Starting phenix.real_space_refine on Sat Feb 7 00:04:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ujl_64216/02_2026/9ujl_64216.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ujl_64216/02_2026/9ujl_64216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ujl_64216/02_2026/9ujl_64216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ujl_64216/02_2026/9ujl_64216.map" model { file = "/net/cci-nas-00/data/ceres_data/9ujl_64216/02_2026/9ujl_64216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ujl_64216/02_2026/9ujl_64216.cif" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.029 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 89 5.49 5 Mg 3 5.21 5 S 70 5.16 5 C 17728 2.51 5 N 5058 2.21 5 O 5492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28442 Number of models: 1 Model: "" Number of chains: 12 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: 10719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1358, 10719 Classifications: {'peptide': 1358} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1289} Chain breaks: 2 Chain: "G" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 881 Classifications: {'DNA': 43} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 42} Chain breaks: 1 Chain: "F" Number of atoms: 2726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2726 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 13, 'TRANS': 322} Chain breaks: 1 Chain: "E" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 754 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain: "C" Number of atoms: 8783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1113, 8783 Classifications: {'peptide': 1113} Link IDs: {'PCIS': 1, 'PTRANS': 71, 'TRANS': 1040} Chain breaks: 1 Chain: "A" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1781 Classifications: {'peptide': 226} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 211} Chain: "B" Number of atoms: 1776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1776 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 210} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 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 8812 SG CYS D1112 22.526 60.863 119.744 1.00 46.98 S ATOM 9456 SG CYS D1194 26.270 60.909 118.814 1.00 34.16 S ATOM 9512 SG CYS D1201 24.762 62.576 121.977 1.00 40.42 S ATOM 9536 SG CYS D1204 25.277 59.122 122.005 1.00 55.94 S ATOM 1456 SG CYS D 58 54.917 105.337 83.229 1.00 85.75 S ATOM 1467 SG CYS D 60 56.155 105.452 79.955 1.00 89.43 S ATOM 1578 SG CYS D 73 52.902 105.878 79.625 1.00 83.60 S ATOM 1604 SG CYS D 76 54.570 102.596 80.252 1.00 71.84 S Time building chain proxies: 6.00, per 1000 atoms: 0.21 Number of scatterers: 28442 At special positions: 0 Unit cell: (131.61, 158.36, 207.58, 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 89 15.00 Mg 3 11.99 O 5492 8.00 N 5058 7.00 C 17728 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1601 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1112 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1194 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1201 " pdb="ZN ZN D1601 " - pdb=" SG CYS D1204 " pdb=" ZN D1602 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 73 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 60 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 58 " pdb="ZN ZN D1602 " - pdb=" SG CYS D 76 " Number of angles added : 12 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6204 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 50 sheets defined 43.7% alpha, 17.5% beta 31 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 4.16 Creating SS restraints... Processing helix chain 'D' and resid 14 through 22 Processing helix chain 'D' and resid 46 through 51 Processing helix chain 'D' and resid 65 through 69 removed outlier: 3.506A pdb=" N PHE D 68 " --> pdb=" O ARG D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 88 removed outlier: 3.540A pdb=" N VAL D 85 " --> pdb=" O LYS D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.649A pdb=" N ASP D 107 " --> pdb=" O TRP D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 117 Processing helix chain 'D' and resid 119 through 128 Processing helix chain 'D' and resid 154 through 164 Processing helix chain 'D' and resid 423 through 426 removed outlier: 3.573A pdb=" N LYS D 426 " --> pdb=" O ASP D 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 423 through 426' Processing helix chain 'D' and resid 456 through 468 removed outlier: 3.832A 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: 4.259A pdb=" N ASP D 542 " --> pdb=" O SER D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 583 Processing helix chain 'D' and resid 602 through 608 Processing helix chain 'D' and resid 612 through 618 Processing helix chain 'D' and resid 646 through 653 Processing helix chain 'D' and resid 653 through 664 Processing helix chain 'D' and resid 669 through 679 removed outlier: 4.046A 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: 3.959A 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: 3.553A pdb=" N ILE D 792 " --> pdb=" O GLY D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 808 through 818 Processing helix chain 'D' and resid 835 through 841 removed outlier: 3.527A pdb=" N LEU D 839 " --> pdb=" O SER D 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 855 Processing helix chain 'D' and resid 876 through 891 Processing helix chain 'D' and resid 892 through 900 removed outlier: 3.533A 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: 3.570A pdb=" N THR D 944 " --> pdb=" O THR D 940 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLY D 946 " --> pdb=" O SER D 942 " (cutoff:3.500A) Processing helix chain 'D' and resid 950 through 954 Processing helix chain 'D' and resid 958 through 980 removed outlier: 4.161A 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: 3.741A pdb=" N HIS D1075 " --> pdb=" O PHE D1071 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLY D1076 " --> pdb=" O ILE D1072 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA D1089 " --> pdb=" O ALA D1085 " (cutoff:3.500A) removed outlier: 4.034A 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 1190 through 1194 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 1234 No H-bonds generated for 'chain 'D' and resid 1232 through 1234' Processing helix chain 'D' and resid 1255 through 1264 Processing helix chain 'D' and resid 1331 through 1339 Processing helix chain 'D' and resid 1340 through 1359 removed outlier: 3.824A pdb=" N VAL D1355 " --> pdb=" O GLU D1351 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR D1356 " --> pdb=" O ILE D1352 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN D1359 " --> pdb=" O VAL D1355 " (cutoff:3.500A) Processing helix chain 'D' and resid 1364 through 1376 removed outlier: 4.180A pdb=" N ILE D1368 " --> pdb=" O HIS D1364 " (cutoff:3.500A) Processing helix chain 'D' and resid 1397 through 1410 Processing helix chain 'D' and resid 1423 through 1430 Processing helix chain 'D' and resid 1433 through 1441 removed outlier: 3.570A pdb=" N GLN D1441 " --> pdb=" O ALA D1437 " (cutoff:3.500A) Processing helix chain 'D' and resid 1442 through 1454 Processing helix chain 'D' and resid 1461 through 1468 removed outlier: 4.262A pdb=" N ASN D1465 " --> pdb=" O GLY D1461 " (cutoff:3.500A) Processing helix chain 'D' and resid 1474 through 1478 Processing helix chain 'D' and resid 1489 through 1496 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: 4.326A pdb=" N TYR F 173 " --> pdb=" O GLU F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 200 removed outlier: 3.659A pdb=" N VAL F 195 " --> pdb=" O ASN F 191 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL F 196 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 227 Processing helix chain 'F' and resid 228 through 232 removed outlier: 3.745A pdb=" N ARG F 231 