Starting phenix.real_space_refine on Sat Aug 8 08:47:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x6g_38088/08_2026/8x6g_38088.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x6g_38088/08_2026/8x6g_38088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8x6g_38088/08_2026/8x6g_38088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x6g_38088/08_2026/8x6g_38088.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x6g_38088/08_2026/8x6g_38088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x6g_38088/08_2026/8x6g_38088.map" } resolution = 3.3 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= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians P 81 5.49 5 S 98 5.16 5 C 16892 2.51 5 N 4745 2.21 5 O 5455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27271 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1726 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 214} Chain: "B" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1708 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 213} Chain: "C" Number of atoms: 9121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1153, 9121 Classifications: {'peptide': 1153} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1102} Chain: "D" Number of atoms: 9281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1176, 9281 Classifications: {'peptide': 1176} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1122} Chain breaks: 1 Chain: "E" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 709 Classifications: {'peptide': 84} Link IDs: {'TRANS': 83} Chain: "F" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 491 Classifications: {'peptide': 62} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 56} Chain: "G" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 596 Classifications: {'peptide': 69} Link IDs: {'TRANS': 68} Chain: "H" Number of atoms: 1978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1978 Classifications: {'peptide': 244} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "T" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 809 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain breaks: 1 Chain: "N" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 852 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain breaks: 1 Time building chain proxies: 5.72, per 1000 atoms: 0.21 Number of scatterers: 27271 At special positions: 0 Unit cell: (149.94, 145.18, 136.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 98 16.00 P 81 15.00 O 5455 8.00 N 4745 7.00 C 16892 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: 2.20 Conformation dependent library (CDL) restraints added in 1.1 seconds 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6014 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 45 sheets defined 44.6% alpha, 18.1% beta 36 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 3.73 Creating SS restraints... Processing helix chain 'A' and resid 31 through 47 Processing helix chain 'A' and resid 74 through 84 removed outlier: 3.516A pdb=" N GLN A 84 " --> pdb=" O MET A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 150 through 155 Processing helix chain 'A' and resid 205 through 226 removed outlier: 4.090A pdb=" N ILE A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE A 224 " --> pdb=" O HIS A 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 47 removed outlier: 3.614A pdb=" N THR B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 84 removed outlier: 3.554A pdb=" N GLN B 84 " --> pdb=" O MET B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 155 Processing helix chain 'B' and resid 205 through 226 removed outlier: 4.067A pdb=" N ILE B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE B 224 " --> pdb=" O HIS B 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 removed outlier: 3.804A pdb=" N SER C 36 " --> pdb=" O ILE C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 53 Processing helix chain 'C' and resid 77 through 84 Processing helix chain 'C' and resid 192 through 200 Processing helix chain 'C' and resid 203 through 212 Processing helix chain 'C' and resid 214 through 224 Processing helix chain 'C' and resid 228 through 241 Processing helix chain 'C' and resid 247 through 260 Processing helix chain 'C' and resid 267 through 279 Processing helix chain 'C' and resid 280 through 286 removed outlier: 4.127A pdb=" N ARG C 284 " --> pdb=" O HIS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 318 Processing helix chain 'C' and resid 318 through 325 removed outlier: 3.731A pdb=" N SER C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 392 Processing helix chain 'C' and resid 410 through 437 Processing helix chain 'C' and resid 443 through 448 removed outlier: 3.683A pdb=" N LEU C 447 " --> pdb=" O THR C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 463 Processing helix chain 'C' and resid 474 through 483 Processing helix chain 'C' and resid 499 through 504 removed outlier: 4.064A pdb=" N ARG C 503 " --> pdb=" O GLN C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 510 removed outlier: 3.634A pdb=" N TYR C 510 " --> pdb=" O TYR C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 569 Processing helix chain 'C' and resid 605 through 607 No H-bonds generated for 'chain 'C' and resid 605 through 607' Processing helix chain 'C' and resid 613 through 617 removed outlier: 3.715A pdb=" N VAL C 617 " --> pdb=" O PRO C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 625 Processing helix chain 'C' and resid 627 through 631 Processing helix chain 'C' and resid 632 through 644 