Starting phenix.real_space_refine on Fri Feb 6 20:20:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fp3_50634/02_2026/9fp3_50634.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fp3_50634/02_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_50634/02_2026/9fp3_50634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fp3_50634/02_2026/9fp3_50634.map" model { file = "/net/cci-nas-00/data/ceres_data/9fp3_50634/02_2026/9fp3_50634.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fp3_50634/02_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 9.14, 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: 2.21 Conformation dependent library (CDL) restraints added in 1.6 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: 3.42 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: 6.68 Time building geometry restraints manager: 2.94 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=" 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 bond pdb=" O5F B4P C1202 " pdb=" PD B4P C1202 " ideal model delta sigma weight residual 1.650 1.596 0.054 2.00e-02 2.50e+03 7.25e+00 bond pdb=" C LEU D 127 " pdb=" N TYR D 128 " ideal model delta sigma weight residual 1.333 1.301 0.032 1.27e-02 6.20e+03 6.44e+00 bond pdb=" O3G B4P C1202 " pdb=" PG B4P C1202 " ideal model delta sigma weight residual 1.650 1.599 0.051 2.00e-02 2.50e+03 6.42e+00 ... (remaining 27922 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 37827 2.76 - 5.52: 242 5.52 - 8.28: 14 8.28 - 11.04: 1 11.04 - 13.80: 4 Bond angle restraints: 38088 Sorted by residual: 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=" PA G2P G2201 " pdb=" C3A G2P G2201 " pdb=" PB G2P G2201 " ideal model delta sigma weight residual 120.83 133.70 -12.87 3.00e+00 1.11e-01 1.84e+01 angle pdb=" PD B4P C1202 " pdb=" O3G B4P C1202 " pdb=" PG B4P C1202 " ideal model delta sigma weight residual 122.47 135.15 -12.68 3.00e+00 1.11e-01 1.79e+01 angle pdb=" N ASN D 737 " pdb=" CA ASN D 737 " pdb=" C ASN D 737 " ideal model delta sigma weight residual 111.74 106.21 5.53 1.35e+00 5.49e-01 1.68e+01 angle pdb=" C GLN D 66 " pdb=" N ARG D 67 " pdb=" CA ARG D 67 " ideal model delta sigma weight residual 126.45 133.61 -7.16 1.77e+00 3.19e-01 1.64e+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: 3535 0.056 - 0.111: 656 0.111 - 0.167: 91 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 2.42 2.17 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB ILE F 88 " pdb=" CA ILE F 88 " pdb=" CG1 ILE F 88 " pdb=" CG2 ILE F 88 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.20e+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: 9.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 34.300 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 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= 0.140 Angle : 0.591 13.804 38100 Z= 0.310 Chirality : 0.044 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 covalent geometry : bond 0.00291 (27927) covalent geometry : angle 0.58874 (38088) hydrogen bonds : bond 0.13537 ( 1258) hydrogen bonds : angle 5.74371 ( 3462) metal coordination : bond 0.00303 ( 8) metal coordination : angle 2.64712 ( 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 : 1.136 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: 0.9212 time to fit residues: 263.5554 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 : 1.037 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: C 920 GLN D 350 HIS D 816 HIS D1323 GLN E 78 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.067660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.045747 restraints weight = 205476.315| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 3.47 r_work: 0.2689 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- 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 = 0.50 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 = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27935 Z= 0.167 Angle : 0.587 9.513 38100 Z= 0.311 Chirality : 0.044 0.216 4287 Planarity : 0.005 0.055 4744 Dihedral : 14.287 127.611 4439 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.73 % Allowed : 20.16 % Favored : 78.11 % 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: 1.23 (0.15), residues: 3255 helix: 1.77 (0.15), residues: 1242 sheet: 0.35 (0.24), residues: 446 loop : 0.29 (0.15), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D1406 TYR 0.020 0.001 TYR D1198 PHE 0.016 0.001 PHE C 684 TRP 0.022 0.002 TRP F 241 HIS 0.007 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00389 (27927) covalent geometry : angle 0.58506 (38088) hydrogen bonds : bond 0.05036 ( 1258) hydrogen bonds : angle 4.73690 ( 3462) metal coordination : bond 0.00494 ( 8) metal coordination : angle 2.59016 ( 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 : 0.870 Fit side-chains revert: symmetry clash REVERT: A 185 ARG cc_start: 0.7533 (ptm-80) cc_final: 0.7247 (ptm-80) REVERT: B 95 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8531 (mp10) REVERT: B 141 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8292 (pt0) REVERT: B 188 GLN cc_start: 0.8062 (mm110) cc_final: 0.7669 (mm-40) REVERT: C 1 MET cc_start: 0.7024 (pp-130) cc_final: 0.6719 (ttm) REVERT: C 648 ARG cc_start: 0.8667 (mtp85) cc_final: 0.8204 (mmp80) REVERT: D 832 ARG cc_start: 0.8499 (ptm-80) cc_final: 0.8243 (ptm160) REVERT: D 979 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8412 (tm-30) REVERT: D 1239 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6711 (ttm-80) REVERT: D 1407 LEU cc_start: 0.9323 (mt) cc_final: 0.9122 (mt) REVERT: E 65 MET cc_start: 0.9416 (mtt) cc_final: 0.9134 (mtt) REVERT: E 83 ASP cc_start: 0.9118 (p0) cc_final: 0.8754 (p0) REVERT: E 87 LYS cc_start: 0.9212 (mtpm) cc_final: 0.8856 (mtmm) REVERT: E 88 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8146 (tp30) outliers start: 48 outliers final: 8 residues processed: 213 average time/residue: 0.8393 time to fit residues: 202.4949 Evaluate side-chains 170 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 1239 ARG 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: 3.9990 chunk 234 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 233 optimal weight: 0.6980 chunk 189 optimal weight: 3.9990 chunk 296 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 670 GLN C 999 HIS D 350 HIS D1172 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 = 0.3464 r_free = 0.3464 target = 0.065923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.044202 restraints weight = 192324.878| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 3.29 r_work: 0.2649 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 27935 Z= 0.228 Angle : 0.594 8.977 38100 Z= 0.317 Chirality : 0.045 0.188 4287 Planarity : 0.005 0.050 4744 Dihedral : 14.099 128.195 4437 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.84 % Allowed : 19.91 % Favored : 78.26 % 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: 1.23 (0.15), residues: 3255 helix: 1.73 (0.15), residues: 1252 sheet: 0.22 (0.24), residues: 474 loop : 0.36 (0.16), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 198 TYR 0.022 0.002 TYR D1198 PHE 0.016 0.002 PHE C 896 TRP 0.022 0.002 TRP F 241 HIS 0.007 0.001 HIS F 170 Details of bonding type rmsd covalent geometry : bond 0.00539 (27927) covalent geometry : angle 0.59225 (38088) hydrogen bonds : bond 0.05528 ( 1258) hydrogen bonds : angle 4.67412 ( 3462) metal coordination : bond 0.00712 ( 8) metal coordination : angle 2.96260 ( 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 208 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 157 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: A 185 ARG cc_start: 0.7769 (ptm-80) cc_final: 0.7286 (ptm-80) REVERT: B 95 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8507 (mp10) REVERT: B 110 LYS cc_start: 0.8825 (mmmm) cc_final: 0.8548 (mptm) REVERT: B 141 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8208 (pt0) REVERT: C 384 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7731 (tm-30) REVERT: D 351 MET cc_start: 0.9114 (pmm) cc_final: 0.8735 (pmm) REVERT: D 832 ARG cc_start: 0.8457 (ptm-80) cc_final: 0.8216 (ptm160) REVERT: D 1317 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.7790 (m-30) REVERT: E 44 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8869 (pt0) REVERT: E 65 MET cc_start: 0.9439 (mtt) cc_final: 0.9228 (mtt) REVERT: E 83 ASP cc_start: 0.9158 (OUTLIER) cc_final: 0.8729 (p0) REVERT: E 87 LYS cc_start: 0.9198 (mtpm) cc_final: 0.8863 (mtmm) REVERT: E 88 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8108 (tp30) REVERT: F 170 HIS cc_start: 0.7733 (p-80) cc_final: 0.7085 (p90) outliers start: 51 outliers final: 17 residues processed: 195 average time/residue: 0.8082 time to fit residues: 178.1099 Evaluate side-chains 165 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain C residue 101 ILE 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 211 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 372 ASP 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 1286 THR Chi-restraints excluded: chain D residue 1299 PHE Chi-restraints excluded: chain D residue 1317 ASP Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 83 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 45 optimal weight: 2.9990 chunk 192 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 291 optimal weight: 1.9990 chunk 177 optimal weight: 8.9990 chunk 178 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 