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 255 removed outlier: 3.668A pdb=" N TYR F 238 " --> pdb=" O LYS F 234 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TRP F 241 " --> pdb=" O THR F 237 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TRP F 242 " --> pdb=" O TYR F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 283 Processing helix chain 'F' and resid 287 through 296 Processing helix chain 'F' and resid 300 through 311 Processing helix chain 'F' and resid 328 through 333 removed outlier: 3.801A pdb=" N ILE F 333 " --> pdb=" O GLY F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 360 removed outlier: 4.092A pdb=" N LYS F 360 " --> pdb=" O LYS F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 373 removed outlier: 3.541A pdb=" N MET F 367 " --> pdb=" O GLU F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 391 Processing helix chain 'F' and resid 393 through 416 removed outlier: 3.886A pdb=" N ILE F 397 " --> pdb=" O THR F 393 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG F 398 " --> pdb=" O ARG F 394 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN F 399 " --> pdb=" O GLU F 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 12 Processing helix chain 'E' and resid 15 through 33 removed outlier: 3.504A pdb=" N LEU E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 71 removed outlier: 3.679A pdb=" N GLY E 71 " --> pdb=" O GLU E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 93 Processing helix chain 'C' and resid 19 through 31 removed outlier: 4.163A pdb=" N SER C 25 " --> pdb=" O ILE C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 39 Processing helix chain 'C' and resid 43 through 52 Processing helix chain 'C' and resid 79 through 86 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 203 through 212 Processing helix chain 'C' and resid 215 through 220 removed outlier: 4.291A pdb=" N GLN C 219 " --> pdb=" O GLY C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 228 removed outlier: 3.818A pdb=" N PHE C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 3.924A 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: 3.734A pdb=" N SER C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 408 removed outlier: 3.628A pdb=" N ARG C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 429 removed outlier: 3.707A pdb=" N ARG C 428 " --> pdb=" O GLY C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 435 removed outlier: 3.644A pdb=" N TYR C 435 " --> pdb=" O ARG C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 525 through 529 Processing helix chain 'C' and resid 535 through 540 Processing helix chain 'C' and resid 543 through 547 Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 554 through 567 removed outlier: 3.799A pdb=" N MET C 560 " --> pdb=" O ASN C 556 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR C 566 " --> pdb=" O SER C 562 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN C 567 " --> pdb=" O ASN C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 591 removed outlier: 3.523A pdb=" N VAL C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 687 removed outlier: 3.825A 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 872 through 876 Processing helix chain 'C' and resid 882 through 898 removed outlier: 3.531A pdb=" N PHE C 896 " --> pdb=" O LEU C 892 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 933 removed outlier: 4.166A pdb=" N ARG C 929 " --> pdb=" O TYR C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 950 removed outlier: 3.579A pdb=" N LYS C 949 " --> pdb=" O ARG C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 969 Processing helix chain 'C' and resid 1000 through 1004 Processing helix chain 'C' and resid 1033 through 1044 Processing helix chain 'C' and resid 1045 through 1054 Processing helix chain 'C' and resid 1059 through 1072 Processing helix chain 'C' and resid 1082 through 1094 removed outlier: 3.634A 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 removed outlier: 3.545A pdb=" N HIS A 156 " --> pdb=" O PRO A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 223 Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'B' and resid 31 through 47 Proline residue: B 39 - end of helix Processing helix chain 'B' and resid 74 through 83 Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 206 through 223 removed outlier: 3.560A pdb=" N THR B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 1456 through 1457 Processing sheet with id=AA2, first strand: chain 'D' and resid 71 through 72 removed outlier: 4.230A pdb=" N LYS D 71 " --> pdb=" O VAL D 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 91 through 100 removed outlier: 10.165A pdb=" N LEU D 95 " --> pdb=" O PRO D 518 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N THR D 97 " --> pdb=" O ALA D 516 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ALA D 516 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 152 through 153 removed outlier: 6.753A pdb=" N ASP D 453 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AA6, first strand: chain 'D' and resid 166 through 170 removed outlier: 3.688A pdb=" N GLU D 183 " --> pdb=" O ALA D 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 342 through 346 removed outlier: 6.849A pdb=" N GLU D 389 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL D 211 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU D 387 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL D 213 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL D 385 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TYR D 215 " --> pdb=" O GLY D 383 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLY D 383 " --> pdb=" O TYR D 215 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA D 359 " --> pdb=" O VAL D 385 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 353 removed outlier: 6.928A pdb=" N VAL D 377 " --> pdb=" O ILE D 367 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 398 through 402 Processing sheet with id=AB1, first strand: chain 'D' and resid 420 through 422 removed outlier: 7.036A pdb=" N VAL D 427 " --> pdb=" O LEU D 421 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 527 through 529 removed outlier: 6.529A pdb=" N PHE D 535 " --> pdb=" O VAL F 315 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 621 through 623 removed outlier: 3.697A pdb=" N GLN C1030 " --> pdb=" O VAL D 623 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 626 through 633 removed outlier: 6.299A 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: 6.187A pdb=" N LEU D 644 " --> pdb=" O VAL D 721 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 827 through 828 Processing sheet with id=AB6, first strand: chain 'D' and resid 842 through 843 Processing sheet with id=AB7, first strand: chain 'D' and resid 1106 through 1109 Processing sheet with id=AB8, first strand: chain 'D' and resid 1118 through 1121 Processing sheet with id=AB9, first strand: chain 'D' and resid 1123 through 1126 Processing sheet with id=AC1, first strand: chain 'D' and resid 1153 through 1155 Processing sheet with id=AC2, first strand: chain 'D' and resid 1300 through 1303 Processing sheet with id=AC3, first strand: chain 'D' and resid 1394 through 1396 removed outlier: 6.763A pdb=" N ALA D1416 " --> pdb=" O THR D1382 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 1485 through 1488 Processing sheet with id=AC5, first strand: chain 'E' and resid 47 through 49 Processing sheet with id=AC6, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AC7, first strand: chain 'C' and resid 54 through 55 removed outlier: 5.542A pdb=" N LEU C 66 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ILE C 101 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N PHE C 68 " --> pdb=" O GLN C 99 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN C 99 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU C 70 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY C 116 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA C 96 " --> pdb=" O PHE C 114 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N PHE C 114 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU C 98 " --> pdb=" O GLU C 112 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU C 112 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LEU C 100 " --> pdb=" O GLU C 110 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N GLU C 110 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N HIS C 102 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE C 108 " --> pdb=" O HIS C 102 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AC9, first strand: chain 'C' and resid 331 through 334 removed outlier: 6.348A pdb=" N SER C 138 " --> pdb=" O SER C 411 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 145 through 150 removed outlier: 6.810A pdb=" N TYR C 158 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL C 176 " --> pdb=" O TYR C 158 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 291 through 294 Processing sheet with id=AD3, first strand: chain 'C' and resid 460 through 461 removed outlier: 5.455A pdb=" N GLU C 482 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N VAL C 475 " --> pdb=" O THR C 480 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR C 480 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 460 through 461 removed outlier: 3.546A pdb=" N ASP C 533 " --> pdb=" O ALA C 497 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 503 through 504 removed outlier: 3.649A pdb=" N ARG C 507 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 595 through 596 removed outlier: 6.522A pdb=" N LEU C 595 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 620 through 624 removed outlier: 6.778A pdb=" N ARG C 610 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL C 606 " --> pdb=" O ARG C 610 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL C 612 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 629 through 630 Processing sheet with id=AD9, first strand: chain 'C' and resid 661 through 662 Processing sheet with id=AE1, first strand: chain 'C' and resid 971 through 972 removed outlier: 7.169A pdb=" N ILE C 688 " --> pdb=" O ALA C 850 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE C 852 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE C 690 " --> pdb=" O ILE C 852 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 689 " --> pdb=" O ILE C 870 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N VAL C 869 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU C 673 " --> pdb=" O VAL C 869 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU C 871 " --> pdb=" O LEU C 673 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ALA C 675 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL C 988 " --> pdb=" O ILE C 676 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 718 through 719 removed outlier: 6.409A pdb=" N ASP C 714 " --> pdb=" O VAL C 819 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL C 819 " --> pdb=" O ASP C 714 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG C 802 " --> pdb=" O TYR C 826 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA C 828 " --> pdb=" O VAL C 800 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N VAL C 800 " --> pdb=" O ALA C 828 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N LYS C 830 " --> pdb=" O GLY C 798 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N GLY C 798 " --> pdb=" O LYS C 830 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 721 through 722 Processing sheet with id=AE4, first strand: chain 'C' and resid 754 through 756 removed outlier: 6.730A pdb=" N LEU C 790 " --> pdb=" O LEU C 755 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 10 through 16 removed outlier: 3.565A pdb=" N TYR A 20 " --> pdb=" O GLN A 16 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ASP A 193 " --> pdb=" O PRO A 27 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N THR A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU A 186 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 192 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR A 184 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 96 through 104 removed outlier: 7.292A pdb=" N ASN A 139 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE A 58 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLU A 141 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL A 56 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ARG A 143 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AE8, first strand: chain 'A' and resid 107 through 110 Processing sheet with id=AE9, first strand: chain 'A' and resid 150 through 151 Processing sheet with id=AF1, first strand: chain 'B' and resid 10 through 16 removed outlier: 3.677A pdb=" N TYR B 20 " --> pdb=" O GLN B 16 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASP B 193 " --> pdb=" O PRO B 27 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N THR B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU B 186 " --> pdb=" O THR B 190 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 97 through 104 removed outlier: 3.637A pdb=" N SER B 55 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP B 145 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N VAL B 53 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLY B 147 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR B 51 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 87 through 89 Processing sheet with id=AF4, first strand: chain 'B' and resid 108 through 110 removed outlier: 6.841A pdb=" N VAL B 109 " --> pdb=" O ILE B 129 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 150 through 151 1238 hydrogen bonds defined for protein. 3453 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 73 hydrogen bonds 146 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 8.10 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4696 1.31 - 1.44: 7460 1.44 - 1.56: 16675 1.56 - 1.69: 179 1.69 - 1.82: 127 Bond restraints: 29137 Sorted by residual: bond pdb=" C23 1N7 B 401 " pdb=" C24 1N7 B 401 " ideal model delta sigma weight residual 1.512 1.573 -0.061 2.00e-02 2.50e+03 9.41e+00 bond pdb=" C ASN D 703 " pdb=" O ASN D 703 " ideal model delta sigma weight residual 1.234 1.205 0.030 1.11e-02 8.12e+03 7.18e+00 bond pdb=" C GLN C1100 " pdb=" O GLN C1100 " ideal model delta sigma weight residual 1.235 1.206 0.029 1.22e-02 6.72e+03 5.67e+00 bond pdb=" CA ASN D 703 " pdb=" C ASN D 703 " ideal model delta sigma weight residual 1.520 1.492 0.028 1.20e-02 6.94e+03 5.60e+00 bond pdb=" C ASN D 703 " pdb=" N ARG D 704 " ideal model delta sigma weight residual 1.331 1.300 0.031 1.34e-02 5.57e+03 5.25e+00 ... (remaining 29132 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 38428 1.19 - 2.39: 1060 2.39 - 3.58: 252 3.58 - 4.78: 48 4.78 - 5.97: 10 Bond angle restraints: 39798 Sorted by residual: angle pdb=" C ASN A 227 " pdb=" CA ASN A 227 " pdb=" CB ASN A 227 " ideal model delta sigma weight residual 110.17 113.42 -3.25 9.90e-01 1.02e+00 1.08e+01 angle pdb=" CA ASN A 227 " pdb=" C ASN A 227 " pdb=" O ASN A 227 " ideal model delta sigma weight residual 119.36 121.95 -2.59 8.40e-01 1.42e+00 9.48e+00 angle pdb=" CA TYR D1207 " pdb=" CB TYR D1207 " pdb=" CG TYR D1207 " ideal model delta sigma weight residual 113.90 119.40 -5.50 1.80e+00 3.09e-01 9.34e+00 angle pdb=" N SER C1009 " pdb=" CA SER C1009 " pdb=" C SER C1009 " ideal model delta sigma weight residual 111.56 107.41 4.15 1.53e+00 4.27e-01 7.34e+00 angle pdb=" CB ARG D 546 " pdb=" CG ARG D 546 " pdb=" CD ARG D 546 " ideal model delta sigma weight residual 111.30 105.33 5.97 2.30e+00 1.89e-01 6.74e+00 ... (remaining 39793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 16061 17.96 - 35.92: 1133 35.92 - 53.89: 399 53.89 - 71.85: 124 71.85 - 89.81: 22 Dihedral