 TRP 0.028 0.002 TRP F 241 HIS 0.007 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (27927) covalent geometry : angle 0.60343 / 0.32 (38088) hydrogen bonds : bond 0.05191 / 3.44 ( 1258) hydrogen bonds : angle 4.81961 / 3.31 ( 3462) metal coordination : bond 0.00466 / 0.24 ( 8) metal coordination : angle 2.57845 / 1.43 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 176 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.7525 (ptm-80) cc_final: 0.7242 (ptm-80) REVERT: B 95 GLN cc_start: 0.8812 (mm-40) cc_final: 0.8542 (mp10) REVERT: B 141 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8295 (pt0) REVERT: B 188 GLN cc_start: 0.8032 (mm110) cc_final: 0.7649 (mm-40) REVERT: C 1 MET cc_start: 0.6957 (pp-130) cc_final: 0.6701 (ttm) REVERT: C 648 ARG cc_start: 0.8665 (mtp85) cc_final: 0.8190 (mmp80) REVERT: D 202 VAL cc_start: 0.8549 (OUTLIER) cc_final: 0.8298 (p) REVERT: D 380 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7777 (pm20) REVERT: D 832 ARG cc_start: 0.8485 (ptm-80) cc_final: 0.8237 (ptm160) REVERT: D 1407 LEU cc_start: 0.9335 (mt) cc_final: 0.9132 (mt) REVERT: E 65 MET cc_start: 0.9400 (mtt) cc_final: 0.9118 (mtt) REVERT: E 84 ARG cc_start: 0.9083 (ptm160) cc_final: 0.8784 (mtp-110) REVERT: E 87 LYS cc_start: 0.9208 (mtpm) cc_final: 0.8790 (mtmm) REVERT: E 88 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8218 (tp30) outliers start: 48 outliers final: 11 residues processed: 213 average time/residue: 0.7815 time to fit residues: 189.3596 Evaluate side-chains 173 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 380 GLU Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 709 HIS Chi-restraints excluded: chain D residue 820 GLU Chi-restraints excluded: chain D residue 1072 ILE Chi-restraints excluded: chain F residue 151 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 62 optimal weight: 0.8980 chunk 234 optimal weight: 2.9990 chunk 208 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 233 optimal weight: 0.5980 chunk 189 optimal weight: 3.9990 chunk 296 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 350 HIS D 816 HIS E 78 ASN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.067613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.045974 restraints weight = 195476.408| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.25 r_work: 0.2704 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9194 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27935 Z= 0.136 Angle : 0.551 9.521 38100 Z= 0.295 Chirality : 0.043 0.276 4287 Planarity : 0.005 0.046 4744 Dihedral : 14.289 129.683 4437 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.26 % Allowed : 20.30 % Favored : 78.44 % 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: 1.34 (0.15), residues: 3255 helix: 1.85 (0.15), residues: 1249 sheet: 0.42 (0.25), residues: 446 loop : 0.36 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 198 TYR 0.021 0.001 TYR D1198 PHE 0.014 0.001 PHE C 684 TRP 0.013 0.001 TRP F 241 HIS 0.007 0.001 HIS F 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (27927) covalent geometry : angle 0.54996 / 0.29 (38088) hydrogen bonds : bond 0.04684 / 3.08 ( 1258) hydrogen bonds : angle 4.58518 / 3.16 ( 3462) metal coordination : bond 0.00369 / 0.21 ( 8) metal coordination : angle 2.35989 / 1.31 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.7644 (ptm-80) cc_final: 0.7281 (ptm-80) REVERT: A 227 ASN cc_start: 0.8174 (OUTLIER) cc_final: 0.7870 (t160) REVERT: B 95 GLN cc_start: 0.8812 (mm-40) cc_final: 0.8514 (mp10) REVERT: B 141 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8241 (pt0) REVERT: B 188 GLN cc_start: 0.8014 (mm110) cc_final: 0.7628 (mm-40) REVERT: C 1 MET cc_start: 0.7058 (pp-130) cc_final: 0.6732 (ttm) REVERT: D 65 ARG cc_start: 0.7941 (ttp-170) cc_final: 0.7715 (ttp-170) REVERT: D 199 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9090 (pt) REVERT: D 351 MET cc_start: 0.9065 (pmm) cc_final: 0.8766 (pmm) REVERT: D 832 ARG cc_start: 0.8481 (ptm-80) cc_final: 0.8260 (ptm160) REVERT: D 1023 MET cc_start: 0.9217 (mtt) cc_final: 0.8953 (mtt) REVERT: E 65 MET cc_start: 0.9395 (mtt) cc_final: 0.9139 (mtt) REVERT: E 83 ASP cc_start: 0.9087 (p0) cc_final: 0.8747 (p0) REVERT: E 87 LYS cc_start: 0.9191 (mtpm) cc_final: 0.8935 (mtmm) REVERT: E 88 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8287 (tt0) REVERT: F 170 HIS cc_start: 0.7595 (p-80) cc_final: 0.6885 (p90) outliers start: 35 outliers final: 16 residues processed: 195 average time/residue: 0.8192 time to fit residues: 182.2135 Evaluate side-chains 178 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 709 HIS Chi-restraints excluded: chain D residue 1072 ILE Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain D residue 1185 GLU Chi-restraints excluded: chain D residue 1299 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 45 optimal weight: 0.0470 chunk 192 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 291 optimal weight: 4.9990 chunk 177 optimal weight: 8.9990 chunk 178 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 209 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 252 optimal weight: 2.9990 overall best weight: 1.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 63 HIS C 670 GLN C 999 HIS D 350 HIS E 78 ASN ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.066925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.045458 restraints weight = 159502.841| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 2.99 r_work: 0.2691 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9209 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 27935 Z= 0.169 Angle : 0.556 9.281 38100 Z= 0.297 Chirality : 0.044 0.237 4287 Planarity : 0.005 0.053 4744 Dihedral : 14.137 129.898 4437 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.62 % Allowed : 19.69 % Favored : 78.69 % 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: 1.43 (0.15), residues: 3255 helix: 1.96 (0.15), residues: 1243 sheet: 0.30 (0.24), residues: 473 loop : 0.43 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 360 TYR 0.019 0.001 TYR D1198 PHE 0.017 0.001 PHE C 684 TRP 0.022 0.002 TRP F 241 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (27927) covalent geometry : angle 0.55422 / 0.30 (38088) hydrogen bonds : bond 0.04888 / 3.23 ( 1258) hydrogen bonds : angle 4.53186 / 3.13 ( 3462) metal coordination : bond 0.00517 / 0.29 ( 8) metal coordination : angle 2.52901 / 1.39 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 166 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.7730 (ptm-80) cc_final: 0.7306 (ptm-80) REVERT: B 95 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8497 (mp10) REVERT: B 141 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8199 (pt0) REVERT: B 188 GLN cc_start: 0.8014 (mm110) cc_final: 0.7606 (mm-40) REVERT: C 1 MET cc_start: 0.7134 (pp-130) cc_final: 0.6917 (ttm) REVERT: C 252 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8804 (pttt) REVERT: C 384 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7646 (tm-30) REVERT: D 199 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9028 (pt) REVERT: D 351 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8643 (pmm) REVERT: D 832 ARG cc_start: 0.8459 (ptm-80) cc_final: 0.8223 (ptm160) REVERT: D 1023 MET cc_start: 0.9246 (mtt) cc_final: 0.8973 (mtt) REVERT: E 44 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8857 (pt0) REVERT: E 65 MET cc_start: 0.9398 (mtt) cc_final: 0.9192 (mtt) REVERT: E 83 ASP cc_start: 0.9093 (OUTLIER) cc_final: 0.8768 (p0) REVERT: E 87 LYS cc_start: 0.9174 (mtpm) cc_final: 0.8921 (mtmm) REVERT: E 88 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8145 (tp30) REVERT: F 170 HIS cc_start: 0.7600 (p-80) cc_final: 0.6927 (p90) outliers start: 45 outliers final: 15 residues processed: 200 average time/residue: 0.8454 time to fit residues: 192.3178 Evaluate side-chains 177 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 351 MET Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 820 GLU Chi-restraints excluded: chain D residue 1072 ILE Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain D residue 1185 GLU Chi-restraints excluded: chain D residue 1299 PHE Chi-restraints excluded: chain E residue 83 