removed outlier: 3.904A pdb=" N ARG C 644 " --> pdb=" O ALA C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 670 removed outlier: 4.602A pdb=" N VAL C 664 " --> pdb=" O GLY C 660 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLY C 670 " --> pdb=" O ALA C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 783 Processing helix chain 'C' and resid 816 through 821 Processing helix chain 'C' and resid 854 through 865 Processing helix chain 'C' and resid 960 through 966 removed outlier: 4.263A pdb=" N SER C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG C 965 " --> pdb=" O GLY C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 984 Processing helix chain 'C' and resid 996 through 1007 Processing helix chain 'C' and resid 1066 through 1070 Processing helix chain 'C' and resid 1076 through 1087 Processing helix chain 'C' and resid 1088 through 1097 Processing helix chain 'C' and resid 1102 through 1116 removed outlier: 4.107A pdb=" N VAL C1107 " --> pdb=" O THR C1103 " (cutoff:3.500A) Processing helix chain 'C' and resid 1125 through 1138 Processing helix chain 'D' and resid 16 through 23 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 67 through 71 removed outlier: 3.637A pdb=" N TYR D 70 " --> pdb=" O ARG D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 103 through 109 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 151 through 162 Processing helix chain 'D' and resid 170 through 181 removed outlier: 3.716A pdb=" N GLY D 174 " --> pdb=" O MET D 170 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE D 175 " --> pdb=" O GLY D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 196 Processing helix chain 'D' and resid 200 through 220 Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 235 through 239 Processing helix chain 'D' and resid 245 through 247 No H-bonds generated for 'chain 'D' and resid 245 through 247' Processing helix chain 'D' and resid 252 through 275 removed outlier: 3.903A pdb=" N ASP D 256 " --> pdb=" O SER D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 297 Processing helix chain 'D' and resid 315 through 321 removed outlier: 3.520A pdb=" N MET D 319 " --> pdb=" O SER D 315 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU D 320 " --> pdb=" O LEU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 330 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 366 through 377 Processing helix chain 'D' and resid 382 through 393 Processing helix chain 'D' and resid 394 through 405 removed outlier: 4.026A pdb=" N TRP D 398 " --> pdb=" O ASP D 394 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL D 400 " --> pdb=" O GLU D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 421 No H-bonds generated for 'chain 'D' and resid 419 through 421' Processing helix chain 'D' and resid 439 through 441 No H-bonds generated for 'chain 'D' and resid 439 through 441' Processing helix chain 'D' and resid 442 through 447 Processing helix chain 'D' and resid 462 through 473 Processing helix chain 'D' and resid 493 through 503 Processing helix chain 'D' and resid 518 through 528 Processing helix chain 'D' and resid 542 through 545 removed outlier: 3.653A pdb=" N ASN D 545 " --> pdb=" O SER D 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 542 through 545' Processing helix chain 'D' and resid 552 through 555 Processing helix chain 'D' and resid 562 through 569 Processing helix chain 'D' and resid 582 through 588 Processing helix chain 'D' and resid 591 through 593 No H-bonds generated for 'chain 'D' and resid 591 through 593' Processing helix chain 'D' and resid 597 through 601 Processing helix chain 'D' and resid 604 through 613 Processing helix chain 'D' and resid 620 through 635 Processing helix chain 'D' and resid 636 through 659 Processing helix chain 'D' and resid 663 through 667 Processing helix chain 'D' and resid 672 through 693 Processing helix chain 'D' and resid 697 through 723 Processing helix chain 'D' and resid 728 through 736 Processing helix chain 'D' and resid 741 through 750 Processing helix chain 'D' and resid 776 through 812 removed outlier: 4.018A pdb=" N HIS D 785 " --> pdb=" O PHE D 781 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY D 786 " --> pdb=" O ILE D 782 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA D 799 " --> pdb=" O ALA D 795 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP D 800 " --> pdb=" O LEU D 796 " (cutoff:3.500A) Processing helix chain 'D' and resid 842 through 848 Processing helix chain 'D' and resid 873 through 883 Processing helix chain 'D' and resid 892 through 896 Processing helix chain 'D' and resid 904 through 908 Processing helix chain 'D' and resid 922 through 938 Proline residue: D 934 - end of helix removed outlier: 4.035A pdb=" N GLN D 937 " --> pdb=" O GLU D 933 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 965 Processing helix chain 'D' and resid 989 through 991 No H-bonds generated for 'chain 'D' and resid 989 through 991' Processing helix chain 'D' and resid 1034 through 1043 Processing helix chain 'D' and resid 1043 through 1062 removed outlier: 3.750A pdb=" N GLN D1062 " --> pdb=" O VAL D1058 " (cutoff:3.500A) Processing helix chain 'D' and resid 1067 through 1079 removed outlier: 4.163A pdb=" N VAL D1071 " --> pdb=" O ASP D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1100 through 1113 Processing helix chain 'D' and resid 1126 through 1133 Processing helix chain 'D' and resid 1136 through 1144 removed outlier: 3.842A pdb=" N ALA D1140 " --> pdb=" O SER D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1145 