angle restraints: 17739 sinusoidal: 8099 harmonic: 9640 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 180.00 150.81 29.19 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA SER D 782 " pdb=" C SER D 782 " pdb=" N ARG D 783 " pdb=" CA ARG D 783 " ideal model delta harmonic sigma weight residual 180.00 -162.76 -17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA ASP D 685 " pdb=" CB ASP D 685 " pdb=" CG ASP D 685 " pdb=" OD1 ASP D 685 " ideal model delta sinusoidal sigma weight residual -30.00 -88.65 58.65 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 17736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2819 0.034 - 0.067: 1135 0.067 - 0.101: 358 0.101 - 0.134: 163 0.134 - 0.168: 12 Chirality restraints: 4487 Sorted by residual: chirality pdb=" CB VAL D 354 " pdb=" CA VAL D 354 " pdb=" CG1 VAL D 354 " pdb=" CG2 VAL D 354 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.03e-01 chirality pdb=" CA ILE D 956 " pdb=" N ILE D 956 " pdb=" C ILE D 956 " pdb=" CB ILE D 956 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.41e-01 chirality pdb=" C20 1N7 B 401 " pdb=" C21 1N7 B 401 " pdb=" C22 1N7 B 401 " pdb=" C9 1N7 B 401 " both_signs ideal model delta sigma weight residual False 2.59 2.73 -0.14 2.00e-01 2.50e+01 5.25e-01 ... (remaining 4484 not shown) Planarity restraints: 4886 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D1207 " 0.023 2.00e-02 2.50e+03 1.85e-02 6.82e+00 pdb=" CG TYR D1207 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR D1207 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D1207 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR D1207 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR D1207 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR D1207 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR D1207 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 546 " 0.207 9.50e-02 1.11e+02 9.29e-02 5.65e+00 pdb=" NE ARG D 546 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG D 546 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG D 546 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 546 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D1093 " 0.014 2.00e-02 2.50e+03 1.20e-02 2.90e+00 pdb=" CG TYR D1093 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR D1093 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR D1093 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR D1093 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D1093 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR D1093 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR D1093 " 0.000 2.00e-02 2.50e+03 ... (remaining 4883 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 232 2.61 - 3.19: 23343 3.19 - 3.76: 43504 3.76 - 4.33: 64455 4.33 - 4.90: 105110 Nonbonded interactions: 236644 Sorted by model distance: nonbonded pdb=" OD1 ASP D 741 " pdb="MG MG D1603 " model vdw 2.043 2.170 nonbonded pdb="MG MG D1603 " pdb=" O HOH D1701 " model vdw 2.058 2.170 nonbonded pdb=" OD1 ASP D 743 " pdb="MG MG D1603 " model vdw 2.075 2.170 nonbonded pdb=" OD1 ASP D 739 " pdb="MG MG D1603 " model vdw 2.090 2.170 nonbonded pdb=" NH1 ARG D 65 " pdb=" O GLY F 378 " model vdw 2.202 3.120 ... (remaining 236639 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 5 through 229) selection = (chain 'B' and resid 5 through 229) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.05 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 35.360 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 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 : 0.004 0.061 29145 Z= 0.173 Angle : 0.564 19.180 39810 Z= 0.285 Chirality : 0.043 0.168 4487 Planarity : 0.004 0.093 4886 Dihedral : 14.976 89.811 11535 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: 0.84 (0.14), residues: 3331 helix: 1.06 (0.14), residues: 1276 sheet: 0.56 (0.25), residues: 430 loop : 0.29 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 546 TYR 0.043 0.002 TYR D1207 PHE 0.026 0.002 PHE C 699 TRP 0.027 0.002 TRP D1398 HIS 0.011 0.001 HIS C 434 Details of bonding type rmsd covalent geometry : bond 0.00408 (29137) covalent geometry : angle 0.52569 (39798) hydrogen bonds : bond 0.20519 ( 1309) hydrogen bonds : angle 6.93225 ( 3599) metal coordination : bond 0.01814 ( 8) metal coordination : angle 11.77995 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 361 VAL cc_start: 0.8659 (t) cc_final: 0.8172 (m) REVERT: D 594 PRO cc_start: 0.8433 (Cg_exo) cc_final: 0.8201 (Cg_endo) REVERT: E 44 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8574 (mt-10) REVERT: C 775 ARG cc_start: 0.8714 (mmt180) cc_final: 0.8381 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 1.1067 time to fit residues: 428.5436 Evaluate side-chains 175 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 197 optimal weight: 0.0870 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.0060 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.9980 overall best weight: 1.0178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 762 GLN D 901 GLN D 976 GLN D1441 GLN ** C 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 GLN C 670 GLN A 180 GLN B 139 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.089730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.060046 restraints weight = 52112.377| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.38 r_work: 0.2720 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2613 r_free = 0.2613 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2613 r_free = 0.2613 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29145 Z= 0.141 Angle : 0.542 8.006 39810 Z= 0.289 Chirality : 0.042 0.146 4487 Planarity : 0.005 0.045 4886 Dihedral : 15.437 76.168 4793 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.98 % Allowed : 6.62 % Favored : 92.40 % 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: 3331 helix: 1.55 (0.14), residues: 1307 sheet: 0.58 (0.26), residues: 414 loop : 0.40 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D1133 TYR 0.019 0.001 TYR D1093 PHE 0.011 0.001 PHE A 179 TRP 0.011 0.001 TRP B 200 HIS 0.007 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00324 (29137) covalent geometry : angle 0.53958 (39798) hydrogen bonds : bond 0.04847 ( 1309) hydrogen bonds : angle 4.78798 ( 3599) metal coordination : bond 0.00551 ( 8) metal coordination : angle 2.84752 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 346 ARG cc_start: 0.8150 (tpp-160) cc_final: 0.7822 (tpp-160) REVERT: D 351 MET cc_start: 0.9034 (mtp) cc_final: 0.8736 (ptp) REVERT: D 486 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7703 (mpp-170) REVERT: D 594 PRO cc_start: 0.8973 (Cg_exo) cc_final: 0.8748 (Cg_endo) REVERT: F 129 GLU cc_start: 0.8648 (tp30) cc_final: 0.8403 (tp30) REVERT: F 179 GLU cc_start: 0.8982 (tp30) cc_final: 0.8520 (tp30) REVERT: F 248 ASN cc_start: 0.8829 (OUTLIER) cc_final: 0.8516 (m110) REVERT: F 402 ASN cc_start: 0.8935 (m-40) cc_final: 0.8455 (m110) REVERT: F 410 TYR cc_start: 0.8790 (t80) cc_final: 0.8492 (t80) REVERT: E 43 GLU cc_start: 0.8883 (pm20) cc_final: 0.8645 (pm20) REVERT: E 44 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8305 (mt-10) REVERT: E 67 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8863 (mt-10) REVERT: C 1061 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7787 (pm20) REVERT: C 1091 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8314 (mt-10) REVERT: A 133 GLU cc_start: 0.8400 (tt0) cc_final: 0.8187 (tt0) REVERT: B 72 LYS cc_start: 0.9139 (mtpm) cc_final: 0.8676 (mttm) REVERT: B 91 ASN cc_start: 0.8746 (t0) cc_final: 0.8423 (t0) outliers start: 28 outliers final: 5 residues processed: 202 average time/residue: 0.9477 time to fit residues: 216.9171 Evaluate side-chains 176 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 167 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 486 ARG Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 