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 47 optimal weight: 0.6980 chunk 282 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 316 optimal weight: 4.9990 chunk 309 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 294 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 128 HIS C 434 HIS C 670 GLN D 350 HIS E 78 ASN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.067171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.045904 restraints weight = 184352.913| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.21 r_work: 0.2697 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9202 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27935 Z= 0.127 Angle : 0.528 10.190 38100 Z= 0.281 Chirality : 0.043 0.259 4287 Planarity : 0.004 0.061 4744 Dihedral : 13.989 129.001 4437 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.51 % Allowed : 19.55 % Favored : 78.94 % 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: 1.51 (0.15), residues: 3255 helix: 2.00 (0.15), residues: 1246 sheet: 0.41 (0.24), residues: 459 loop : 0.48 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1310 TYR 0.019 0.001 TYR D1198 PHE 0.013 0.001 PHE D 982 TRP 0.018 0.001 TRP F 241 HIS 0.006 0.001 HIS F 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (27927) covalent geometry : angle 0.52600 / 0.28 (38088) hydrogen bonds : bond 0.04379 / 2.88 ( 1258) hydrogen bonds : angle 4.41068 / 3.05 ( 3462) metal coordination : bond 0.00368 / 0.21 ( 8) metal coordination : angle 2.32191 / 1.29 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 164 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: A 185 ARG cc_start: 0.7827 (ptm-80) cc_final: 0.7488 (ptm-80) REVERT: A 227 ASN cc_start: 0.8140 (OUTLIER) cc_final: 0.7886 (t160) REVERT: B 95 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8501 (mp10) REVERT: B 141 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8237 (pt0) REVERT: B 188 GLN cc_start: 0.8008 (mm110) cc_final: 0.7617 (mm-40) REVERT: C 1 MET cc_start: 0.7275 (pp-130) cc_final: 0.7039 (ttm) REVERT: C 252 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8838 (pttt) REVERT: C 648 ARG cc_start: 0.8762 (mtp85) cc_final: 0.8205 (mmp80) REVERT: C 762 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8243 (ptpp) REVERT: D 199 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9040 (pt) REVERT: D 351 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8735 (pmm) REVERT: D 436 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7596 (pp20) REVERT: D 832 ARG cc_start: 0.8481 (ptm-80) cc_final: 0.8255 (ptm160) REVERT: D 1023 MET cc_start: 0.9234 (mtt) cc_final: 0.8968 (mtt) REVERT: D 1315 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7899 (m-30) REVERT: E 44 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8867 (pt0) REVERT: E 83 ASP cc_start: 0.9089 (OUTLIER) cc_final: 0.8868 (p0) REVERT: E 87 LYS cc_start: 0.9171 (mtpm) cc_final: 0.8881 (mtmm) REVERT: E 88 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8086 (tp30) REVERT: F 170 HIS cc_start: 0.7525 (p-80) cc_final: 0.6797 (p90) outliers start: 42 outliers final: 15 residues processed: 197 average time/residue: 0.7748 time to fit residues: 174.2776 Evaluate side-chains 179 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain C residue 762 LYS Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 351 MET Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 1072 ILE Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain D residue 1185 GLU Chi-restraints excluded: chain D residue 1299 PHE Chi-restraints excluded: chain D residue 1315 ASP Chi-restraints excluded: chain E residue 83 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 257 optimal weight: 2.9990 chunk 208 optimal weight: 4.9990 chunk 170 optimal weight: 0.0770 chunk 138 optimal weight: 2.9990 chunk 302 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 272 optimal weight: 2.9990 chunk 177 optimal weight: 10.0000 chunk 174 optimal weight: 4.9990 chunk 236 optimal weight: 2.