Starting phenix.real_space_refine on Sun Jul 5 17:45:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ukp_64252/07_2026/9ukp_64252.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ukp_64252/07_2026/9ukp_64252.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ukp_64252/07_2026/9ukp_64252.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ukp_64252/07_2026/9ukp_64252.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ukp_64252/07_2026/9ukp_64252.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ukp_64252/07_2026/9ukp_64252.map" } resolution = 2.73 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= 0.002 sd= 0.027 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 95 5.49 5 Mg 4 5.21 5 S 70 5.16 5 C 17833 2.51 5 N 5099 2.21 5 O 5551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28654 Number of models: 1 Model: "" Number of chains: 13 Chain: "F" Number of atoms: 2747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2747 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 13, 'TRANS': 325} Chain breaks: 1 Chain: "E" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 761 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 6, 'TRANS': 87} Chain: "D" Number of atoms: 10776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1365, 10776 Classifications: {'peptide': 1365} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1296} Chain breaks: 2 Chain: "C" Number of atoms: 8794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8794 Classifications: {'peptide': 1114} Link IDs: {'PCIS': 1, 'PTRANS': 71, 'TRANS': 1041} Chain breaks: 1 Chain: "A" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1795 Classifications: {'peptide': 228} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 213} Chain: "B" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1782 Classifications: {'peptide': 226} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 211} Chain: "G" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 903 Classifications: {'DNA': 44} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 43} Chain breaks: 1 Chain: "H" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 987 Classifications: {'DNA': 48} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 47} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 24 Unusual residues: {' MG': 2, ' ZN': 2, 'C5P%rna3p': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "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: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11342 SG CYS D1112 22.465 59.782 119.705 1.00 68.51 S ATOM 11986 SG CYS D1194 26.257 59.928 118.850 1.00 62.36 S ATOM 12042 SG CYS D1201 24.782 61.532 121.989 1.00 55.91 S ATOM 12066 SG CYS D1204 25.293 58.109 121.974 1.00 67.37 S ATOM 3986 SG CYS D 58 54.729 104.187 83.270 1.00106.27 S ATOM 3997 SG CYS D 60 55.911 104.214 80.155 1.00106.68 S ATOM 4108 SG CYS D 73 52.846 104.488 79.646 1.00106.30 S ATOM 4134 SG CYS D 76 54.632 101.312 80.221 1.00 95.90 S Time building chain proxies: 5.12, per 1000 atoms: 0.18 Number of scatterers: 28654 At special positions: 0 Unit cell: (131.61, 157.29, 205.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 70 16.00 P 95 15.00 Mg 4 11.99 O 5551 8.00 N 5099 7.00 C 17833 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 810.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1601 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1201 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1112 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1194 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1204 " pdb=" ZN D1602 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 60 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 58 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 76 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 73 " Number of angles added : 12 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6234 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 52 sheets defined 43.7% alpha, 17.6% beta 24 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'F' and resid 79 through 89 Processing helix chain 'F' and resid 95 through 121 Processing helix chain 'F' and resid 123 through 137 Processing helix chain 'F' and resid 138 through 140 No H-bonds generated for 'chain 'F' and resid 138 through 140' Processing helix chain 'F' and resid 152 through 165 Processing helix chain 'F' and resid 167 through 190 removed outlier: 4.430A pdb=" N TYR F 173 " --> pdb=" O GLU F 169 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU F 174 " --> pdb=" O HIS F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 200 removed outlier: 3.626A pdb=" N VAL F 195 " --> pdb=" O ASN F 191 " (cutoff:3.500A) removed outlier: 3.526A 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 234 through 255 removed outlier: 3.615A pdb=" N TYR F 238 " --> pdb=" O LYS F 234 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TRP F 241 " --> pdb=" O THR F 237 " (cutoff:3.500A) removed outlier: 3.912A 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: 3.545A pdb=" N GLY F 296 " --> pdb=" O ALA F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 311 Processing helix chain 'F' and resid 328 through 333 removed outlier: 3.661A pdb=" N ILE F 333 " --> pdb=" O GLY F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 360 removed outlier: 3.728A pdb=" N LYS F 360 " --> pdb=" O LYS F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 373 removed outlier: 3.612A pdb=" N MET F 367 " --> pdb=" O GLU F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 391 removed outlier: 3.737A pdb=" N PHE F 389 " --> pdb=" O GLU F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 416 Processing helix chain 'F' and resid 419 through 423 Processing helix chain 'E' and resid 5 through 11 Processing helix chain 'E' and resid 15 through 33 removed outlier: 3.656A pdb=" N LEU E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 71 removed outlier: 3.706A pdb=" N GLY E 71 " --> pdb=" O GLU E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 93 removed outlier: 3.531A pdb=" N GLN E 86 " --> pdb=" O GLU E 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 46 through 51 Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 102 through 107 Processing helix chain 'D' and resid 110 through 117 Processing helix chain 'D' and resid 119 through 128 Processing helix chain 'D' and resid 154 through 164 Processing helix chain 'D' and resid 456 through 468 removed outlier: 3.735A pdb=" N ALA D 460 " --> pdb=" O MET D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 481 Processing helix chain 'D' and resid 485 through 506 Processing helix chain 'D' and resid 508 through 511 Processing helix chain 'D' and resid 521 through 525 Processing helix chain 'D' and resid 538 through 560 removed outlier: 4.112A 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 removed outlier: 3.559A pdb=" N GLU D 651 " --> pdb=" O ARG D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 664 Processing helix chain 'D' and resid 669 through 679 removed outlier: 3.905A 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: 3.835A pdb=" N ASP D 689 " --> pdb=" O ASP D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 711 No H-bonds generated for 'chain 'D' and resid 709 through 711' Processing helix chain 'D' and resid 729 through 731 No H-bonds generated for 'chain 'D' and resid 729 through 731' Processing helix chain 'D' and resid 732 through 737 Processing helix chain 'D' and resid 752 through 762 Processing helix chain 'D' and resid 764 through 768 Processing helix chain 'D' and resid 782 through 794 removed outlier: 3.568A pdb=" N ILE D 792 " --> pdb=" O GLY D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 808 through 818 removed outlier: 3.517A pdb=" N GLU D 817 " --> pdb=" O LEU D 813 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG D 818 " --> pdb=" O ALA D 814 " (cutoff:3.500A) 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 removed outlier: 3.560A pdb=" N GLU D 898 " --> pdb=" O LYS D 894 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 907 through 922 Processing helix chain 'D' and resid 923 through 946 removed outlier: 3.607A pdb=" N THR D 944 " --> pdb=" O THR D 940 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLY D 946 " --> pdb=" O SER D 942 " (cutoff:3.500A) Processing