1061 GLU Chi-restraints excluded: chain C residue 1091 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 301 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 207 optimal weight: 3.9990 chunk 290 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 109 optimal weight: 0.3980 chunk 155 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 254 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 GLN B 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.088813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.059090 restraints weight = 52580.001| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 2.39 r_work: 0.2702 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29145 Z= 0.148 Angle : 0.500 6.799 39810 Z= 0.265 Chirality : 0.042 0.146 4487 Planarity : 0.004 0.042 4886 Dihedral : 15.490 84.152 4793 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.98 % Allowed : 7.98 % Favored : 91.04 % 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: 1.36 (0.15), residues: 3331 helix: 1.74 (0.14), residues: 1308 sheet: 0.49 (0.25), residues: 412 loop : 0.45 (0.16), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 30 TYR 0.016 0.001 TYR D1093 PHE 0.014 0.001 PHE C 227 TRP 0.011 0.001 TRP B 200 HIS 0.006 0.001 HIS C 434 Details of bonding type rmsd covalent geometry : bond 0.00349 (29137) covalent geometry : angle 0.49832 (39798) hydrogen bonds : bond 0.04342 ( 1309) hydrogen bonds : angle 4.47589 ( 3599) metal coordination : bond 0.00555 ( 8) metal coordination : angle 2.23947 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 1.137 Fit side-chains revert: symmetry clash REVERT: D 346 ARG cc_start: 0.8175 (tpp-160) cc_final: 0.7886 (tpp-160) REVERT: D 386 HIS cc_start: 0.7560 (m-70) cc_final: 0.7293 (m90) REVERT: D 486 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7717 (mpp-170) REVERT: D 594 PRO cc_start: 0.9042 (Cg_exo) cc_final: 0.8831 (Cg_endo) REVERT: D 1310 ARG cc_start: 0.8234 (mtp85) cc_final: 0.7853 (mtm-85) REVERT: F 129 GLU cc_start: 0.8685 (tp30) cc_final: 0.8238 (tp30) REVERT: F 179 GLU cc_start: 0.9041 (tp30) cc_final: 0.8537 (tp30) REVERT: F 248 ASN cc_start: 0.8844 (t0) cc_final: 0.8537 (m110) REVERT: F 306 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8161 (mm-30) REVERT: F 402 ASN cc_start: 0.8952 (m-40) cc_final: 0.8474 (m110) REVERT: F 410 TYR cc_start: 0.8798 (t80) cc_final: 0.8514 (t80) REVERT: E 43 GLU cc_start: 0.8948 (pm20) cc_final: 0.8671 (pm20) REVERT: E 44 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8338 (mt-10) REVERT: E 67 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8919 (mt-10) REVERT: E 88 GLU cc_start: 0.8377 (tp30) cc_final: 0.8018 (tp30) REVERT: C 390 GLN cc_start: 0.8905 (tt0) cc_final: 0.8018 (tm-30) REVERT: C 820 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7425 (mtm-85) REVERT: C 1061 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7931 (pm20) REVERT: C 1091 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8343 (mt-10) REVERT: A 133 GLU cc_start: 0.8421 (tt0) cc_final: 0.8219 (tt0) REVERT: B 91 ASN cc_start: 0.8729 (t0) cc_final: 0.8346 (t0) outliers start: 28 outliers final: 10 residues processed: 204 average time/residue: 0.9124 time to fit residues: 210.7535 Evaluate side-chains 178 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 486 ARG Chi-restraints excluded: chain D residue 980 MET Chi-restraints excluded: chain D residue 1452 ILE Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 820 ARG Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 1061 GLU Chi-restraints excluded: chain C residue 1091 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 233 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 200 optimal weight: 7.9990 chunk 319 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 336 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS B 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.088589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.058869 restraints weight = 52377.816| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.39 r_work: 0.2698 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29145 Z= 0.143 Angle : 0.491 7.274 39810 Z= 0.259 Chirality : 0.042 0.143 4487 Planarity : 0.004 0.042 4886 Dihedral : 15.428 85.030 4793 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.26 % Allowed : 8.79 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.15), residues: 3331 helix: 1.84 (0.14), residues: 1308 sheet: 0.50 (0.26), residues: 404 loop : 0.46 (0.16), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 414 TYR 0.014 0.001 TYR D1093 PHE 0.011 0.001 PHE D 68 TRP 0.012 0.001 TRP B 200 HIS 0.005 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00338 (29137) covalent geometry : angle 0.48965 (39798) hydrogen bonds : bond 0.03932 ( 1309) hydrogen bonds : angle 4.29233 ( 3599) metal coordination : bond 0.00479 ( 8) metal coordination : angle 1.85347 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 176 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 167 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8443 (tt0) REVERT: D 346 ARG cc_start: 0.8126 (tpp-160) cc_final: 0.7911 (tpp-160) REVERT: D 386 HIS cc_start: 0.7545 (m-70) cc_final: 0.7197 (m90) REVERT: D 486 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7702 (mpp-170) REVERT: D 1289 LYS cc_start: 0.7124 (ptmt) cc_final: 0.6865 (pptt) REVERT: D 1310 ARG cc_start: 0.8264 (mtp85) cc_final: 0.7840 (mtm-85) REVERT: F 129 GLU cc_start: 0.8708 (tp30) cc_final: 0.8199 (tp30) REVERT: F 179 GLU cc_start: 0.9042 (tp30) cc_final: 0.8535 (tp30) REVERT: F 248 ASN cc_start: 0.8845 (OUTLIER) cc_final: 0.8533 (m110) REVERT: F 306 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8162 (mm-30) REVERT: F 402 ASN cc_start: 0.8953 (m-40) cc_final: 0.8472 (m110) REVERT: F 410 TYR cc_start: 0.8797 (t80) cc_final: 0.8539 (t80) REVERT: E 43 GLU cc_start: 0.8981 (pm20) cc_final: 0.8694 (pm20) REVERT: E 44 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8323 (mt-10) REVERT: E 67 GLU cc_start: 0.9187 (mt-10) cc_final: 0.8942 (mt-10) REVERT: E 88 GLU cc_start: 0.8441 (tp30) cc_final: 0.8095 (tp30) REVERT: C 184 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7540 (tmm) REVERT: C 390 GLN cc_start: 0.8914 (tt0) cc_final: 0.8043 (tm-30) REVERT: C 425 PHE cc_start: 0.7702 (m-80) cc_final: 0.7498 (m-80) REVERT: C 820 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7390 (mtm-85) REVERT: C 1061 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7935 (pm20) REVERT: A 133 GLU cc_start: 0.8464 (tt0) cc_final: 0.8197 (tt0) REVERT: A 189 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7193 (ptm160) REVERT: B 91 ASN cc_start: 0.8738 (t0) cc_final: 0.8311 (t0) outliers start: 36 outliers final: 12 residues processed: 200 average time/residue: 0.8623 time to fit residues: 195.9474 Evaluate side-chains 181 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 486 ARG Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 607 LEU Chi-restraints excluded: chain D residue 952 ASP Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 820 ARG Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 1061 GLU Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain A residue 189 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 182 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 200 optimal weight: 7.9990 chunk 27 optimal weight: 0.0000 chunk 173 optimal weight: 5.9990 chunk 254 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 214 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 305 optimal weight: 10.0000 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.089029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.059372 restraints weight = 52383.552| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.40 r_work: 0.2710 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29145 Z= 0.119 Angle : 