209 optimal weight: 1.9990 chunk 117 optimal weight: 0.3980 chunk 252 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.066325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.045017 restraints weight = 157849.873| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.93 r_work: 0.2689 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 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 = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 27935 Z= 0.158 Angle : 0.544 9.916 38100 Z= 0.289 Chirality : 0.043 0.153 4287 Planarity : 0.004 0.046 4744 Dihedral : 13.924 126.623 4437 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.69 % Allowed : 19.91 % Favored : 78.40 % 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: 1.44 (0.15), residues: 3255 helix: 1.97 (0.15), residues: 1236 sheet: 0.28 (0.24), residues: 472 loop : 0.46 (0.16), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D1310 TYR 0.019 0.001 TYR D1198 PHE 0.013 0.001 PHE C 684 TRP 0.020 0.001 TRP F 241 HIS 0.006 0.001 HIS C 102 Details of bonding type rmsd covalent geometry : bond 0.00369 (27927) covalent geometry : angle 0.54251 (38088) hydrogen bonds : bond 0.04668 ( 1258) hydrogen bonds : angle 4.48936 ( 3462) metal coordination : bond 0.00474 ( 8) metal coordination : angle 2.59005 ( 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 208 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.7824 (ptm-80) cc_final: 0.7419 (ptm-80) REVERT: B 95 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8474 (mp10) REVERT: B 110 LYS cc_start: 0.8896 (mmmm) cc_final: 0.8656 (mptm) REVERT: B 188 GLN cc_start: 0.7885 (mm110) cc_final: 0.7494 (mm-40) REVERT: C 252 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8819 (pttt) REVERT: C 648 ARG cc_start: 0.8724 (mtp85) cc_final: 0.8167 (mmp80) REVERT: C 858 MET cc_start: 0.9105 (mmm) cc_final: 0.8824 (mmm) REVERT: D 1023 MET cc_start: 0.9240 (mtt) cc_final: 0.8964 (mtt) REVERT: D 1315 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7845 (m-30) REVERT: E 44 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8846 (pt0) REVERT: E 65 MET cc_start: 0.9381 (mtt) cc_final: 0.9180 (mtt) REVERT: E 83 ASP cc_start: 0.9123 (OUTLIER) cc_final: 0.8795 (p0) REVERT: E 87 LYS cc_start: 0.9155 (mtpm) cc_final: 0.8814 (mtmm) REVERT: E 88 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8179 (tp30) REVERT: F 170 HIS cc_start: 0.7667 (p-80) cc_final: 0.7004 (p90) outliers start: 47 outliers final: 20 residues processed: 196 average time/residue: 0.9040 time to fit residues: 202.0204 Evaluate side-chains 170 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 182 GLU 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 848 VAL Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 1105 LYS 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 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 Chi-restraints excluded: chain F residue 127 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 47 optimal weight: 3.9990 chunk 282 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 316 optimal weight: 4.9990 chunk 309 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 294 optimal weight: 0.0980 chunk 0 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.066284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.044728 restraints weight = 183356.042| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.26 r_work: 0.2666 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 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 = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27935 Z= 0.158 Angle : 0.542 9.234 38100 Z= 0.287 Chirality : 0.043 0.163 4287 Planarity : 0.005 0.058 4744 Dihedral : 13.829 126.315 4437 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.62 % Allowed : 19.87 % Favored : 78.51 % 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: 1.50 (0.15), residues: 3255 helix: 2.02 (0.15), residues: 1237 sheet: 0.29 (0.23), residues: 485 loop : 0.51 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D1310 TYR 0.020 0.001 TYR D1198 PHE 0.016 0.001 PHE D 982 TRP 0.022 0.001 TRP F 241 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00371 (27927) covalent geometry : angle 0.54003 (38088) hydrogen bonds : bond 0.04669 ( 1258) hydrogen bonds : angle 4.45376 ( 3462) metal coordination : bond 0.00482 ( 8) metal coordination : angle 2.66009 ( 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 200 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 155 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 185 ARG cc_start: 0.7958 (ptm-80) cc_final: 0.7523 (ptm-80) REVERT: A 227 ASN cc_start: 0.8265 (OUTLIER) cc_final: 0.8028 (t0) REVERT: B 95 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8485 (mp10) REVERT: B 107 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7946 (ptpt) REVERT: B 110 LYS cc_start: 0.8862 (mmmm) cc_final: 0.8616 (mptm) REVERT: B 188 GLN cc_start: 0.7881 (mm110) cc_final: 0.7509 (mm-40) REVERT: C 252 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8856 (pttt) REVERT: D 436 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7501 (pp20) REVERT: D 1023 MET cc_start: 0.9264 (mtt) cc_final: 0.8990 (mtt) REVERT: D 1239 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6683 (ttm-80) REVERT: E 44 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8887 (pt0) REVERT: E 83 ASP cc_start: 0.9162 (OUTLIER) cc_final: 0.8900 (p0) REVERT: E 84 ARG cc_start: 0.9046 (ptm160) cc_final: 0.8679 (ptm-80) REVERT: E 87 LYS cc_start: 0.9181 (mtpm) cc_final: 0.8922 (mtmm) REVERT: E 91 ARG cc_start: 0.9084 (tmm-80) cc_final: 0.8864 (ttp80) REVERT: F 170 HIS cc_start: 0.7665 (p-80) cc_final: 0.7014 (p90) outliers start: 45 outliers final: 19 residues processed: 191 average time/residue: 0.8615 time to fit residues: 187.7071 Evaluate side-chains 169 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 107 LYS 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 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 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 1239 ARG Chi-restraints excluded: chain D residue 1299 PHE 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 127 ILE 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: 0.8980 chunk 170 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 302 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 272 optimal weight: 2.9990 chunk 177 optimal weight: 8.9990 chunk 174 optimal weight: 4.9990 chunk 236 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.065750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.044213 restraints weight = 160271.517| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.99 r_work: 0.2664 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 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 = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 27935 Z= 0.205 Angle : 0.570 9.678 38100 Z= 0.301 Chirality : 0.044 0.178 4287 Planarity : 0.005 0.054 4744 Dihedral : 13.843 126.724 4437 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.87 % Allowed : 19.65 % Favored : 78.47 % 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: 1.45 (0.15), residues: 3255 helix: 1.97 (0.15), residues: 1241 sheet: 0.29 (0.23), residues: 477 loop : 0.47 (0.16), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D1310 TYR 0.020 0.001 TYR D1198 PHE 0.015 0.002 PHE C 896 TRP 0.027 0.002 TRP F 241 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00485 (27927) covalent geometry : angle 0.56758 (38088) hydrogen bonds : bond 0.05092 ( 1258) hydrogen bonds : angle 4.51576 ( 3462) metal coordination : bond 0.00639 ( 8) metal coordination : angle 2.84121 ( 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 206 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 154 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.7990 (ptm-80) cc_final: 0.7746 (ptm-80) REVERT: A 227 ASN cc_start: 0.8425 (OUTLIER) cc_final: 0.8091 (t0) REVERT: B 95 GLN cc_start: 0.8745 (mm-40) cc_final: 0.8475 (mp10) REVERT: B 107 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7990 (ptpt) REVERT: B 110 LYS cc_start: 0.8897 (mmmm) cc_final: 0.8661 (mptm) REVERT: C 252 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8854 (pttt) REVERT: C 648 ARG cc_start: 0.8647 (mtp85) cc_final: 0.8090 (mmp80) REVERT: D 1023 MET cc_start: 0.9270 (mtt) cc_final: 0.8987 (mtt) REVERT: E 44 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8843 (pt0) outliers start: 52 outliers final: 22 residues processed: 196 average time/residue: 0.8281 time to fit residues: 185.7993 Evaluate side-chains 172 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain B residue 107 LYS 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 848 VAL Chi-restraints excluded: chain C residue 1105 LYS 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 1132 LEU 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 E residue 50 THR Chi-restraints excluded: chain F residue 127 ILE 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: 5.9990 chunk 83 optimal weight: 0.7980 chunk 279 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 248 optimal weight: 0.8980 chunk 175 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 670 GLN D 350 HIS E 78 ASN ** E 86 GLN ** 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 = 0.3464 r_free = 0.3464 target = 0.065869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.044308 restraints weight = 165638.679| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 