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 670 GLN D 350 HIS E 78 ASN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.065769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.044423 restraints weight = 159999.391| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.99 r_work: 0.2660 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9231 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 27935 Z= 0.226 Angle : 0.585 8.749 38100 Z= 0.311 Chirality : 0.045 0.265 4287 Planarity : 0.005 0.051 4744 Dihedral : 14.035 129.385 4437 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.73 % Allowed : 19.58 % Favored : 78.69 % 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: 1.43 (0.15), residues: 3255 helix: 1.90 (0.15), residues: 1251 sheet: 0.37 (0.23), residues: 475 loop : 0.46 (0.16), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D1310 TYR 0.018 0.001 TYR D1198 PHE 0.018 0.002 PHE C 896 TRP 0.031 0.002 TRP F 241 HIS 0.007 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.23 (27927) covalent geometry : angle 0.58258 / 0.31 (38088) hydrogen bonds : bond 0.05346 / 3.54 ( 1258) hydrogen bonds : angle 4.55717 / 3.16 ( 3462) metal coordination : bond 0.00746 / 0.43 ( 8) metal coordination : angle 2.88168 / 1.58 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 154 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: A 185 ARG cc_start: 0.7847 (ptm-80) cc_final: 0.7419 (ptm-80) REVERT: B 95 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8495 (mp10) REVERT: B 107 LYS cc_start: 0.8269 (ttpt) cc_final: 0.7791 (pttt) REVERT: B 110 LYS cc_start: 0.8814 (mmmm) cc_final: 0.8564 (mptm) REVERT: C 1 MET cc_start: 0.7300 (pp-130) cc_final: 0.7078 (ttm) REVERT: C 252 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8793 (pttt) REVERT: C 648 ARG cc_start: 0.8767 (mtp85) cc_final: 0.8166 (mmp80) REVERT: C 762 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8286 (ptpp) REVERT: D 199 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9033 (pt) REVERT: D 436 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7641 (pp20) REVERT: D 832 ARG cc_start: 0.8471 (ptm-80) cc_final: 0.8271 (ptm160) REVERT: D 1023 MET cc_start: 0.9267 (mtt) cc_final: 0.8973 (mtt) REVERT: D 1315 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7805 (m-30) REVERT: D 1317 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7805 (m-30) REVERT: E 44 GLU cc_start: 0.9168 (mt-10) cc_final: 0.8862 (pt0) REVERT: E 83 ASP cc_start: 0.9140 (OUTLIER) cc_final: 0.8923 (p0) REVERT: E 87 LYS cc_start: 0.9182 (mtpm) cc_final: 0.8972 (mtmm) REVERT: F 170 HIS cc_start: 0.7633 (p-80) cc_final: 0.6959 (p90) outliers start: 48 outliers final: 20 residues processed: 193 average time/residue: 0.8389 time to fit residues: 184.4656 Evaluate side-chains 173 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain C residue 762 LYS Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 1072 ILE Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain D residue 1185 GLU Chi-restraints excluded: chain D residue 1299 PHE Chi-restraints excluded: chain D residue 1315 ASP Chi-restraints excluded: chain D residue 1317 ASP Chi-restraints excluded: chain D residue 1408 ILE Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain F residue 338 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 222 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 279 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 ASN A 229 GLN C 670 GLN D 350 HIS E 78 ASN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.066416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.044920 restraints weight = 166947.141| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.03 r_work: 0.2684 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9211 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27935 Z= 0.148 Angle : 0.547 9.446 38100 Z= 0.291 Chirality : 0.043 0.322 4287 Planarity : 0.004 0.055 4744 Dihedral : 13.936 128.370 4437 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.44 % Allowed : 19.91 % Favored : 78.65 % 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: 1.51 (0.15), residues: 3255 helix: 2.00 (0.15), residues: 1244 sheet: 0.37 (0.24), residues: 471 loop : 0.50 