helix chain 'D' and resid 958 through 980 removed outlier: 4.150A pdb=" N GLN D 962 " --> pdb=" O GLU D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 984 through 1015 Processing helix chain 'D' and resid 1018 through 1026 Processing helix chain 'D' and resid 1031 through 1040 Processing helix chain 'D' and resid 1066 through 1103 removed outlier: 3.848A pdb=" N HIS D1075 " --> pdb=" O PHE D1071 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLY D1076 " --> pdb=" O ILE D1072 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA D1089 " --> pdb=" O ALA D1085 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP D1090 " --> pdb=" O LEU D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 1136 through 1145 Processing helix chain 'D' and resid 1167 through 1180 Processing helix chain 'D' and resid 1202 through 1206 Processing helix chain 'D' and resid 1220 through 1231 Processing helix chain 'D' and resid 1232 through 1236 Processing helix chain 'D' and resid 1255 through 1264 Processing helix chain 'D' and resid 1331 through 1339 Processing helix chain 'D' and resid 1340 through 1359 removed outlier: 4.069A pdb=" N VAL D1355 " --> pdb=" O GLU D1351 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR D1356 " --> pdb=" O ILE D1352 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN D1359 " --> pdb=" O VAL D1355 " (cutoff:3.500A) Processing helix chain 'D' and resid 1364 through 1376 removed outlier: 4.159A pdb=" N ILE D1368 " --> pdb=" O HIS D1364 " (cutoff:3.500A) Processing helix chain 'D' and resid 1397 through 1410 removed outlier: 3.584A pdb=" N GLU D1410 " --> pdb=" O ARG D1406 " (cutoff:3.500A) Processing helix chain 'D' and resid 1423 through 1430 Processing helix chain 'D' and resid 1433 through 1439 Processing helix chain 'D' and resid 1442 through 1454 Processing helix chain 'D' and resid 1462 through 1469 Processing helix chain 'D' and resid 1474 through 1477 Processing helix chain 'D' and resid 1478 through 1483 removed outlier: 4.411A pdb=" N PHE D1483 " --> pdb=" O ASP D1479 " (cutoff:3.500A) Processing helix chain 'D' and resid 1489 through 1501 Processing helix chain 'C' and resid 19 through 31 removed outlier: 4.095A pdb=" N SER C 25 " --> pdb=" O ILE C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 39 Processing helix chain 'C' and resid 42 through 52 Processing helix chain 'C' and resid 79 through 87 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 203 through 212 removed outlier: 3.691A pdb=" N LEU C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA C 208 " --> pdb=" O GLN C 204 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU C 210 " --> pdb=" O THR C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 222 removed outlier: 3.555A pdb=" N MET C 222 " --> pdb=" O GLN C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 228 removed outlier: 3.584A pdb=" N PHE C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 223 through 228' Processing helix chain 'C' and resid 230 through 243 Processing helix chain 'C' and resid 249 through 262 Processing helix chain 'C' and resid 270 through 282 Processing helix chain 'C' and resid 302 through 316 Processing helix chain 'C' and resid 335 through 359 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 375 through 389 removed outlier: 3.558A pdb=" N SER C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 408 removed outlier: 3.563A pdb=" N SER C 403 " --> pdb=" O ASN C 399 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 429 removed outlier: 3.715A pdb=" N ARG C 428 " --> pdb=" O GLY C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 435 Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 525 through 529 Processing helix chain 'C' and resid 535 through 540 Processing helix chain 'C' and resid 543 through 547 removed outlier: 3.603A 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 removed outlier: 3.880A pdb=" N MET C 560 " --> pdb=" O ASN C 556 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN C 565 " --> pdb=" O GLY C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 568 No H-bonds generated for 'chain 'C' and resid 566 through 568' Processing helix chain 'C' and resid 583 through 591 Processing helix chain 'C' and resid 683 through 687 removed outlier: 3.655A pdb=" N ASP C 686 " --> pdb=" O ASN C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 697 Processing helix chain 'C' and resid 768 through 779 Processing helix chain 'C' and resid 854 through 858 Processing helix chain 'C' and resid 874 through 880 removed outlier: 4.631A pdb=" N SER C 878 " --> pdb=" O LEU C 874 " (cutoff:3.500A) removed outlier: 3.734A 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 932 removed outlier: 3.660A pdb=" N GLU C 923 " --> pdb=" O ALA C 919 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 924 " --> pdb=" O GLN C 920 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS C 928 " --> pdb=" O VAL C 924 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ARG C 929 " --> pdb=" O TYR C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 950 Processing helix chain 'C' and resid 958 through 969 removed outlier: 3.566A pdb=" N GLN C 969 " --> pdb=" O GLU C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1004 Processing helix chain 'C' and resid 1033 through 1044 Processing helix chain 'C' and resid 1045 through 1054 Processing helix chain 'C' and resid 1059 through 1072 Processing helix chain 'C' and resid 1082 through 1094 removed outlier: 3.671A pdb=" N ARG C1086 " --> pdb=" O PRO C1082 " (cutoff:3.500A) 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 222 Processing helix chain 'A' and resid 223 through 226 removed outlier: 3.818A pdb=" N SER A 226 " --> pdb=" O THR A 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 223 through 226' Processing helix chain 'B' and resid 31 through 47 Proline residue: B 39 - end of helix Processing helix chain 'B' and resid 74 through 84 removed outlier: 3.595A 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 Processing helix chain 'B' and resid 206 through 223 removed outlier: 3.551A pdb=" N THR B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 315 through 316 Processing sheet with id=AA2, first strand: chain 'E' and resid 47 through 49 Processing sheet with id=AA3, first strand: chain 'E' and resid 73 through 76 Processing sheet with id=AA4, first strand: chain 'D' and resid 1456 through 1457 Processing sheet with id=AA5, first strand: chain 'D' and resid 22 through 25 removed outlier: 7.636A pdb=" N HIS D 92 " --> pdb=" O TYR D 23 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLU D 25 " --> pdb=" O HIS D 92 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N GLU D 94 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 10.206A pdb=" N LEU D 95 " --> pdb=" O PRO D 518 " (cutoff:3.500A) removed outlier: 10.684A pdb=" N THR D 97 " --> pdb=" O ALA D 516 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ALA D 516 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 71 through 72 removed outlier: 4.032A pdb=" N LYS D 71 " --> pdb=" O VAL D 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 152 through 153 removed outlier: 6.699A pdb=" N ASP D 453 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AA9, first strand: chain 'D' and resid 166 through 170 removed outlier: 3.657A pdb=" N GLU D 183 " --> pdb=" O ALA D 203 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 342 through 346 removed outlier: 3.547A pdb=" N GLY D 383 " --> pdb=" O VAL D 361 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 342 through 346 Processing sheet with id=AB3, first strand: chain 'D' and resid 351 through 353 Processing sheet with id=AB4, first strand: chain 'D' and resid 398 through 402 removed outlier: 3.776A pdb=" N ASP D 413 " --> pdb=" O VAL D 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 420 through 422 removed outlier: 6.906A pdb=" N VAL D 427 " --> pdb=" O LEU D 421 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 621 through 623 removed outlier: 3.638A pdb=" N GLN C1030 " --> pdb=" O VAL D 623 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 626 through 633 removed outlier: 6.451A pdb=" N CYS D 642 " --> pdb=" O VAL D 719 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL D 721 " --> pdb=" O CYS D 642 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU D 644 " --> pdb=" O VAL D 721 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 827 through 828 Processing sheet with id=AB9, first strand: chain 'D' and resid 842 through 843 Processing sheet with id=AC1, first strand: chain 'D' and resid 1106 through 1109 Processing sheet with id=AC2, first strand: chain 'D' and resid 1118 through 1121 Processing sheet with id=AC3, first strand: chain 'D' and resid 1123 through 1126 Processing sheet with id=AC4, first strand: chain 'D' and resid 1153 through 1155 Processing sheet with id=AC5, first strand: chain 'D' and resid 1300 through 1303 Processing sheet with id=AC6, first strand: chain 'D' and resid 1394 through 1396 removed outlier: 6.716A pdb=" N ALA D1416 " --> pdb=" O THR D1382 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AC8, first strand: chain 'C' and resid 54 through 55 removed outlier: 5.392A pdb=" N LEU C 66 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE C 101 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N PHE C 68 " --> pdb=" O GLN C 99 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLN C 99 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU C 70 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY C 116 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA C 96 " --> pdb=" O PHE C 114 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N PHE C 114 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU C 98 " --> pdb=" O GLU C 112 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU C 112 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU C 100 " --> pdb=" O GLU C 110 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLU C 110 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N HIS C 102 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE C 108 " --> pdb=" O HIS C 102 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AD1, first strand: chain 'C' and resid 331 through 334 removed outlier: 6.388A pdb=" N SER C 138 " --> pdb=" O SER C 411 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 145 through 150 removed outlier: 6.877A pdb=" N TYR C 158 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL C 176 " --> pdb=" O TYR C 158 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 291 through 294 Processing sheet with id=AD4, first strand: chain 'C' and resid 460 through 461 removed outlier: 5.357A pdb=" N GLU C 482 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL C 475 " --> pdb=" O THR C 480 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR C 480 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 460 through 461 Processing sheet with id=AD6, first strand: chain 'C' and resid 495 through 497 Processing sheet with id=AD7, first strand: chain 'C' and resid 503 through 504 removed outlier: 3.833A pdb=" N ARG C 507 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 595 through 596 removed outlier: 6.484A pdb=" N LEU C 595 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 620 through 624 removed outlier: 6.910A pdb=" N ARG C 610 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N VAL C 606 " --> pdb=" O ARG C 610 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL C 612 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 629 through 630 Processing sheet with id=AE2, first strand: chain 'C' and resid 661 through 662 Processing sheet with id=AE3, first strand: chain 'C' and resid 971 through 972 removed outlier: 6.831A pdb=" N ILE C 688 " --> pdb=" O LYS C 851 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N LEU C 853 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE C 690 " --> pdb=" O LEU C 853 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 689 " --> pdb=" O ILE C 870 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N VAL C 869 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU C 673 " --> pdb=" O VAL C 869 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU C 871 " --> pdb=" O LEU C 673 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ALA C 675 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL C 988 " --> pdb=" O ILE C 676 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 702 through 713 removed outlier: 3.602A pdb=" N ARG C 802 " --> pdb=" O TYR C 826 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA C 828 " --> pdb=" O VAL C 800 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL C 800 " --> pdb=" O ALA C 828 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N LYS C 830 " --> pdb=" O GLY C 798 " (cutoff:3.500A) removed outlier: 9.098A pdb=" N GLY C 798 " --> pdb=" O LYS C 830 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 721 through 722 Processing sheet with id=AE6, first strand: chain 'C' and resid 754 through 756 removed outlier: 6.707A pdb=" N LEU C 790 " --> pdb=" O LEU C 755 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 10 through 16 removed outlier: 3.567A pdb=" N GLU A 26 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR A 20 " --> pdb=" O GLN A 16 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ASP A 193 " --> pdb=" O PRO A 27 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 96 through 104 removed outlier: 3.614A pdb=" N SER A 55 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP A 145 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL A 53 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLY A 147 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N THR A 51 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AF1, first strand: chain 'A' and resid 107 through 110 Processing sheet with id=AF2, first strand: chain 'A' and resid 150 through 151 Processing sheet with id=AF3, first strand: chain 'B' and resid 10 through 16 removed outlier: 3.737A pdb=" N TYR B 20 " --> pdb=" O GLN B 16 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N TYR B 20 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N THR B 201 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLU B 22 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE B 199 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N VAL B 24 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LEU B 197 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N GLU B 26 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU B 195 " --> pdb=" O GLU B 26 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N THR B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU B 186 " --> pdb=" O THR B 190 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 97 through 104 removed outlier: 3.540A pdb=" N LEU B 138 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASP B 145 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N VAL B 53 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLY B 147 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N THR B 51 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 87 through 89 Processing sheet with id=AF6, first strand: chain 'B' and resid 108 through 110 removed outlier: 6.882A pdb=" N VAL B 109 " --> pdb=" O ILE B 129 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 150 through 151 1233 hydrogen bonds defined for protein. 