through 1157 Processing helix chain 'D' and resid 1164 through 1172 removed outlier: 3.848A pdb=" N ASN D1168 " --> pdb=" O GLY D1164 " (cutoff:3.500A) Processing helix chain 'D' and resid 1177 through 1180 Processing helix chain 'D' and resid 1181 through 1186 Processing helix chain 'E' and resid 9 through 14 Processing helix chain 'E' and resid 15 through 28 Processing helix chain 'E' and resid 33 through 45 Processing helix chain 'E' and resid 47 through 65 removed outlier: 4.365A pdb=" N ASN E 53 " --> pdb=" O GLU E 49 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG E 54 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN E 57 " --> pdb=" O ASN E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing helix chain 'E' and resid 83 through 91 Processing helix chain 'F' and resid 5 through 11 Processing helix chain 'F' and resid 15 through 33 Processing helix chain 'F' and resid 34 through 37 removed outlier: 3.862A pdb=" N GLU F 37 " --> pdb=" O PRO F 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 34 through 37' Processing helix chain 'F' and resid 46 through 57 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 30 through 38 Processing helix chain 'G' and resid 53 through 63 Processing helix chain 'H' and resid 14 through 27 Processing helix chain 'H' and resid 28 through 52 removed outlier: 3.568A pdb=" N GLN H 32 " --> pdb=" O ASN H 28 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LYS H 41 " --> pdb=" O LYS H 37 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LEU H 42 " --> pdb=" O HIS H 38 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR H 50 " --> pdb=" O LEU H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 75 Processing helix chain 'H' and resid 83 through 102 Proline residue: H 89 - end of helix Processing helix chain 'H' and resid 109 through 131 Proline residue: H 117 - end of helix Processing helix chain 'H' and resid 135 through 144 Processing helix chain 'H' and resid 146 through 159 Processing helix chain 'H' and resid 180 through 184 Processing helix chain 'H' and resid 189 through 204 Processing helix chain 'H' and resid 205 through 207 No H-bonds generated for 'chain 'H' and resid 205 through 207' Processing helix chain 'H' and resid 208 through 219 Processing helix chain 'H' and resid 224 through 233 Processing helix chain 'H' and resid 235 through 256 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 14 removed outlier: 5.019A pdb=" N ILE A 9 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N GLU A 26 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N THR A 11 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL A 24 " --> pdb=" O THR A 11 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP A 192 " --> pdb=" O PRO A 27 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N SER A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL A 185 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 101 removed outlier: 3.740A pdb=" N TYR A 55 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASN A 143 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N VAL A 53 " --> pdb=" O ASN A 143 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLY A 145 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA A 51 " --> pdb=" O GLY A 145 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 105 through 108 Processing sheet with id=AA5, first strand: chain 'A' and resid 148 through 149 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 14 removed outlier: 5.066A pdb=" N ILE B 9 " --> pdb=" O GLU B 26 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLU B 26 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N THR B 11 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL B 24 " --> pdb=" O THR B 11 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N PHE B 20 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR B 200 " --> pdb=" O PHE B 20 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LYS B 22 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL B 198 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL B 24 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU B 196 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N GLU B 26 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU B 194 " --> pdb=" O GLU B 26 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N SER B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL B 185 " --> pdb=" O SER B 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 112 through 113 removed outlier: 3.716A pdb=" N TYR B 55 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ASN B 143 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N VAL B 53 " --> pdb=" O ASN B 143 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY B 145 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ALA B 51 " --> pdb=" O GLY B 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 89 Processing sheet with id=AA9, first strand: chain 'B' and resid 105 through 108 removed outlier: 6.499A pdb=" N GLY B 105 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THR B 129 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL B 107 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 148 through 149 Processing sheet with id=AB2, first strand: chain 'C' and resid 4 through 8 removed outlier: 4.483A pdb=" N HIS C 986 " --> pdb=" O LYS C 13 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 988 " --> pdb=" O ARG C 15 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 55 through 56 removed outlier: 5.507A pdb=" N LEU C 64 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE C 99 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N PHE C 66 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG C 97 " --> pdb=" O PHE C 66 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP C 68 " --> pdb=" O LYS C 95 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ALA C 90 " --> pdb=" O ASP C 115 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP C 115 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU C 92 " --> pdb=" O MET C 113 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU C 105 " --> pdb=" O ILE C 100 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 125 through 127 Processing sheet with id=AB5, first strand: chain 'C' and resid 406 through 409 removed outlier: 6.374A pdb=" N SER C 136 " --> pdb=" O SER C 486 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 144 through 150 removed outlier: 6.704A pdb=" N TYR C 158 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR C 174 " --> pdb=" O TYR C 158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 288 through 289 removed outlier: 3.825A pdb=" N GLN C 288 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 294 through 295 removed outlier: 6.793A pdb=" N ILE C 294 " --> pdb=" O VAL C 303 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 328 through 331 removed outlier: 3.888A pdb=" N GLN C 345 " --> pdb=" O GLY C 364 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 535 through 536 removed outlier: 5.561A pdb=" N GLN C 559 " --> pdb=" O LYS C 548 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 535 through 536 Processing sheet with id=AC3, first strand: chain 'C' and resid 673 through 674 removed outlier: 6.421A pdb=" N ILE C 673 " --> pdb=" O LEU C 741 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 700 through 710 removed outlier: 5.107A pdb=" N GLU C 701 " --> pdb=" O GLU C 697 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU C 697 " --> pdb=" O GLU C 701 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N GLU C 703 " --> pdb=" O VAL C 695 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL C 695 " --> pdb=" O GLU C 703 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N GLU C 705 " --> pdb=" O ARG C 693 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLU C 688 " --> pdb=" O VAL C 684 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N VAL C 684 " --> pdb=" O GLU C 688 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU C 690 " --> pdb=" O GLU C 682 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 715 through 716 Processing sheet with id=AC6, first strand: chain 'C' and resid 747 through 748 Processing sheet with id=AC7, first strand: chain 'C' and resid 1014 through 1015 removed outlier: 6.897A pdb=" N VAL C 774 " --> pdb=" O LYS C 937 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL C 939 " --> pdb=" O VAL C 774 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N MET C 776 " --> pdb=" O VAL C 939 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 775 " --> pdb=" O MET C 956 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ILE C 955 " --> pdb=" O ASN C 757 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL C 759 " --> pdb=" O ILE C 955 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU C 957 " --> pdb=" O VAL C 759 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY C 761 " --> pdb=" O LEU C 957 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N SER C1031 " --> pdb=" O PHE C 762 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 804 through 805 removed outlier: 6.005A pdb=" N SER C 788 " --> pdb=" O LYS C 916 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS C 916 " --> pdb=" O SER C 788 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N HIS C 790 " --> pdb=" O VAL C 914 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL C 914 " --> pdb=" O HIS C 790 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU C 792 " --> pdb=" O TYR C 912 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR C 912 " --> pdb=" O GLU C 792 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR C 794 " --> pdb=" O ARG C 910 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ARG C 910 " --> pdb=" O TYR C 794 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N SER C 796 " --> pdb=" O LEU C 908 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU C 908 " --> pdb=" O SER C 796 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA C 798 " --> pdb=" O ASN C 906 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ASN C 906 " --> pdb=" O ASN C 893 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASN C 893 " --> pdb=" O ASN C 906 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU C 908 " --> pdb=" O VAL C 891 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL C 891 " --> pdb=" O LEU C 908 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG C 910 " --> pdb=" O VAL C 889 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL C 889 " --> pdb=" O ARG C 910 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR C 912 " --> pdb=" O LEU C 887 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 807 through 808 Processing sheet with id=AD1, first strand: chain 'C' and resid 840 through 842 removed outlier: 6.418A pdb=" N LEU C 876 " --> pdb=" O LEU C 841 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1049 through 1051 removed outlier: 7.856A pdb=" N ILE D 436 " --> pdb=" O ARG D 341 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL D 343 " --> pdb=" O ILE D 436 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU D 438 