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D1310 TYR 0.019 0.001 TYR D1198 PHE 0.015 0.001 PHE D 982 TRP 0.026 0.001 TRP F 241 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (27927) covalent geometry : angle 0.54518 / 0.29 (38088) hydrogen bonds : bond 0.04669 / 3.07 ( 1258) hydrogen bonds : angle 4.43855 / 3.08 ( 3462) metal coordination : bond 0.00472 / 0.28 ( 8) metal coordination : angle 2.58005 / 1.42 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: A 185 ARG cc_start: 0.7844 (ptm-80) cc_final: 0.7452 (ptm-80) REVERT: B 95 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8502 (mp10) REVERT: B 107 LYS cc_start: 0.8312 (ttpt) cc_final: 0.7914 (ptpt) REVERT: B 110 LYS cc_start: 0.8857 (mmmm) cc_final: 0.8612 (mptm) REVERT: C 1 MET cc_start: 0.7318 (pp-130) cc_final: 0.7075 (ttm) REVERT: C 252 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8823 (pttt) REVERT: C 648 ARG cc_start: 0.8749 (mtp85) cc_final: 0.8186 (mmp80) REVERT: C 762 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8284 (ptpp) REVERT: D 199 LEU cc_start: 0.9244 (pt) cc_final: 0.9011 (pt) REVERT: D 436 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7612 (pp20) REVERT: D 1023 MET cc_start: 0.9259 (mtt) cc_final: 0.8986 (mtt) REVERT: D 1315 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7857 (m-30) REVERT: E 44 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8889 (pt0) REVERT: E 84 ARG cc_start: 0.9036 (mtp-110) cc_final: 0.8526 (mtp180) REVERT: F 170 HIS cc_start: 0.7595 (p-80) cc_final: 0.6710 (p90) outliers start: 40 outliers final: 17 residues processed: 188 average time/residue: 0.8187 time to fit residues: 175.8590 Evaluate side-chains 168 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain C residue 762 LYS Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 1072 ILE Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain D residue 1185 GLU Chi-restraints excluded: chain D residue 1299 PHE Chi-restraints excluded: chain D residue 1315 ASP Chi-restraints excluded: chain D residue 1408 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 20 optimal weight: 0.8980 chunk 328 optimal weight: 10.0000 chunk 181 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 chunk 200 optimal weight: 0.6980 chunk 320 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 169 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 ASN C 670 GLN D 350 HIS E 78 ASN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.066924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.045574 restraints weight = 157201.727| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.00 r_work: 0.2701 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9200 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27935 Z= 0.127 Angle : 0.542 10.955 38100 Z= 0.287 Chirality : 0.043 0.252 4287 Planarity : 0.004 0.057 4744 Dihedral : 13.841 127.882 4437 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.86 % Allowed : 20.37 % Favored : 78.76 % 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: 1.58 (0.15), residues: 3255 helix: 2.06 (0.15), residues: 1244 sheet: 0.37 (0.23), residues: 477 loop : 0.55 (0.16), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D1310 TYR 0.018 0.001 TYR D1198 PHE 0.012 0.001 PHE C 684 TRP 0.025 0.001 TRP F 241 HIS 0.008 0.001 HIS F 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (27927) covalent geometry : angle 0.54002 / 0.29 (38088) hydrogen bonds : bond 0.04352 / 2.86 ( 1258) hydrogen bonds : angle 4.36085 / 3.02 ( 3462) metal coordination : bond 0.00362 / 0.21 ( 8) metal coordination : angle 2.45213 / 1.