0.474 7.673 39810 Z= 0.251 Chirality : 0.041 0.157 4487 Planarity : 0.004 0.042 4886 Dihedral : 15.359 85.673 4793 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.16 % Allowed : 9.07 % Favored : 89.78 % 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: 3331 helix: 1.94 (0.14), residues: 1309 sheet: 0.54 (0.26), residues: 401 loop : 0.48 (0.16), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 650 TYR 0.012 0.001 TYR D1093 PHE 0.014 0.001 PHE C 227 TRP 0.011 0.001 TRP B 200 HIS 0.005 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00276 (29137) covalent geometry : angle 0.47332 (39798) hydrogen bonds : bond 0.03646 ( 1309) hydrogen bonds : angle 4.18571 ( 3599) metal coordination : bond 0.00379 ( 8) metal coordination : angle 1.57835 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 124 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.8006 (tp30) REVERT: D 386 HIS cc_start: 0.7561 (m-70) cc_final: 0.7179 (m90) REVERT: D 486 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7848 (mtm-85) REVERT: D 1289 LYS cc_start: 0.7144 (ptmt) cc_final: 0.6726 (pptt) REVERT: D 1304 LYS cc_start: 0.8975 (mttm) cc_final: 0.8565 (mmtt) REVERT: D 1310 ARG cc_start: 0.8207 (mtp85) cc_final: 0.7798 (mtm-85) REVERT: F 129 GLU cc_start: 0.8723 (tp30) cc_final: 0.8192 (tp30) REVERT: F 179 GLU cc_start: 0.9024 (tp30) cc_final: 0.8502 (tp30) REVERT: F 248 ASN cc_start: 0.8841 (OUTLIER) cc_final: 0.8536 (m110) REVERT: F 306 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8185 (mm-30) REVERT: F 402 ASN cc_start: 0.8951 (m-40) cc_final: 0.8468 (m110) REVERT: F 410 TYR cc_start: 0.8778 (t80) cc_final: 0.8525 (t80) REVERT: E 43 GLU cc_start: 0.9001 (pm20) cc_final: 0.8701 (pm20) REVERT: E 44 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8302 (mt-10) REVERT: E 67 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8908 (mt-10) REVERT: E 88 GLU cc_start: 0.8446 (tp30) cc_final: 0.8040 (tp30) REVERT: C 390 GLN cc_start: 0.8908 (tt0) cc_final: 0.8049 (tm-30) REVERT: C 820 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7382 (mtm-85) REVERT: C 1061 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7865 (pm20) REVERT: A 133 GLU cc_start: 0.8484 (tt0) cc_final: 0.8261 (tt0) REVERT: A 189 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7131 (ptm160) REVERT: A 227 ASN cc_start: 0.8208 (OUTLIER) cc_final: 0.7884 (t0) REVERT: B 72 LYS cc_start: 0.9213 (mtpm) cc_final: 0.8665 (mtpp) REVERT: B 91 ASN cc_start: 0.8734 (t0) cc_final: 0.8310 (t0) outliers start: 33 outliers final: 10 residues processed: 197 average time/residue: 0.9125 time to fit residues: 204.0876 Evaluate side-chains 180 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 486 ARG Chi-restraints excluded: chain D residue 607 LEU Chi-restraints excluded: chain D residue 980 MET Chi-restraints excluded: chain D residue 1452 ILE Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 820 ARG Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 1061 GLU Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 227 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 189 optimal weight: 0.1980 chunk 275 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 249 optimal weight: 4.9990 chunk 190 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 160 optimal weight: 0.8980 chunk 323 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.088204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.058715 restraints weight = 52301.914| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.37 r_work: 0.2676 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2552 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29145 Z= 0.148 Angle : 0.490 7.535 39810 Z= 0.258 Chirality : 0.041 0.143 4487 Planarity : 0.004 0.042 4886 Dihedral : 15.339 84.999 4793 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.26 % Allowed : 9.35 % Favored : 89.39 % 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: 1.53 (0.15), residues: 3331 helix: 1.96 (0.14), residues: 1310 sheet: 0.44 (0.26), residues: 408 loop : 0.51 (0.16), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 650 TYR 0.012 0.001 TYR D 989 PHE 0.010 0.001 PHE D1008 TRP 0.012 0.001 TRP B 200 HIS 0.005 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00353 (29137) covalent geometry : angle 0.48927 (39798) hydrogen bonds : bond 0.03795 ( 1309) hydrogen bonds : angle 4.15929 ( 3599) metal coordination : bond 0.00481 ( 8) metal coordination : angle 1.48580 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 124 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7979 (tp30) REVERT: D 209 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7637 (mtt90) REVERT: D 386 HIS cc_start: 0.7527 (m-70) cc_final: 0.7134 (m90) REVERT: D 486 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7847 (mtm-85) REVERT: D 1100 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8000 (m-30) REVERT: D 1289 LYS cc_start: 0.7156 (ptmt) cc_final: 0.6849 (pptt) REVERT: D 1310 ARG cc_start: 0.8184 (mtp85) cc_final: 0.7780 (mtm-85) REVERT: F 129 GLU cc_start: 0.8728 (tp30) cc_final: 0.8191 (tp30) REVERT: F 179 GLU cc_start: 0.9021 (tp30) cc_final: 0.8502 (tp30) REVERT: F 248 ASN cc_start: 0.8809 (OUTLIER) cc_final: 0.8495 (m110) REVERT: F 402 ASN cc_start: 0.8940 (m-40) cc_final: 0.8461 (m110) REVERT: F 410 TYR cc_start: 0.8780 (t80) cc_final: 0.8558 (t80) REVERT: E 43 GLU cc_start: 0.8975 (pm20) cc_final: 0.8675 (pm20) REVERT: E 44 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8235 (mt-10) REVERT: E 67 GLU cc_start: 0.9136 (mt-10) cc_final: 0.8809 (mt-10) REVERT: E 88 GLU cc_start: 0.8447 (tp30) cc_final: 0.8124 (tp30) REVERT: C 390 GLN cc_start: 0.8891 (tt0) cc_final: 0.8021 (tm-30) REVERT: C 820 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7342 (mtm-85) REVERT: C 1061 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7834 (pm20) REVERT: A 189 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7074 (ptm160) REVERT: A 201 THR cc_start: 0.9256 (OUTLIER) cc_final: 0.8983 (p) REVERT: B 72 LYS cc_start: 0.9198 (mtpm) cc_final: 0.8644 (mtpp) REVERT: B 91 ASN cc_start: 0.8705 (t0) cc_final: 0.8270 (t0) REVERT: B 107 LYS cc_start: 0.8782 (ptmm) cc_final: 0.8394 (pttm) outliers start: 36 outliers final: 13 residues processed: 193 average time/residue: 0.9378 time to fit residues: 204.5071 Evaluate side-chains 182 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 486 ARG Chi-restraints excluded: chain D residue 607 LEU Chi-restraints excluded: chain D residue 952 ASP Chi-restraints excluded: chain D residue 980 MET Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 820 ARG Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 1061 GLU Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 201 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 103 optimal weight: 3.9990 chunk 327 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 333 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 249 optimal weight: 0.3980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.087914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.058243 restraints weight = 52266.374| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 2.39 r_work: 0.2668 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29145 Z= 0.155 Angle : 0.491 7.520 39810 Z= 0.259 Chirality : 0.042 0.162 4487 Planarity : 0.004 0.043 4886 Dihedral : 15.316 84.376 4793 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.09 % Allowed : 9.98 % Favored : 88.94 % 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: 3331 helix: 1.98 (0.14), residues: 1306 sheet: 0.39 (0.25), residues: 408 loop : 0.48 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 414 TYR 0.012 0.001 TYR D 989 PHE 0.011 0.001 PHE D1008 TRP 0.012 0.001 TRP B 200 HIS 0.005 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00370 (29137) covalent geometry : angle 0.49064 (39798) hydrogen bonds : bond 0.03824 ( 1309) hydrogen bonds : angle 4.14326 ( 3599) metal coordination : bond 0.00476 ( 8) metal coordination : angle 1.33526 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 209 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7725 (mtt90) REVERT: D 386 HIS cc_start: 0.7517 (m-70) cc_final: 0.7126 (m90) REVERT: D 486 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7664 (mpp-170) REVERT: D 1100 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.8011 (m-30) REVERT: D 1289 LYS cc_start: 0.7161 (ptmt) cc_final: 0.6851 (pptt) REVERT: D 1310 ARG cc_start: 0.8181 (mtp85) cc_final: 0.7782 (mtm-85) REVERT: F 129 GLU cc_start: 0.8737 (tp30) cc_final: 0.8193 (tp30) REVERT: F 179 GLU cc_start: 0.9025 (tp30) cc_final: 0.8404 (tp30) REVERT: F 248 ASN cc_start: 0.8822 (OUTLIER) cc_final: 0.8496 (m110) REVERT: F 402 ASN cc_start: 0.8943 (m-40) cc_final: 0.8453 (m110) REVERT: F 410 TYR cc_start: 0.8806 (t80) cc_final: 0.8602 (t80) REVERT: E 43 GLU cc_start: 0.8978 (pm20) cc_final: 0.8670 (pm20) REVERT: E 44 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8224 (mt-10) REVERT: E 67 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8817 (mt-10) REVERT: E 87 LYS cc_start: 0.8518 (mtmm) cc_final: 0.8270 (mmpt) REVERT: E 88 GLU cc_start: 0.8420 (tp30) cc_final: 0.8024 (tp30) REVERT: C 390 GLN cc_start: 0.8898 (tt0) cc_final: 0.8031 (tm-30) REVERT: C 650 ARG cc_start: 0.7986 (mtp-110) cc_final: 0.7468 (mmp80) REVERT: C 820 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7300 (mtm-85) REVERT: C 1061 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7854 (pm20) REVERT: A 7 LYS cc_start: 0.8970 (ttpp) cc_final: 0.8723 (tppt) REVERT: A 189 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7066 (ptm160) REVERT: A 201 THR cc_start: 0.9287 (OUTLIER) cc_final: 0.9028 (p) REVERT: A 227 ASN cc_start: 0.8235 (OUTLIER) cc_final: 0.7898 (t0) REVERT: B 91 ASN cc_start: 0.8704 (t0) cc_final: 0.8257 (t0) REVERT: B 107 LYS cc_start: 0.8744 (ptmm) cc_final: 0.8422 (pttm) outliers start: 31 outliers final: 13 residues processed: 189 average time/residue: 0.9007 time to fit residues: 192.8540 Evaluate side-chains 180 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 486 ARG Chi-restraints excluded: chain D residue 952 ASP Chi-restraints excluded: chain D residue 980 MET Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 820 ARG Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 1061 GLU Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 293 optimal weight: 3.9990 chunk 303 optimal weight: 0.9990 chunk 339 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 277 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 154 optimal weight: 5.9990 chunk 270 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.088063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.058429 restraints weight = 52440.860| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.40 r_work: 0.2685 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2583 r_free = 0.2583 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2583 r_free = 0.2583 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29145 Z= 0.142 Angle : 0.487 8.149 39810 Z= 0.256 Chirality : 0.041 0.142 4487 Planarity : 0.004 0.044 4886 Dihedral : 15.285 84.823 4793 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.19 % Allowed : 10.26 % Favored : 88.55 % 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: 3331 helix: 1.99 (0.14), residues: 1311 sheet: 0.42 (0.25), residues: 408 loop : 0.51 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 346 TYR 0.011 0.001 TYR D 158 PHE 0.010 0.001 PHE D1008 TRP 0.013 0.001 TRP B 200 HIS 0.005 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00337 (29137) covalent geometry : angle 0.48665 (39798) hydrogen bonds : bond 0.03701 ( 1309) hydrogen bonds : angle 4.10718 ( 3599) metal coordination : bond 0.00421 ( 8) metal coordination : angle 1.29774 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 209 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7692 (mtt90) REVERT: D 386 HIS cc_start: 0.7595 (m-70) cc_final: 0.7162 (m90) REVERT: D 486 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7828 (mtm-85) REVERT: D 1100 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.7978 (m-30) REVERT: D 1310 ARG cc_start: 0.8174 (mtp85) cc_final: 0.7776 (mtm-85) REVERT: F 129 GLU cc_start: 0.8736 (tp30) cc_final: 0.8174 (tp30) REVERT: F 179 GLU cc_start: 0.9019 (tp30) cc_final: 0.8400 (tp30) REVERT: F 248 ASN cc_start: 0.8810 (OUTLIER) cc_final: 0.8491 (m110) REVERT: F 402 ASN cc_start: 0.8938 (m-40) cc_final: 0.8448 (m110) REVERT: F 410 TYR cc_start: 0.8813 (t80) cc_final: 0.8594 (t80) REVERT: E 43 GLU cc_start: 0.8988 (pm20) cc_final: 0.8674 (pm20) REVERT: E 44 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8187 (mt-10) REVERT: E 67 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8845 (mt-10) REVERT: E 88 GLU cc_start: 0.8428 (tp30) cc_final: 0.8085 (tp30) REVERT: C 390 GLN cc_start: 0.8885 (tt0) cc_final: 0.8014 (tm-30) REVERT: C 650 ARG cc_start: 0.8010 (mtp-110) cc_final: 0.7477 (mmp80) REVERT: C 820 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7288 (mtm-85) REVERT: C 1061 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7874 (pm20) REVERT: C 1091 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8326 (mt-10) REVERT: A 189 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7135 (ptm160) REVERT: A 201 THR cc_start: 0.9266 (OUTLIER) cc_final: 0.9004 (p) REVERT: A 227 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7966 (m-40) REVERT: B 91 ASN cc_start: 0.8697 (t0) cc_final: 0.8244 (t0) REVERT: B 107 LYS cc_start: 0.8745 (ptmm) cc_final: 0.8440 (pttm) REVERT: B 113 ASP cc_start: 0.8643 (m-30) cc_final: 0.8198 (m-30) outliers start: 34 outliers final: 17 residues processed: 194 average time/residue: 0.8337 time to fit residues: 183.9934 Evaluate side-chains 186 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 486 ARG Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 952 ASP Chi-restraints excluded: chain D residue 980 MET Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 820 ARG Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 1061 GLU Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain C residue 1091 GLU Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 294 optimal weight: 2.9990 chunk 145 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 69 optimal weight: 0.0020 chunk 159 optimal weight: 2.9990 chunk 326 optimal weight: 5.9990 chunk 276 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 317 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.088204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.058558 restraints weight = 52476.344| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.40 r_work: 0.2691 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29145 Z= 0.132 Angle : 0.487 8.232 39810 Z= 0.256 Chirality : 0.041 0.141 4487 Planarity : 0.004 0.049 4886 Dihedral : 15.259 85.313 4793 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.05 % Allowed : 10.57 % Favored : 88.38 % 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: 1.58 (0.15), residues: 3331 helix: 2.01 (0.14), residues: 1311 sheet: 0.45 (0.26), residues: 407 loop : 0.53 (0.16), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 346 TYR 0.010 0.001 TYR D1093 PHE 0.010 0.001 PHE A 179 TRP 0.013 0.001 TRP B 200 HIS 0.005 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00314 (29137) covalent geometry : angle 0.48679 (39798) hydrogen bonds : bond 0.03615 ( 1309) hydrogen bonds : angle 4.08032 ( 3599) metal coordination : bond 0.00382 ( 8) metal coordination : angle 1.26908 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 209 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7725 (mtt90) REVERT: D 386 HIS cc_start: 0.7620 (m-70) cc_final: 0.7008 (m90) REVERT: D 486 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7845 (mtm-85) REVERT: D 1100 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7969 (m-30) REVERT: D 1310 ARG cc_start: 0.8160 (mtp85) cc_final: 0.7767 (mtm-85) REVERT: F 129 GLU cc_start: 0.8751 (tp30) cc_final: 0.8186 (tp30) REVERT: F 179 GLU cc_start: 0.9008 (tp30) cc_final: 0.8386 (tp30) REVERT: F 248 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8485 (m110) REVERT: F 402 ASN cc_start: 0.8939 (m-40) cc_final: 0.8448 (m110) REVERT: F 410 TYR cc_start: 0.8814 (t80) cc_final: 0.8604 (t80) REVERT: E 43 GLU cc_start: 0.8991 (pm20) cc_final: 0.8674 (pm20) REVERT: E 44 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8250 (mt-10) REVERT: E 67 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8851 (mt-10) REVERT: E 88 GLU cc_start: 0.8435 (tp30) cc_final: 0.8169 (tp30) REVERT: C 28 ARG cc_start: 0.8517 (mmm-85) cc_final: 0.7921 (ttm110) REVERT: C 361 MET cc_start: 0.8170 (pp-130) cc_final: 0.7702 (ppp) REVERT: C 390 GLN cc_start: 0.8877 (tt0) cc_final: 0.8009 (tm-30) REVERT: C 650 ARG cc_start: 0.8005 (mtp-110) cc_final: 0.7459 (mmp80) REVERT: C 820 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7253 (mtm-85) REVERT: C 1061 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7873 (pm20) REVERT: C 1091 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8312 (mt-10) REVERT: A 189 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7156 (ptm160) REVERT: A 201 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.8990 (p) REVERT: A 227 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7969 (m-40) REVERT: B 91 ASN cc_start: 0.8697 (t0) cc_final: 0.8247 (t0) REVERT: B 107 LYS cc_start: 0.8736 (ptmm) cc_final: 0.8425 (pttm) outliers start: 30 outliers final: 17 residues processed: 187 average time/residue: 0.8327 time to fit residues: 177.9181 Evaluate side-chains 186 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 486 ARG Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 952 ASP Chi-restraints excluded: chain D residue 980 MET Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1452 ILE Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 820 ARG Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 1061 GLU Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain C residue 1091 GLU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 274 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 288 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 325 optimal weight: 0.9980 chunk 173 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 chunk 104 optimal weight: 0.3980 chunk 11 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.088799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.059326 restraints weight = 52272.859| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.39 r_work: 0.2707 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29145 Z= 0.113 Angle : 0.482 9.599 39810 Z= 0.253 Chirality : 0.041 0.139 4487 Planarity : 0.004 0.058 4886 Dihedral : 15.229 86.259 4793 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.95 % Allowed : 10.75 % Favored : 88.31 % 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: 3331 helix: 2.04 (0.14), residues: 1312 sheet: 0.49 (0.26), residues: 401 loop : 0.55 (0.16), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 346 TYR 0.011 0.001 TYR D1093 PHE 0.010 0.001 PHE A 179 TRP 0.013 0.001 TRP B 200 HIS 0.006 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00263 (29137) covalent geometry : angle 0.48186 (39798) hydrogen bonds : bond 0.03424 ( 1309) hydrogen bonds : angle 4.02343 ( 3599) metal coordination : bond 0.00292 ( 8) metal coordination : angle 1.25683 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6662 Ramachandran restraints generated. 3331 Oldfield, 0 Emsley, 3331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 ARG cc_start: 0.7528 (tpp-160) cc_final: 0.7090 (tpp80) REVERT: D 351 MET cc_start: 0.8138 (ptp) cc_final: 0.7917 (pmt) REVERT: D 386 HIS cc_start: 0.7449 (m-70) cc_final: 0.6995 (m90) REVERT: D 486 ARG cc_start: 0.8137 (mpp-170) cc_final: 0.7855 (mtm-85) REVERT: D 1100 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7926 (m-30) REVERT: D 1310 ARG cc_start: 0.8138 (mtp85) cc_final: 0.7753 (mtm-85) REVERT: F 129 GLU cc_start: 0.8730 (tp30) cc_final: 0.8180 (tp30) REVERT: F 179 GLU cc_start: 0.8973 (tp30) cc_final: 0.8449 (tp30) REVERT: F 248 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8483 (m110) REVERT: F 402 ASN cc_start: 0.8936 (m-40) cc_final: 0.8453 (m110) REVERT: F 410 TYR cc_start: 0.8820 (t80) cc_final: 0.8593 (t80) REVERT: E 43 GLU cc_start: 0.8992 (pm20) cc_final: 0.8676 (pm20) REVERT: E 44 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8256 (mt-10) REVERT: E 67 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8841 (mt-10) REVERT: E 88 GLU cc_start: 0.8414 (tp30) cc_final: 0.8071 (tp30) REVERT: C 28 ARG cc_start: 0.8504 (mmm-85) cc_final: 0.7864 (mtm-85) REVERT: C 361 MET cc_start: 0.8233 (pp-130) cc_final: 0.7761 (ppp) REVERT: C 390 GLN cc_start: 0.8871 (tt0) cc_final: 0.8005 (tm-30) REVERT: C 650 ARG cc_start: 0.7999 (mtp-110) cc_final: 0.7458 (mmp80) REVERT: C 820 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7228 (mtm-85) REVERT: C 1061 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7883 (pm20) REVERT: C 1091 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8247 (mt-10) REVERT: A 7 LYS cc_start: 0.8956 (ttpp) cc_final: 0.8723 (tppt) REVERT: A 189 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7081 (ptm160) REVERT: A 201 THR cc_start: 0.9203 (OUTLIER) cc_final: 0.8925 (p) REVERT: A 227 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.7974 (m-40) REVERT: B 91 ASN cc_start: 0.8696 (t0) cc_final: 0.8246 (t0) REVERT: B 107 LYS cc_start: 0.8732 (ptmm) cc_final: 0.8422 (pttm) outliers start: 27 outliers final: 15 residues processed: 183 average time/residue: 0.9021 time to fit residues: 188.1765 Evaluate side-chains 182 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 952 ASP Chi-restraints excluded: chain D residue 980 MET Chi-restraints excluded: chain D residue 1100 ASP Chi-restraints excluded: chain D residue 1452 ILE Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 820 ARG Chi-restraints excluded: chain C residue 1061 GLU Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain C residue 1091 GLU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 68 optimal weight: 0.0030 chunk 227 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 chunk 308 optimal weight: 5.9990 chunk 278 optimal weight: 5.9990 chunk 298 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 282 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 175 optimal weight: 10.0000 overall best weight: 1.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.087859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.058208 restraints weight = 52246.716| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 2.39 r_work: 0.2670 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 29145 Z= 0.158 Angle : 0.499 9.166 39810 Z= 0.262 Chirality : 0.042 0.219 4487 Planarity : 0.004 0.058 4886 Dihedral : 15.253 85.591 4793 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.98 % Allowed : 10.68 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.15), residues: 3331 helix: 2.03 (0.14), residues: 1305 sheet: 0.44 (0.26), residues: 404 loop : 0.52 (0.16), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 346 TYR 0.012 0.001 TYR D 128 PHE 0.011 0.001 PHE D1008 TRP 0.012 0.001 TRP B 200 HIS 0.005 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00378 (29137) covalent geometry : angle 0.49895 (39798) hydrogen bonds : bond 0.03751 ( 1309) hydrogen bonds : angle 4.08630 ( 3599) metal coordination : bond 0.00495 ( 8) metal coordination : angle 1.42980 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11209.60 seconds wall clock time: 190 minutes 51.38 seconds (11451.38 seconds total)