3.03 r_work: 0.2666 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9039 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 27935 Z= 0.186 Angle : 0.568 9.114 38100 Z= 0.300 Chirality : 0.044 0.199 4287 Planarity : 0.005 0.051 4744 Dihedral : 13.827 126.285 4437 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.48 % Allowed : 19.98 % Favored : 78.55 % 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: 1.46 (0.15), residues: 3255 helix: 1.98 (0.15), residues: 1241 sheet: 0.28 (0.23), residues: 477 loop : 0.49 (0.16), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D1310 TYR 0.019 0.001 TYR D1198 PHE 0.018 0.001 PHE D 982 TRP 0.028 0.002 TRP F 241 HIS 0.008 0.001 HIS F 170 Details of bonding type rmsd covalent geometry : bond 0.00438 (27927) covalent geometry : angle 0.56609 (38088) hydrogen bonds : bond 0.04921 ( 1258) hydrogen bonds : angle 4.49279 ( 3462) metal coordination : bond 0.00587 ( 8) metal coordination : angle 2.80762 ( 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 192 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.8000 (ptm-80) cc_final: 0.7786 (ptm-80) REVERT: A 227 ASN cc_start: 0.8369 (OUTLIER) cc_final: 0.8133 (t0) REVERT: B 95 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8481 (mp10) REVERT: B 107 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8016 (ptpt) REVERT: B 110 LYS cc_start: 0.8896 (mmmm) cc_final: 0.8663 (mptm) REVERT: C 252 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8860 (pttt) REVERT: D 436 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7618 (pp20) REVERT: D 1023 MET cc_start: 0.9276 (mtt) cc_final: 0.8999 (mtt) REVERT: D 1239 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6257 (ttm-80) REVERT: E 44 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8871 (pt0) outliers start: 41 outliers final: 25 residues processed: 183 average time/residue: 0.8571 time to fit residues: 178.7798 Evaluate side-chains 177 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain B residue 107 LYS 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 226 VAL Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain C residue 1105 LYS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 123 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 1238 MET Chi-restraints excluded: chain D residue 1239 ARG Chi-restraints excluded: chain D residue 1299 PHE Chi-restraints excluded: chain D residue 1408 ILE Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 338 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 20 optimal weight: 0.9980 chunk 328 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 203 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 200 optimal weight: 0.9980 chunk 320 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 169 optimal weight: 0.6980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 434 HIS C 670 GLN D 350 HIS E 78 ASN E 86 GLN F 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.066402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.045157 restraints weight = 157454.625| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.07 r_work: 0.2683 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 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 = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27935 Z= 0.135 Angle : 0.549 11.029 38100 Z= 0.289 Chirality : 0.042 0.187 4287 Planarity : 0.004 0.057 4744 Dihedral : 13.758 125.670 4437 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.37 % Allowed : 20.05 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.15), residues: 3255 helix: 2.03 (0.15), residues: 1249 sheet: 0.36 (0.23), residues: 474 loop : 0.55 (0.16), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D1310 TYR 0.018 0.001 TYR D1198 PHE 0.012 0.001 PHE C 684 TRP 0.021 0.001 TRP F 241 HIS 0.011 0.001 HIS F 170 Details of bonding type rmsd covalent geometry : bond 0.00313 (27927) covalent geometry : angle 0.54687 (38088) hydrogen bonds : bond 0.04385 ( 1258) hydrogen bonds : angle 4.38275 ( 3462) metal coordination : bond 0.00384 ( 8) metal coordination : angle 2.58117 ( 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 190 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.8032 (ptm-80) cc_final: 0.7829 (ptm-80) REVERT: A 227 ASN cc_start: 0.8357 (OUTLIER) cc_final: 0.8064 (t0) REVERT: B 95 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8493 (mp10) REVERT: B 107 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7978 (pttt) REVERT: B 110 LYS cc_start: 0.8872 (mmmm) cc_final: 0.8653 (mptm) REVERT: C 252 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8873 (pttt) REVERT: C 384 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7714 (tm-30) REVERT: C 648 ARG cc_start: 0.8678 (mtp85) cc_final: 0.8139 (mmp80) REVERT: D 436 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7504 (pp20) REVERT: D 1023 MET cc_start: 0.9233 (mtt) cc_final: 0.8962 (mtt) REVERT: E 44 GLU cc_start: 0.9185 (mt-10) cc_final: 0.8876 (pt0) REVERT: E 84 ARG cc_start: 0.9069 (ptm160) cc_final: 0.8699 (ptm-80) outliers start: 38 outliers final: 21 residues processed: 183 average time/residue: 0.7810 time to fit residues: 163.5350 Evaluate side-chains 171 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain B residue 107 LYS 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 226 VAL 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 1105 LYS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 123 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 1299 PHE Chi-restraints excluded: chain D residue 1408 ILE Chi-restraints excluded: chain E residue 86 GLN Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 338 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 15 optimal weight: 2.9990 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: 1.9990 chunk 191 optimal weight: 0.7980 chunk 168 optimal weight: 2.9990 chunk 296 optimal weight: 3.9990 chunk 264 optimal weight: 4.9990 chunk 253 optimal weight: 0.0670 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 670 GLN D 350 HIS E 78 ASN ** E 86 GLN ** 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 = 0.3459 r_free = 0.3459 target = 0.065803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.044043 restraints weight = 183531.538| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 3.17 r_work: 0.2653 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 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 = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 27935 Z= 0.208 Angle : 0.582 8.039 38100 Z= 0.307 Chirality : 0.044 0.244 4287 Planarity : 0.005 0.070 4744 Dihedral : 13.841 126.407 4437 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.30 % Allowed : 20.16 % Favored : 78.55 % 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: 1.49 (0.15), residues: 3255 helix: 1.99 (0.15), residues: 1242 sheet: 0.30 (0.23), residues: 476 loop : 0.50 (0.16), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D1310 TYR 0.018 0.001 TYR D1198 PHE 0.020 0.002 PHE D 982 TRP 0.031 0.002 TRP F 241 HIS 0.011 0.001 HIS F 170 Details of bonding type rmsd covalent geometry : bond 0.00491 (27927) covalent geometry : angle 0.57942 (38088) hydrogen bonds : bond 0.05049 ( 1258) hydrogen bonds : angle 4.50092 ( 3462) metal coordination : bond 0.00629 ( 8) metal coordination : angle 2.86353 ( 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 184 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.8185 (t0) REVERT: B 95 GLN cc_start: 0.8790 (mm-40) cc_final: 0.8508 (mp10) REVERT: B 107 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7998 (ptpt) REVERT: B 110 LYS cc_start: 0.8893 (mmmm) cc_final: 0.8670 (mptm) REVERT: C 252 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8869 (pttt) REVERT: C 384 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7716 (tm-30) REVERT: C 648 ARG cc_start: 0.8658 (mtp85) cc_final: 0.8091 (mmp80) REVERT: D 436 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7584 (pp20) REVERT: D 576 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8510 (mp0) REVERT: D 1023 MET cc_start: 0.9283 (mtt) cc_final: 0.8987 (mtt) REVERT: E 44 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8852 (pt0) REVERT: E 84 ARG cc_start: 0.9119 (ptm160) cc_final: 0.8760 (ptm-80) outliers start: 36 outliers final: 22 residues processed: 178 average time/residue: 0.8357 time to fit residues: 169.4891 Evaluate side-chains 175 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain B residue 107 LYS 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 226 VAL 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 C residue 1105 LYS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 123 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 576 GLU Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 1072 ILE Chi-restraints excluded: chain D residue 1299 PHE Chi-restraints excluded: chain D residue 1408 ILE Chi-restraints excluded: chain F residue 127 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 113 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 chunk 321 optimal weight: 3.9990 chunk 152 optimal weight: 0.0030 chunk 254 optimal weight: 3.9990 chunk 141 optimal weight: 0.0970 chunk 245 optimal weight: 3.9990 chunk 322 optimal weight: 2.9990 chunk 307 optimal weight: 8.