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: A 185 ARG cc_start: 0.7957 (ptm-80) cc_final: 0.7562 (ptm-80) REVERT: B 95 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8492 (mp10) REVERT: B 107 LYS cc_start: 0.8354 (ttpt) cc_final: 0.8013 (ptpt) REVERT: B 110 LYS cc_start: 0.8865 (mmmm) cc_final: 0.8633 (mptm) REVERT: C 1 MET cc_start: 0.7302 (pp-130) cc_final: 0.7037 (ttm) REVERT: C 252 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8838 (pttt) REVERT: C 762 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8317 (ptpp) REVERT: D 199 LEU cc_start: 0.9233 (pt) cc_final: 0.9010 (pt) REVERT: D 1023 MET cc_start: 0.9238 (mtt) cc_final: 0.8967 (mtt) REVERT: D 1315 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7829 (m-30) REVERT: E 44 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8891 (pt0) REVERT: E 84 ARG cc_start: 0.9069 (mtp-110) cc_final: 0.8485 (mtp180) REVERT: F 170 HIS cc_start: 0.7609 (p-80) cc_final: 0.6836 (p90) outliers start: 24 outliers final: 15 residues processed: 176 average time/residue: 0.8028 time to fit residues: 161.4444 Evaluate side-chains 167 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain C residue 762 LYS Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 1072 ILE Chi-restraints excluded: chain D residue 1185 GLU Chi-restraints excluded: chain D residue 1299 PHE Chi-restraints excluded: chain D residue 1315 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 15 optimal weight: 0.5980 chunk 144 optimal weight: 2.9990 chunk 228 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 296 optimal weight: 3.9990 chunk 264 optimal weight: 5.9990 chunk 253 optimal weight: 0.5980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 670 GLN D 350 HIS E 78 ASN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.065964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.044208 restraints weight = 183459.656| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 3.28 r_work: 0.2651 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9238 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 27935 Z= 0.212 Angle : 0.589 9.413 38100 Z= 0.313 Chirality : 0.045 0.279 4287 Planarity : 0.005 0.098 4744 Dihedral : 13.915 128.524 4437 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.72 % Allowed : 20.48 % Favored : 78.80 % 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: 3255 helix: 1.96 (0.15), residues: 1245 sheet: 0.32 (0.23), residues: 480 loop : 0.50 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG D1310 TYR 0.018 0.001 TYR D1198 PHE 0.020 0.002 PHE D 982 TRP 0.036 0.002 TRP F 241 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 (27927) covalent geometry : angle 0.58718 / 0.31 (38088) hydrogen bonds : bond 0.05175 / 3.42 ( 1258) hydrogen bonds : angle 4.51549 / 3.13 ( 3462) metal coordination : bond 0.00696 / 0.40 ( 8) metal coordination : angle 2.85234 / 1.56 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: A 185 ARG cc_start: 0.8013 (ptm-80) cc_final: 0.7742 (ptm-80) REVERT: B 95 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8512 (mp10) REVERT: B 107 LYS cc_start: 0.8323 (ttpt) cc_final: 0.7986 (ptpt) REVERT: B 110 LYS cc_start: 0.8878 (mmmm) cc_final: 0.8662 (mptm) REVERT: C 1 MET cc_start: 0.7377 (pp-130) cc_final: 0.7068 (ttm) REVERT: C 252 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8864 (pttt) REVERT: C 762 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8270 (ptpp) REVERT: D 199 LEU cc_start: 0.9220 (pt) cc_final: 0.9000 (pt) REVERT: D 1023 MET cc_start: 0.9286 (mtt) cc_final: 0.8991 (mtt) REVERT: E 44 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8914 (pt0) REVERT: E 84 ARG cc_start: 0.9140 (mtp-110) cc_final: 0.8576 (mtp180) REVERT: F 170 HIS cc_start: 0.7620 (p-80) cc_final: 0.6818 (p90) outliers start: 20 outliers final: 15 residues processed: 168 average time/residue: 0.8703 time to fit residues: 166.8392 Evaluate side-chains 162 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain C residue 762 LYS Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 1072 ILE Chi-restraints excluded: chain D residue 1185 GLU 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 113 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 208 optimal weight: 0.9980 chunk 173 optimal weight: 8.9990 chunk 321 optimal weight: 0.9980 chunk 152 optimal weight: 0.0470 chunk 254 optimal weight: 2.9990 chunk 141 optimal weight: 0.5980 chunk 245 optimal weight: 1.9990 chunk 322 optimal weight: 5.9990 chunk 307 optimal weight: 7.