3441 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 57 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 7.23 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4686 1.30 - 1.43: 7379 1.43 - 1.55: 16971 1.55 - 1.68: 194 1.68 - 1.81: 127 Bond restraints: 29357 Sorted by residual: bond pdb=" O5' C5P D1605 " pdb=" P C5P D1605 " ideal model delta sigma weight residual 1.709 1.592 0.117 2.00e-02 2.50e+03 3.42e+01 bond pdb=" C ASP D 624 " pdb=" O ASP D 624 " ideal model delta sigma weight residual 1.233 1.171 0.062 1.28e-02 6.10e+03 2.37e+01 bond pdb=" CA ASP D 624 " pdb=" C ASP D 624 " ideal model delta sigma weight residual 1.528 1.470 0.058 1.35e-02 5.49e+03 1.83e+01 bond pdb=" C3' DA H 45 " pdb=" C2' DA H 45 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.26e+01 bond pdb=" C3' DC G 28 " pdb=" C2' DC G 28 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 ... (remaining 29352 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 39919 2.79 - 5.57: 177 5.57 - 8.36: 11 8.36 - 11.14: 3 11.14 - 13.93: 2 Bond angle restraints: 40112 Sorted by residual: angle pdb=" O3B B4P C1201 " pdb=" PG B4P C1201 " pdb=" O3G B4P C1201 " ideal model delta sigma weight residual 95.27 109.20 -13.93 3.00e+00 1.11e-01 2.16e+01 angle pdb=" N3 DT H 39 " pdb=" C4 DT H 39 " pdb=" O4 DT H 39 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT G 40 " pdb=" C4 DT G 40 " pdb=" O4 DT G 40 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT G 8 " pdb=" C4 DT G 8 " pdb=" O4 DT G 8 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT H 15 " pdb=" C4 DT H 15 " pdb=" O4 DT H 15 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 ... (remaining 40107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.95: 16807 24.95 - 49.89: 867 49.89 - 74.84: 217 74.84 - 99.79: 20 99.79 - 124.74: 3 Dihedral angle restraints: 17914 sinusoidal: 8229 harmonic: 9685 Sorted by residual: dihedral pdb=" CA TYR D1207 " pdb=" C TYR D1207 " pdb=" N ASP D1208 " pdb=" CA ASP D1208 " ideal model delta harmonic sigma weight residual 180.00 153.86 26.14 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" C ASP D 624 " pdb=" N ASP D 624 " pdb=" CA ASP D 624 " pdb=" CB ASP D 624 " ideal model delta harmonic sigma weight residual -122.60 -110.97 -11.63 0 2.50e+00 1.60e-01 2.17e+01 dihedral pdb=" C22 1N7 B 401 " pdb=" C23 1N7 B 401 " pdb=" C24 1N7 B 401 " pdb=" N1 1N7 B 401 " ideal model delta sinusoidal sigma weight residual 227.30 108.60 118.70 1 3.00e+01 1.11e-03 1.58e+01 ... (remaining 17911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3565 0.046 - 0.092: 672 0.092 - 0.138: 276 0.138 - 0.184: 4 0.184 - 0.231: 3 Chirality restraints: 4520 Sorted by residual: chirality pdb=" C1' C5P D1605 " pdb=" C2' C5P D1605 " pdb=" N1 C5P D1605 " pdb=" O4' C5P D1605 " both_signs ideal model delta sigma weight residual False 2.22 2.45 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C1F B4P C1201 " pdb=" C2F B4P C1201 " pdb=" N9B B4P C1201 " pdb=" O4F B4P C1201 " both_signs ideal model delta sigma weight residual False 2.32 2.55 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C20 1N7 B 401 " pdb=" C21 1N7 B 401 " pdb=" C22 1N7 B 401 " pdb=" C9 1N7 B 401 " both_signs ideal model delta sigma weight residual False 2.59 2.79 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 4517 not shown) Planarity restraints: 4911 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP D 624 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" CG ASP D 624 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASP D 624 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP D 624 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN D1323 " -0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO D1324 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO D1324 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D1324 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 634 " -0.022 5.00e-02 4.00e+02 3.37e-02 1.81e+00 pdb=" N PRO D 635 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO D 635 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 635 " -0.019 5.00e-02 4.00e+02 ... (remaining 4908 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 160 2.55 - 3.14: 22237 3.14 - 3.73: 43342 3.73 - 4.31: 66044 4.31 - 4.90: 109015 Nonbonded interactions: 240798 Sorted by model distance: nonbonded pdb=" O2A B4P C1201 " pdb=" O HOH C1301 " model vdw 1.968 3.040 nonbonded pdb=" OD1 ASP D 739 " pdb="MG MG D1603 " model vdw 2.021 2.170 nonbonded pdb="MG MG D1603 " pdb=" O3' C5P D1605 " model vdw 2.026 2.170 nonbonded pdb=" OD1 ASP D 741 " pdb="MG MG D1603 " model vdw 2.065 2.170 nonbonded pdb=" OD1 ASP D 743 " pdb="MG MG D1603 " model vdw 2.078 2.170 ... (remaining 240793 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 4 through 229) selection = (chain 'B' and resid 4 through 229) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.05 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 29.380 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 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 0.117 29366 Z= 0.222 Angle : 0.563 24.775 40124 Z= 0.322 Chirality : 0.042 0.231 4520 Planarity : 0.003 0.037 4911 Dihedral : 15.227 124.736 11680 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.24 % Allowed : 0.38 % Favored : 99.37 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.15), residues: 3346 helix: 1.05 (0.15), residues: 1256 sheet: 0.42 (0.25), residues: 439 loop : 0.55 (0.16), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 704 TYR 0.019 0.001 TYR D1207 PHE 0.020 0.001 PHE D 754 TRP 0.008 0.001 TRP D 688 HIS 0.003 0.001 HIS D 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.22 (29357) covalent geometry : angle 0.50781 / 0.32 (40112) hydrogen bonds : bond 0.22840 / 15.25 ( 1284) hydrogen bonds : angle 7.61152 / 5.51 ( 3555) metal coordination : bond 0.01522 / 0.98 ( 8) metal coordination : angle 14.10302 / 8.80 ( 12) Misc. bond : bond 0.03204 / 1.69 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 266 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 83 GLN cc_start: 0.8802 (tt0) cc_final: 0.8553 (tm-30) REVERT: F 355 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8136 (tm-30) REVERT: E 44 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8631 (mt-10) REVERT: E 50 THR cc_start: 0.8943 (m) cc_final: 0.8622 (p) REVERT: E 87 LYS cc_start: 0.9243 (ttpp) cc_final: 0.8627 (tmmm) REVERT: D 971 LEU cc_start: 0.9287 (tp) cc_final: 0.9078 (tm) REVERT: D 1299 PHE cc_start: 0.8914 (m-80) cc_final: 0.8695 (m-80) REVERT: C 121 MET cc_start: 0.9287 (ttm) cc_final: 0.9023 (ttp) REVERT: C 390 GLN cc_start: 0.8565 (tt0) cc_final: 0.8322 (tp-100) REVERT: A 91 ASN cc_start: 0.8894 (t0) cc_final: 0.8370 (t0) REVERT: A 226 SER cc_start: 0.8783 (p) cc_final: 0.8562 (p) REVERT: B 72 LYS cc_start: 0.9189 (mttt) cc_final: 0.8889 (mmtp) outliers start: 7 outliers final: 2 residues processed: 271 average time/residue: 0.9703 time to fit residues: 292.0782 Evaluate side-chains 154 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 152 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1452 ILE Chi-restraints excluded: chain C residue 402 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.1980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 320 HIS C 670 GLN B 139 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.080176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.053689 restraints weight = 59919.768| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 2.60 r_work: 0.2583 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2442 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2451 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2451 r_free = 0.2451 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2451 r_free = 0.2451 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2451 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29366 Z= 0.146 Angle : 0.592 8.995 40124 Z= 0.316 Chirality : 0.044 0.159 4520 Planarity : 0.005 0.074 4911 Dihedral : 15.589 129.606 4910 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.70 % Allowed : 6.17 % Favored : 93.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.15), residues: 3346 helix: 1.45 (0.14), residues: 1300 sheet: 0.56 (0.26), residues: 416 loop : 0.53 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 284 TYR 0.016 0.001 TYR C 925 PHE 0.018 0.001 PHE C 425 TRP 0.009 0.001 TRP A 200 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (29357) covalent geometry : angle 0.58729 / 0.32 (40112) hydrogen bonds : bond 0.05668 / 3.73 ( 1284) hydrogen bonds : angle 5.23996 / 3.79 ( 3555) metal coordination : bond 0.00747 / 0.42 ( 8) metal coordination : angle 4.39566 / 2.64 ( 12) Misc. bond : bond 0.01327 / 0.70 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 83 GLN cc_start: 0.8762 (tt0) cc_final: 0.8299 (tm-30) REVERT: E 44 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8615 (mt-10) REVERT: E 86 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8481 (tm-30) REVERT: E 87 LYS cc_start: 0.9192 (ttpp) cc_final: 0.8917 (tmmm) REVERT: E 88 GLU cc_start: 0.8813 (tp30) cc_final: 0.8586 (tp30) REVERT: D 65 ARG cc_start: 0.7608 (mmt90) cc_final: 0.7265 (mmt90) REVERT: D 1299 PHE cc_start: 0.9206 (m-80) cc_final: 0.8981 (m-80) REVERT: C 102 HIS cc_start: 0.8085 (m-70) cc_final: 0.7856 (m90) REVERT: C 121 MET cc_start: 0.9176 (ttm) cc_final: 0.8934 (ttp) REVERT: C 390 GLN cc_start: 0.9180 (tt0) cc_final: 0.8391 (tp-100) REVERT: C 442 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: A 91 ASN cc_start: 0.8890 (t0) cc_final: 0.8468 (t0) REVERT: A 185 ARG cc_start: 0.8883 (ptm160) cc_final: 0.8606 (ptm160) REVERT: B 7 LYS cc_start: 0.8710 (tppt) cc_final: 0.8329 (pptt) REVERT: B 72 LYS cc_start: 0.9392 (mttt) cc_final: 0.9042 (mmtp) REVERT: B 95 GLN cc_start: 0.8177 (tp40) cc_final: 0.7755 (mm-40) REVERT: B 102 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8650 (mmmt) REVERT: B 140 MET cc_start: 0.9492 (mtm) cc_final: 0.9225 (mtm) outliers start: 20 outliers final: 5 residues processed: 185 average time/residue: 0.8329 time to fit residues: 174.5553 Evaluate side-chains 155 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 148 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 1131 SER Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 172 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 108 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 253 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 243 optimal weight: 6.9990 chunk 331 optimal weight: 0.8980 chunk 270 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 538 GLN B 163 ASN B 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.077384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.050737 restraints weight = 61102.659| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 2.63 r_work: 0.2565 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2426 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2426 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2423 r_free = 0.2423 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2424 r_free = 0.2424 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2424 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 29366 Z= 0.262 Angle : 0.590 7.881 40124 Z= 0.311 Chirality : 0.045 0.153 4520 Planarity : 0.005 0.044 4911 Dihedral : 15.614 130.389 4907 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.87 % Allowed : 7.35 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.14), residues: 3346 helix: 1.60 (0.15), residues: 1286 sheet: 0.39 (0.25), residues: 428 loop : 0.42 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 172 TYR 0.016 0.001 TYR D1207 PHE 0.017 0.002 PHE F 390 TRP 0.010 0.001 TRP B 200 HIS 0.007 0.001 HIS C 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.26 (29357) covalent geometry : angle 0.58697 / 0.31 (40112) hydrogen bonds : bond 0.05459 / 3.57 ( 1284) hydrogen bonds : angle 4.87873 / 3.51 ( 3555) metal coordination : bond 0.01230 / 0.82 ( 8) metal coordination : angle 3.21640 / 1.91 ( 12) Misc. bond : bond 0.00095 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 83 GLN cc_start: 0.8747 (tt0) cc_final: 0.8300 (tm-30) REVERT: F 110 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8597 (mpp) REVERT: F 290 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8536 (mp0) REVERT: F 355 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8354 (pp20) REVERT: E 44 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8752 (mt-10) REVERT: E 86 GLN cc_start: 0.8800 (tm-30) cc_final: 0.8578 (tm-30) REVERT: E 87 LYS cc_start: 0.9183 (ttpp) cc_final: 0.8812 (tmmt) REVERT: E 88 GLU cc_start: 0.8896 (tp30) cc_final: 0.8610 (tp30) REVERT: D 124 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8526 (tm-30) REVERT: D 351 MET cc_start: 0.9469 (mtp) cc_final: 0.8999 (ptp) REVERT: C 33 ASP cc_start: 0.9300 (m-30) cc_final: 0.8886 (t0) REVERT: C 102 HIS cc_start: 0.8099 (OUTLIER) cc_final: 0.7884 (m90) REVERT: C 390 GLN cc_start: 0.9227 (tt0) cc_final: 0.8434 (tp-100) REVERT: C 442 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8209 (tt0) REVERT: A 91 ASN cc_start: 0.8973 (t0) cc_final: 0.8338 (t0) REVERT: B 7 LYS cc_start: 0.8766 (tppt) cc_final: 0.8509 (pttt) REVERT: B 95 GLN cc_start: 0.8272 (tp40) cc_final: 0.7778 (mm-40) REVERT: B 140 MET cc_start: 0.9475 (mtm) cc_final: 0.9184 (mtm) outliers start: 25 outliers final: 9 residues processed: 164 average time/residue: 0.9184 time to fit residues: 170.4597 Evaluate side-chains 151 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 1452 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 580 MET Chi-restraints excluded: chain C residue 1002 GLU Chi-restraints excluded: chain B residue 172 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 303 optimal weight: 0.8980 chunk 212 optimal weight: 0.8980 chunk 225 optimal weight: 5.9990 chunk 232 optimal weight: 0.7980 chunk 197 optimal weight: 0.8980 chunk 276 optimal weight: 2.9990 chunk 324 optimal weight: 2.9990 chunk 23 optimal weight: 0.0970 chunk 91 optimal weight: 0.6980 chunk 209 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 163 ASN B 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.079072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.052667 restraints weight = 60116.565| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 2.60 r_work: 0.2599 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2460 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2465 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2465 r_free = 0.2465 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2465 r_free = 0.2465 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 29366 Z= 0.113 Angle : 0.513 9.087 40124 Z= 0.273 Chirality : 0.042 0.143 4520 Planarity : 0.004 0.044 4911 Dihedral : 15.472 131.750 4907 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.70 % Allowed : 8.50 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.15), residues: 3346 helix: 1.72 (0.15), residues: 1293 sheet: 0.51 (0.26), residues: 398 loop : 0.51 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 84 TYR 0.011 0.001 TYR D 989 PHE 0.020 0.001 PHE F 390 TRP 0.010 0.001 TRP B 200 HIS 0.005 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (29357) covalent geometry : angle 0.51159 / 0.27 (40112) hydrogen bonds : bond 0.04163 / 2.73 ( 1284) hydrogen bonds : angle 4.58635 / 3.30 ( 3555) metal coordination : bond 0.00335 / 0.20 ( 8) metal coordination : angle 2.29722 / 1.34 ( 12) Misc. bond : bond 0.00033 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 83 GLN cc_start: 0.8669 (tt0) cc_final: 0.8251 (tm-30) REVERT: F 110 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8617 (mpp) REVERT: F 290 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8855 (mt-10) REVERT: E 44 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8806 (mt-10) REVERT: E 86 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8574 (tm-30) REVERT: E 87 LYS cc_start: 0.9088 (ttpp) cc_final: 0.8827 (tmmt) REVERT: E 88 GLU cc_start: 0.8945 (tp30) cc_final: 0.8688 (tp30) REVERT: D 65 ARG cc_start: 0.7804 (mmt90) cc_final: 0.7559 (mmt90) REVERT: D 351 MET cc_start: 0.9369 (mtp) cc_final: 0.8846 (ptp) REVERT: D 486 ARG cc_start: 0.8460 (mmm-85) cc_final: 0.8041 (mmm-85) REVERT: D 692 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8262 (mt-10) REVERT: C 33 ASP cc_start: 0.9245 (m-30) cc_final: 0.8853 (t0) REVERT: C 102 HIS cc_start: 0.8063 (m-70) cc_final: 0.7834 (m90) REVERT: C 222 MET cc_start: 0.7138 (tpt) cc_final: 0.6770 (tpt) REVERT: C 390 GLN cc_start: 0.9212 (tt0) cc_final: 0.8453 (tp-100) REVERT: C 771 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8217 (tm-30) REVERT: A 91 ASN cc_start: 0.9004 (t0) cc_final: 0.8398 (t0) REVERT: B 72 LYS cc_start: 0.9410 (mttt) cc_final: 0.9074 (mmtp) REVERT: B 95 GLN cc_start: 0.8285 (tp40) cc_final: 0.7804 (mm-40) REVERT: B 201 THR cc_start: 0.9481 (OUTLIER) cc_final: 0.9242 (p) outliers start: 20 outliers final: 10 residues processed: 162 average time/residue: 0.8131 time to fit residues: 150.2411 Evaluate side-chains 152 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 1131 SER Chi-restraints excluded: chain D residue 1452 ILE Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain B residue 201 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 178 optimal weight: 3.9990 chunk 287 optimal weight: 4.9990 chunk 230 optimal weight: 0.8980 chunk 223 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 281 optimal weight: 2.9990 chunk 231 optimal weight: 0.0980 chunk 87 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 163 ASN B 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.078312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.052077 restraints weight = 60253.783| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 2.57 r_work: 0.2604 