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 670 GLN D 350 HIS E 78 ASN E 86 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.065893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.044381 restraints weight = 179962.689| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 3.14 r_work: 0.2666 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 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 = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27935 Z= 0.171 Angle : 0.572 11.702 38100 Z= 0.300 Chirality : 0.043 0.258 4287 Planarity : 0.005 0.068 4744 Dihedral : 13.850 126.148 4437 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.19 % Allowed : 20.30 % Favored : 78.51 % 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: 1.50 (0.15), residues: 3255 helix: 2.02 (0.15), residues: 1242 sheet: 0.31 (0.23), residues: 471 loop : 0.49 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D1310 TYR 0.018 0.001 TYR D1198 PHE 0.013 0.001 PHE C 684 TRP 0.029 0.001 TRP F 241 HIS 0.012 0.001 HIS F 170 Details of bonding type rmsd covalent geometry : bond 0.00404 (27927) covalent geometry : angle 0.57015 (38088) hydrogen bonds : bond 0.04762 ( 1258) hydrogen bonds : angle 4.44820 ( 3462) metal coordination : bond 0.00536 ( 8) metal coordination : angle 2.73203 ( 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 181 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.7869 (ptm-80) cc_final: 0.7661 (ptm-80) REVERT: A 227 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.8191 (t0) REVERT: B 95 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8523 (mp10) REVERT: B 107 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8073 (ptpt) REVERT: B 110 LYS cc_start: 0.8895 (mmmm) cc_final: 0.8684 (mptm) REVERT: C 252 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8856 (pttt) REVERT: C 384 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7731 (tm-30) REVERT: C 648 ARG cc_start: 0.8681 (mtp85) cc_final: 0.8130 (mmp80) REVERT: D 436 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7551 (pp20) REVERT: D 576 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8512 (mp0) REVERT: D 1023 MET cc_start: 0.9272 (mtt) cc_final: 0.8993 (mtt) REVERT: E 44 GLU cc_start: 0.9182 (mt-10) cc_final: 0.8864 (pt0) REVERT: E 84 ARG cc_start: 0.9045 (ptm160) cc_final: 0.8711 (ptm-80) outliers start: 33 outliers final: 23 residues processed: 173 average time/residue: 0.7802 time to fit residues: 154.0324 Evaluate side-chains 175 residues out of total 2768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain B residue 107 LYS 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 226 VAL 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 1105 LYS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 123 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 576 GLU Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 1072 ILE Chi-restraints excluded: chain D residue 1238 MET Chi-restraints excluded: chain D residue 1299 PHE Chi-restraints excluded: chain D residue 1408 ILE Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain F residue 127 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: 2.9990 chunk 325 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 217 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 266 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 258 optimal weight: 1.9990 chunk 129 optimal weight: 0.0970 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 670 GLN D 350 HIS E 78 ASN ** E 86 GLN ** 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 = 0.3475 r_free = 0.3475 target = 0.066446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.045070 restraints weight = 159858.227| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.97 r_work: 0.2689 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 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 = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27935 Z= 0.142 Angle : 0.547 8.397 38100 Z= 0.287 Chirality : 0.043 0.260 4287 Planarity : 0.005 0.061 4744 Dihedral : 13.767 125.773 4437 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.15 % Allowed : 20.45 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.15), residues: 3255 helix: 2.08 (0.15), residues: 1243 sheet: 0.33 (0.24), residues: 463 loop : 0.51 (0.16), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D1310 TYR 0.018 0.001 TYR D1198 PHE 0.020 0.001 PHE D 982 TRP 0.026 0.001 TRP F 241 HIS 0.011 0.001 HIS F 170 Details of bonding type rmsd covalent geometry : bond 0.00331 (27927) covalent geometry : angle 0.54502 (38088) hydrogen bonds : bond 0.04401 ( 1258) hydrogen bonds : angle 4.37697 ( 3462) metal coordination : bond 0.00418 ( 8) metal coordination : angle 2.58237 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11501.82 seconds wall clock time: 195 minutes 53.13 seconds (11753.13 seconds total)