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 670 GLN D 350 HIS E 78 ASN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.066956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.045442 restraints weight = 179384.766| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.25 r_work: 0.2688 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9209 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27935 Z= 0.123 Angle : 0.554 9.509 38100 Z= 0.293 Chirality : 0.043 0.268 4287 Planarity : 0.005 0.081 4744 Dihedral : 13.804 127.575 4437 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.76 % Allowed : 20.30 % Favored : 78.94 % 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: 1.59 (0.15), residues: 3255 helix: 2.06 (0.15), residues: 1245 sheet: 0.40 (0.23), residues: 474 loop : 0.55 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 284 TYR 0.019 0.001 TYR D1198 PHE 0.011 0.001 PHE C 684 TRP 0.028 0.001 TRP F 241 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (27927) covalent geometry : angle 0.55198 / 0.29 (38088) hydrogen bonds : bond 0.04281 / 2.81 ( 1258) hydrogen bonds : angle 4.36050 / 3.02 ( 3462) metal coordination : bond 0.00348 / 0.21 ( 8) metal coordination : angle 2.42081 / 1.34 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 1.165 Fit side-chains revert: symmetry clash REVERT: A 185 ARG cc_start: 0.7993 (ptm-80) cc_final: 0.7615 (ptm-80) REVERT: B 95 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8502 (mp10) REVERT: B 107 LYS cc_start: 0.8372 (ttpt) cc_final: 0.8031 (ptpt) REVERT: C 1 MET cc_start: 0.7358 (pp-130) cc_final: 0.7068 (ttm) REVERT: C 252 LYS cc_start: 0.9074 (ptpt) cc_final: 0.8856 (pttt) REVERT: C 762 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8322 (ptpp) REVERT: D 199 LEU cc_start: 0.9205 (pt) cc_final: 0.8998 (pt) REVERT: D 1023 MET cc_start: 0.9238 (mtt) cc_final: 0.8975 (mtt) REVERT: E 44 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8927 (pt0) REVERT: E 84 ARG cc_start: 0.9119 (mtp-110) cc_final: 0.8761 (mmm160) REVERT: F 170 HIS cc_start: 0.7578 (p-80) cc_final: 0.6810 (p90) outliers start: 21 outliers final: 17 residues processed: 170 average time/residue: 0.8397 time to fit residues: 163.9621 Evaluate side-chains 163 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain C residue 762 LYS Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 1072 ILE Chi-restraints excluded: chain D residue 1185 GLU Chi-restraints excluded: chain D residue 1299 PHE Chi-restraints excluded: chain D residue 1408 ILE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 338 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 148 optimal weight: 3.9990 chunk 325 optimal weight: 10.0000 chunk 239 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 217 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 266 optimal weight: 0.9990 chunk 145 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 258 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 670 GLN D 350 HIS E 78 ASN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.066261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.044844 restraints weight = 163108.917| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.09 r_work: 0.2676 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9219 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27935 Z= 0.168 Angle : 0.569 9.512 38100 Z= 0.301 Chirality : 0.044 0.245 4287 Planarity : 0.005 0.092 4744 Dihedral : 13.820 128.022 4437 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.68 % Allowed : 20.55 % Favored : 78.76 % 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: 3255 helix: 2.04 (0.15), residues: 1246 sheet: 0.41 (0.23), residues: 476 loop : 0.54 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D1310 TYR 0.017 0.001 TYR D1198 PHE 0.020 0.001 PHE D 982 TRP 0.033 0.002 TRP F 241 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (27927) covalent geometry : angle 0.56676 / 0.30 (38088) hydrogen bonds : bond 0.04707 / 3.11 ( 1258) hydrogen bonds : angle 4.42159 / 3.07 ( 3462) metal coordination : bond 0.00534 / 0.31 ( 8) metal coordination : angle 2.63432 / 1.45 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11716.84 seconds wall clock time: 199 minutes 45.02 seconds (11985.02 seconds total)