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2467 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2454 r_free = 0.2454 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2454 r_free = 0.2454 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29366 Z= 0.149 Angle : 0.507 9.692 40124 Z= 0.268 Chirality : 0.042 0.141 4520 Planarity : 0.004 0.047 4911 Dihedral : 15.448 132.650 4907 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.12 % Allowed : 8.82 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.15), residues: 3346 helix: 1.85 (0.15), residues: 1286 sheet: 0.46 (0.26), residues: 408 loop : 0.52 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 189 TYR 0.011 0.001 TYR D 132 PHE 0.016 0.001 PHE F 390 TRP 0.009 0.001 TRP B 200 HIS 0.005 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (29357) covalent geometry : angle 0.50583 / 0.27 (40112) hydrogen bonds : bond 0.04091 / 2.67 ( 1284) hydrogen bonds : angle 4.43579 / 3.19 ( 3555) metal coordination : bond 0.00596 / 0.39 ( 8) metal coordination : angle 2.28785 / 1.32 ( 12) Misc. bond : bond 0.00068 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 83 GLN cc_start: 0.8739 (tt0) cc_final: 0.8275 (tm-30) REVERT: F 110 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8509 (mpp) REVERT: F 290 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8833 (mt-10) REVERT: F 389 PHE cc_start: 0.8897 (t80) cc_final: 0.8673 (t80) REVERT: E 44 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8749 (mt-10) REVERT: E 86 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8589 (tm-30) REVERT: E 87 LYS cc_start: 0.9109 (ttpp) cc_final: 0.8869 (tmmt) REVERT: E 88 GLU cc_start: 0.8955 (tp30) cc_final: 0.8712 (tp30) REVERT: E 90 GLU cc_start: 0.8569 (pp20) cc_final: 0.8357 (pp20) REVERT: D 351 MET cc_start: 0.9376 (mtp) cc_final: 0.8911 (ptp) REVERT: D 486 ARG cc_start: 0.8488 (mmm-85) cc_final: 0.8273 (mmm-85) REVERT: D 1100 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8306 (m-30) REVERT: D 1433 SER cc_start: 0.8925 (OUTLIER) cc_final: 0.8710 (t) REVERT: C 33 ASP cc_start: 0.9265 (m-30) cc_final: 0.8858 (t0) REVERT: C 102 HIS cc_start: 0.8103 (m-70) cc_final: 0.7776 (m90) REVERT: C 104 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.8141 (p0) REVERT: C 222 MET cc_start: 0.7270 (tpt) cc_final: 0.6935 (tpt) REVERT: C 390 GLN cc_start: 0.9211 (tt0) cc_final: 0.8448 (tp-100) REVERT: C 771 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8237 (tm-30) REVERT: C 816 LYS cc_start: 0.8675 (mtmm) cc_final: 0.8466 (mmmt) REVERT: A 91 ASN cc_start: 0.9030 (t0) cc_final: 0.8397 (t0) REVERT: B 95 GLN cc_start: 0.8291 (tp40) cc_final: 0.7800 (mm-40) REVERT: B 201 THR cc_start: 0.9475 (OUTLIER) cc_final: 0.9158 (p) outliers start: 32 outliers final: 15 residues processed: 164 average time/residue: 0.7280 time to fit residues: 137.7948 Evaluate side-chains 157 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1131 SER Chi-restraints excluded: chain D residue 1433 SER Chi-restraints excluded: chain D residue 1452 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 580 MET Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain B residue 201 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 42 optimal weight: 0.7980 chunk 316 optimal weight: 9.9990 chunk 202 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 304 optimal weight: 0.0470 chunk 5 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 125 optimal weight: 0.2980 chunk 33 optimal weight: 0.7980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 163 ASN B 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.079546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.053252 restraints weight = 60371.669| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 2.61 r_work: 0.2633 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2495 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2510 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2510 r_free = 0.2510 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2510 r_free = 0.2510 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2510 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 29366 Z= 0.101 Angle : 0.484 8.799 40124 Z= 0.257 Chirality : 0.041 0.143 4520 Planarity : 0.004 0.049 4911 Dihedral : 15.364 133.117 4907 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.98 % Allowed : 9.41 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.15), residues: 3346 helix: 1.89 (0.15), residues: 1293 sheet: 0.54 (0.26), residues: 398 loop : 0.55 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 189 TYR 0.010 0.001 TYR D 989 PHE 0.011 0.001 PHE F 390 TRP 0.009 0.001 TRP B 200 HIS 0.005 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (29357) covalent geometry : angle 0.48288 / 0.26 (40112) hydrogen bonds : bond 0.03570 / 2.34 ( 1284) hydrogen bonds : angle 4.29033 / 3.09 ( 3555) metal coordination : bond 0.00290 / 0.19 ( 8) metal coordination : angle 1.85002 / 1.06 ( 12) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 83 GLN cc_start: 0.8757 (tt0) cc_final: 0.8290 (tm-30) REVERT: F 290 GLU cc_start: 0.9172 (OUTLIER) cc_final: 0.8658 (mt-10) REVERT: F 367 MET cc_start: 0.9386 (mmm) cc_final: 0.9158 (tpp) REVERT: E 44 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8806 (mt-10) REVERT: E 86 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8602 (tm-30) REVERT: E 87 LYS cc_start: 0.9109 (ttpp) cc_final: 0.8845 (tmmt) REVERT: E 88 GLU cc_start: 0.8978 (tp30) cc_final: 0.8672 (tp30) REVERT: D 351 MET cc_start: 0.9359 (mtp) cc_final: 0.8904 (ptp) REVERT: D 486 ARG cc_start: 0.8464 (mmm-85) cc_final: 0.8117 (mmm-85) REVERT: D 692 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8174 (mt-10) REVERT: D 804 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8344 (mp) REVERT: D 1086 LEU cc_start: 0.9210 (mp) cc_final: 0.8984 (mt) REVERT: D 1100 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8249 (m-30) REVERT: C 33 ASP cc_start: 0.9244 (m-30) cc_final: 0.8848 (t0) REVERT: C 102 HIS cc_start: 0.8080 (m-70) cc_final: 0.7846 (m90) REVERT: C 222 MET cc_start: 0.7292 (tpt) cc_final: 0.7007 (tpt) REVERT: C 390 GLN cc_start: 0.9200 (tt0) cc_final: 0.8443 (tp-100) REVERT: C 442 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: C 771 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8199 (tm-30) REVERT: C 816 LYS cc_start: 0.8681 (mtmm) cc_final: 0.8469 (mmmt) REVERT: A 91 ASN cc_start: 0.9048 (t0) cc_final: 0.8481 (t0) REVERT: A 155 LYS cc_start: 0.8819 (mtpp) cc_final: 0.8570 (ttpt) REVERT: B 72 LYS cc_start: 0.9449 (mttt) cc_final: 0.9103 (mmtp) REVERT: B 95 GLN cc_start: 0.8330 (tp40) cc_final: 0.7856 (mm-40) REVERT: B 201 THR cc_start: 0.9446 (OUTLIER) cc_final: 0.9119 (t) outliers start: 28 outliers final: 12 residues processed: 165 average time/residue: 0.8943 time to fit residues: 168.6849 Evaluate side-chains 154 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1131 SER Chi-restraints excluded: chain D residue 1452 ILE Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain B residue 201 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 7 optimal weight: 2.9990 chunk 218 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 110 optimal weight: 0.0770 chunk 73 optimal weight: 5.9990 chunk 230 optimal weight: 0.6980 chunk 259 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 139 optimal weight: 0.6980 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 28 GLN B 163 ASN B 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.079083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.052937 restraints weight = 60104.075| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 2.57 r_work: 0.2612 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2475 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2476 r_free = 0.2476 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2476 r_free = 0.2476 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29366 Z= 0.116 Angle : 0.476 8.518 40124 Z= 0.252 Chirality : 0.041 0.139 4520 Planarity : 0.004 0.048 4911 Dihedral : 15.341 133.360 4907 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.98 % Allowed : 9.76 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.15), residues: 3346 helix: 1.95 (0.15), residues: 1293 sheet: 0.49 (0.26), residues: 407 loop : 0.55 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 189 TYR 0.010 0.001 TYR D 989 PHE 0.016 0.001 PHE F 389 TRP 0.008 0.001 TRP B 200 HIS 0.005 0.001 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (29357) covalent geometry : angle 0.47539 / 0.25 (40112) hydrogen bonds : bond 0.03588 / 2.35 ( 1284) hydrogen bonds : angle 4.23698 / 3.05 ( 3555) metal coordination : bond 0.00406 / 0.27 ( 8) metal coordination : angle 1.88952 / 1.08 ( 12) Misc. bond : bond 0.00052 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 83 GLN cc_start: 0.8782 (tt0) cc_final: 0.8347 (tm-30) REVERT: F 290 GLU cc_start: 0.9198 (OUTLIER) cc_final: 0.8986 (mt-10) REVERT: E 44 GLU cc_start: 0.9240 (mt-10) cc_final: 0.8883 (mt-10) REVERT: E 86 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8560 (tm-30) REVERT: E 87 LYS cc_start: 0.9130 (ttpp) cc_final: 0.8922 (tmmt) REVERT: E 88 GLU cc_start: 0.8988 (tp30) cc_final: 0.8650 (tp30) REVERT: D 351 MET cc_start: 0.9374 (mtp) cc_final: 0.8939 (ptp) REVERT: D 486 ARG cc_start: 0.8498 (mmm-85) cc_final: 0.8183 (mmm-85) REVERT: D 804 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8379 (mp) REVERT: D 1086 LEU cc_start: 0.9244 (mp) cc_final: 0.9018 (mt) REVERT: D 1100 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.8286 (m-30) REVERT: C 33 ASP cc_start: 0.9235 (m-30) cc_final: 0.8850 (t0) REVERT: C 102 HIS cc_start: 0.8107 (m-70) cc_final: 0.7758 (m90) REVERT: C 104 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8107 (p0) REVERT: C 189 ARG cc_start: 0.8314 (ttm110) cc_final: 0.8022 (ttm110) REVERT: C 222 MET cc_start: 0.7292 (tpt) cc_final: 0.7012 (tpt) REVERT: C 390 GLN cc_start: 0.9210 (tt0) cc_final: 0.8472 (tp-100) REVERT: C 442 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8078 (tt0) REVERT: C 771 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8222 (tm-30) REVERT: C 816 LYS cc_start: 0.8734 (mtmm) cc_final: 0.8515 (mmmt) REVERT: A 91 ASN cc_start: 0.9101 (t0) cc_final: 0.8534 (t0) REVERT: B 72 LYS cc_start: 0.9457 (mttt) cc_final: 0.9113 (mmtp) REVERT: B 95 GLN cc_start: 0.8393 (tp40) cc_final: 0.7911 (mm-40) REVERT: B 201 THR cc_start: 0.9452 (OUTLIER) cc_final: 0.9112 (t) outliers start: 28 outliers final: 14 residues processed: 162 average time/residue: 0.8525 time to fit residues: 159.0694 Evaluate side-chains 154 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1131 SER Chi-restraints excluded: chain D residue 1452 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain B residue 201 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 112 optimal weight: 2.9990 chunk 315 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 334 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 278 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 187 optimal weight: 8.9990 chunk 29 optimal weight: 0.0470 chunk 226 optimal weight: 3.9990 overall best weight: 1.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 HIS B 163 ASN B 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.078758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.052438 restraints weight = 60612.752| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 2.60 r_work: 0.2607 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2471 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2481 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2481 r_free = 0.2481 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2481 r_free = 0.2481 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.2481 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29366 Z= 0.141 Angle : 0.489 9.456 40124 Z= 0.258 Chirality : 0.041 0.141 4520 Planarity : 0.004 0.043 4911 Dihedral : 15.355 133.400 4907 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.91 % Allowed : 10.04 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.15), residues: 3346 helix: 1.97 (0.15), residues: 1293 sheet: 0.48 (0.26), residues: 406 loop : 0.56 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 189 TYR 0.010 0.001 TYR D 989 PHE 0.011 0.001 PHE F 390 TRP 0.009 0.001 TRP A 200 HIS 0.005 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (29357) covalent geometry : angle 0.48790 / 0.26 (40112) hydrogen bonds : bond 0.03685 / 2.41 ( 1284) hydrogen bonds : angle 4.21035 / 3.03 ( 3555) metal coordination : bond 0.00521 / 0.35 ( 8) metal coordination : angle 1.80286 / 1.03 ( 12) Misc. bond : bond 0.00067 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 83 GLN cc_start: 0.8730 (tt0) cc_final: 0.8278 (tm-30) REVERT: F 290 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8711 (mt-10) REVERT: E 44 GLU cc_start: 0.9309 (mt-10) cc_final: 0.8929 (mt-10) REVERT: E 86 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8546 (tm-30) REVERT: E 88 GLU cc_start: 0.8960 (tp30) cc_final: 0.8608 (tp30) REVERT: E 90 GLU cc_start: 0.8470 (pp20) cc_final: 0.8251 (pp20) REVERT: D 351 MET cc_start: 0.9380 (mtp) cc_final: 0.8943 (ptp) REVERT: D 486 ARG cc_start: 0.8503 (mmm-85) cc_final: 0.8188 (mmm-85) REVERT: D 692 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8196 (mt-10) REVERT: D 804 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8366 (mp) REVERT: D 1100 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8290 (m-30) REVERT: C 33 ASP cc_start: 0.9265 (m-30) cc_final: 0.8850 (t0) REVERT: C 102 HIS cc_start: 0.8126 (m-70) cc_final: 0.7762 (m90) REVERT: C 104 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.8132 (p0) REVERT: C 222 MET cc_start: 0.7548 (tpt) cc_final: 0.6994 (tpt) REVERT: C 390 GLN cc_start: 0.9214 (tt0) cc_final: 0.8465 (tp-100) REVERT: C 442 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8085 (tt0) REVERT: C 771 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8209 (tm-30) REVERT: C 816 LYS cc_start: 0.8712 (mtmm) cc_final: 0.8489 (mmmt) REVERT: A 38 ASN cc_start: 0.8621 (t0) cc_final: 0.8409 (t0) REVERT: A 91 ASN cc_start: 0.9087 (t0) cc_final: 0.8493 (t0) REVERT: A 155 LYS cc_start: 0.8886 (mtpp) cc_final: 0.8618 (ttpt) REVERT: B 72 LYS cc_start: 0.9457 (mttt) cc_final: 0.9112 (mmtp) REVERT: B 95 GLN cc_start: 0.8429 (tp40) cc_final: 0.7951 (mm-40) REVERT: B 201 THR cc_start: 0.9463 (OUTLIER) cc_final: 0.9085 (t) REVERT: B 229 GLN cc_start: 0.7948 (mt0) cc_final: 0.7359 (mp10) outliers start: 26 outliers final: 16 residues processed: 160 average time/residue: 0.8347 time to fit residues: 153.9344 Evaluate side-chains 157 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1131 SER Chi-restraints excluded: chain D residue 1452 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain B residue 201 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 87 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 148 optimal weight: 0.3980 chunk 216 optimal weight: 4.9990 chunk 275 optimal weight: 0.9980 chunk 335 optimal weight: 20.0000 chunk 196 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 170 HIS D 388 HIS B 163 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.079561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.053105 restraints weight = 60346.133| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.63 r_work: 0.2630 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2493 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2504 r_free = 0.2504 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2504 r_free = 0.2504 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 29366 Z= 0.104 Angle : 0.481 8.661 40124 Z= 0.253 Chirality : 0.041 0.140 4520 Planarity : 0.004 0.058 4911 Dihedral : 15.298 133.456 4907 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.05 % Allowed : 10.04 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.15), residues: 3346 helix: 2.02 (0.15), residues: 1292 sheet: 0.52 (0.26), residues: 407 loop : 0.57 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 185 TYR 0.010 0.001 TYR D 989 PHE 0.027 0.001 PHE F 389 TRP 0.009 0.001 TRP B 200 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (29357) covalent geometry : angle 0.48007 / 0.25 (40112) hydrogen bonds : bond 0.03406 / 2.23 ( 1284) hydrogen bonds : angle 4.14022 / 2.98 ( 3555) metal coordination : bond 0.00294 / 0.19 ( 8) metal coordination : angle 1.61392 / 0.92 ( 12) Misc. bond : bond 0.00039 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 83 GLN cc_start: 0.8718 (tt0) cc_final: 0.8255 (tm-30) REVERT: F 110 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8461 (mpp) REVERT: F 290 GLU cc_start: 0.9181 (OUTLIER) cc_final: 0.8750 (mt-10) REVERT: F 367 MET cc_start: 0.9442 (mmm) cc_final: 0.9201 (tpp) REVERT: E 44 GLU cc_start: 0.9271 (mt-10) cc_final: 0.8907 (mt-10) REVERT: E 86 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8509 (tm-30) REVERT: E 88 GLU cc_start: 0.8948 (tp30) cc_final: 0.8667 (tp30) REVERT: E 90 GLU cc_start: 0.8455 (pp20) cc_final: 0.8169 (pp20) REVERT: D 65 ARG cc_start: 0.8093 (mmm-85) cc_final: 0.7370 (mmm-85) REVERT: D 351 MET cc_start: 0.9371 (mtp) cc_final: 0.8963 (ptp) REVERT: D 486 ARG cc_start: 0.8472 (mmm-85) cc_final: 0.8172 (mmm-85) REVERT: D 692 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8176 (mt-10) REVERT: D 804 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8381 (mp) REVERT: D 973 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7674 (tt0) REVERT: D 1100 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8278 (m-30) REVERT: C 33 ASP cc_start: 0.9243 (m-30) cc_final: 0.8845 (t0) REVERT: C 102 HIS cc_start: 0.8159 (m-70) cc_final: 0.7805 (m90) REVERT: C 104 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8118 (p0) REVERT: C 219 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8350 (mp10) REVERT: C 222 MET cc_start: 0.6980 (tpt) cc_final: 0.6699 (tpt) REVERT: C 390 GLN cc_start: 0.9209 (tt0) cc_final: 0.8495 (tp-100) REVERT: C 442 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8061 (tt0) REVERT: C 771 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8163 (tm-30) REVERT: C 816 LYS cc_start: 0.8708 (mtmm) cc_final: 0.8497 (mmmt) REVERT: A 91 ASN cc_start: 0.9087 (t0) cc_final: 0.8505 (t0) REVERT: A 155 LYS cc_start: 0.8868 (mtpp) cc_final: 0.8602 (ttpt) REVERT: B 72 LYS cc_start: 0.9463 (mttt) cc_final: 0.9100 (mmtp) REVERT: B 95 GLN cc_start: 0.8460 (tp40) cc_final: 0.8005 (mm-40) REVERT: B 201 THR cc_start: 0.9431 (OUTLIER) cc_final: 0.9087 (t) REVERT: B 229 GLN cc_start: 0.7979 (mt0) cc_final: 0.7329 (mp10) outliers start: 30 outliers final: 17 residues processed: 164 average time/residue: 0.8061 time to fit residues: 152.1509 Evaluate side-chains 158 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 390 PHE Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 973 GLN Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1131 SER Chi-restraints excluded: chain D residue 1452 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain B residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 116 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 148 optimal weight: 0.4980 chunk 310 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 275 optimal weight: 0.8980 chunk 235 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.079615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.052865 restraints weight = 60372.164| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 2.67 r_work: 0.2628 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2492 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2501 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2501 r_free = 0.2501 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2501 r_free = 0.2501 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (15 function evaluations) r_final: 0.2501 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29366 Z= 0.110 Angle : 0.481 8.901 40124 Z= 0.254 Chirality : 0.041 0.139 4520 Planarity : 0.004 0.060 4911 Dihedral : 15.259 133.494 4907 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.91 % Allowed : 10.35 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.15), residues: 3346 helix: 2.03 (0.15), residues: 1298 sheet: 0.53 (0.26), residues: 407 loop : 0.60 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 189 TYR 0.010 0.001 TYR D 989 PHE 0.009 0.001 PHE D 68 TRP 0.009 0.001 TRP B 200 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (29357) covalent geometry : angle 0.48035 / 0.25 (40112) hydrogen bonds : bond 0.03406 / 2.23 ( 1284) hydrogen bonds : angle 4.10588 / 2.96 ( 3555) metal coordination : bond 0.00339 / 0.22 ( 8) metal coordination : angle 1.57417 / 0.89 ( 12) Misc. bond : bond 0.00042 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 83 GLN cc_start: 0.8755 (tt0) cc_final: 0.8257 (tm-30) REVERT: F 110 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.8473 (mpp) REVERT: F 290 GLU cc_start: 0.9178 (OUTLIER) cc_final: 0.8756 (mt-10) REVERT: F 367 MET cc_start: 0.9442 (mmm) cc_final: 0.9228 (tpp) REVERT: E 44 GLU cc_start: 0.9281 (mt-10) cc_final: 0.8919 (mt-10) REVERT: E 86 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8477 (tm-30) REVERT: E 88 GLU cc_start: 0.8952 (tp30) cc_final: 0.8666 (tp30) REVERT: E 90 GLU cc_start: 0.8481 (pp20) cc_final: 0.8189 (pp20) REVERT: D 65 ARG cc_start: 0.8110 (mmm-85) cc_final: 0.7480 (mmm-85) REVERT: D 351 MET cc_start: 0.9377 (mtp) cc_final: 0.8975 (ptp) REVERT: D 486 ARG cc_start: 0.8485 (mmm-85) cc_final: 0.8186 (mmm-85) REVERT: D 804 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8385 (mp) REVERT: D 987 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8582 (pt0) REVERT: D 1100 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8347 (m-30) REVERT: C 33 ASP cc_start: 0.9245 (m-30) cc_final: 0.8845 (t0) REVERT: C 102 HIS cc_start: 0.8181 (m-70) cc_final: 0.7829 (m90) REVERT: C 104 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8147 (p0) REVERT: C 219 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8318 (mp10) REVERT: C 222 MET cc_start: 0.7141 (tpt) cc_final: 0.6934 (tpt) REVERT: C 284 ARG cc_start: 0.8392 (mpp-170) cc_final: 0.8166 (mpp-170) REVERT: C 390 GLN cc_start: 0.9144 (tt0) cc_final: 0.8411 (tp-100) REVERT: C 442 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8045 (tt0) REVERT: C 771 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8166 (tm-30) REVERT: C 816 LYS cc_start: 0.8722 (mtmm) cc_final: 0.8501 (mmmt) REVERT: A 91 ASN cc_start: 0.9094 (t0) cc_final: 0.8508 (t0) REVERT: A 155 LYS cc_start: 0.8886 (mtpp) cc_final: 0.8627 (ttpt) REVERT: B 72 LYS cc_start: 0.9468 (mttt) cc_final: 0.9103 (mmtp) REVERT: B 95 GLN cc_start: 0.8478 (tp40) cc_final: 0.8025 (mm-40) REVERT: B 140 MET cc_start: 0.9393 (mtm) cc_final: 0.9172 (mmm) REVERT: B 229 GLN cc_start: 0.8002 (mt0) cc_final: 0.7361 (mp10) outliers start: 26 outliers final: 15 residues processed: 156 average time/residue: 0.7928 time to fit residues: 142.7921 Evaluate side-chains 155 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 987 GLU Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1131 SER Chi-restraints excluded: chain D residue 1452 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain A residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 179 optimal weight: 0.0020 chunk 293 optimal weight: 0.2980 chunk 190 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 203 optimal weight: 2.9990 chunk 217 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 855 HIS B 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.079537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.053331 restraints weight = 60937.982| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.63 r_work: 0.2631 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2492 r_free = 0.2492 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2492 r_free = 0.2492 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 29366 Z= 0.101 Angle : 0.479 8.599 40124 Z= 0.252 Chirality : 0.041 0.229 4520 Planarity : 0.004 0.061 4911 Dihedral : 15.211 133.438 4907 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.84 % Allowed : 10.53 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.15), residues: 3346 helix: 2.06 (0.15), residues: 1298 sheet: 0.58 (0.26), residues: 407 loop : 0.62 (0.16), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 189 TYR 0.010 0.001 TYR D 989 PHE 0.033 0.001 PHE F 389 TRP 0.010 0.001 TRP B 200 HIS 0.006 0.001 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (29357) covalent geometry : angle 0.47821 / 0.25 (40112) hydrogen bonds : bond 0.03262 / 2.13 ( 1284) hydrogen bonds : angle 4.07202 / 2.93 ( 3555) metal coordination : bond 0.00262 / 0.17 ( 8) metal coordination : angle 1.55602 / 0.89 ( 12) Misc. bond : bond 0.00033 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9753.70 seconds wall clock time: 166 minutes 32.94 seconds (9992.94 seconds total)