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA D 345 " --> pdb=" O LEU D 438 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1074 through 1075 Processing sheet with id=AD4, first strand: chain 'C' and resid 1143 through 1145 Processing sheet with id=AD5, first strand: chain 'D' and resid 24 through 27 removed outlier: 7.567A pdb=" N HIS D 94 " --> pdb=" O PHE D 25 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU D 27 " --> pdb=" O HIS D 94 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N GLU D 96 " --> pdb=" O GLU D 27 " (cutoff:3.500A) removed outlier: 10.013A pdb=" N LEU D 97 " --> pdb=" O PRO D 232 " (cutoff:3.500A) removed outlier: 10.717A pdb=" N ALA D 99 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL D 230 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 149 through 150 removed outlier: 6.796A pdb=" N VAL D 167 " --> pdb=" O VAL D 137 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 241 through 243 Processing sheet with id=AD8, first strand: chain 'D' and resid 515 through 516 Processing sheet with id=AD9, first strand: chain 'D' and resid 816 through 819 removed outlier: 6.017A pdb=" N ILE D 816 " --> pdb=" O VAL D 902 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 828 through 831 removed outlier: 4.691A pdb=" N TYR D 851 " --> pdb=" O ARG D 891 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 833 through 835 removed outlier: 6.852A pdb=" N GLU D 835 " --> pdb=" O MET D 839 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N MET D 839 " --> pdb=" O GLU D 835 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 856 through 857 removed outlier: 6.813A pdb=" N ILE D 856 " --> pdb=" O ILE D 865 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1003 through 1008 removed outlier: 6.117A pdb=" N LYS D 998 " --> pdb=" O VAL D 982 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL D 982 " --> pdb=" O LYS D 998 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1097 through 1099 removed outlier: 5.413A pdb=" N VAL D1082 " --> pdb=" O VAL D1123 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL D1123 " --> pdb=" O VAL D1082 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ILE D1084 " --> pdb=" O LYS D1121 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LYS D1121 " --> pdb=" O ILE D1084 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU D1086 " --> pdb=" O THR D1119 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1189 through 1191 Processing sheet with id=AE7, first strand: chain 'E' and resid 31 through 32 removed outlier: 6.306A pdb=" N LEU E 75 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 44 through 50 removed outlier: 6.320A pdb=" N PHE G 7 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE G 48 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LYS G 5 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 9.506A pdb=" N GLU G 69 " --> pdb=" O SER G 23 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR G 25 " --> pdb=" O GLU G 69 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 168 through 170 1174 hydrogen bonds defined for protein. 3297 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 84 hydrogen bonds 168 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 7.47 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8393 1.33 - 1.45: 4182 1.45 - 1.57: 14978 1.57 - 1.69: 159 1.69 - 1.81: 179 Bond restraints: 27891 Sorted by residual: bond pdb=" C3' DT T 46 " pdb=" C2' DT T 46 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" N VAL D 669 " pdb=" CA VAL D 669 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.22e-02 6.72e+03 9.58e+00 bond pdb=" N VAL D 668 " pdb=" CA VAL D 668 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.24e-02 6.50e+03 8.79e+00 bond pdb=" C1' DT N 18 " pdb=" N1 DT N 18 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 8.34e+00 bond pdb=" C1' DT N 22 " pdb=" N1 DT N 22 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 8.20e+00 ... (remaining 27886 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 37499 2.27 - 4.54: 486 4.54 - 6.80: 30 6.80 - 9.07: 3 9.07 - 11.34: 2 Bond angle restraints: 38020 Sorted by residual: angle pdb=" N THR C 874 " pdb=" CA THR C 874 " pdb=" C THR C 874 " ideal model delta sigma weight residual 110.61 104.71 5.90 1.25e+00 6.40e-01 2.23e+01 angle pdb=" O4' DA N 26 " pdb=" C4' DA N 26 " pdb=" C3' DA N 26 " ideal model delta sigma weight residual 106.00 103.18 2.82 6.00e-01 2.78e+00 2.21e+01 angle pdb=" O4' DT T 54 " pdb=" C4' DT T 54 " pdb=" C3' DT T 54 " ideal model delta sigma weight residual 106.00 103.20 2.80 6.00e-01 2.78e+00 2.18e+01 angle pdb=" N3 DT T 39 " pdb=" C4 DT T 39 " pdb=" O4 DT T 39 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT N 23 " pdb=" C4 DT N 23 " pdb=" O4 DT N 23 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+01 ... (remaining 38015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.79: 15869 29.79 - 59.57: 982 59.57 - 89.36: 44 89.36 - 119.14: 3 119.14 - 148.93: 1 Dihedral angle restraints: 16899 sinusoidal: 7558 harmonic: 9341 Sorted by residual: dihedral pdb=" CA SER A 171 " pdb=" C SER A 171 " pdb=" N PRO A 172 " pdb=" CA PRO A 172 " ideal model delta harmonic sigma weight residual -180.00 -151.19 -28.81 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ARG C 10 " pdb=" C ARG C 10 " pdb=" N HIS C 11 " pdb=" CA HIS C 11 " ideal model delta harmonic sigma weight residual 180.00 -160.50 -19.50 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" C4' DC T 37 " pdb=" C3' DC T 37 " pdb=" O3' DC T 37 " pdb=" P DA T 38 " ideal model delta sinusoidal sigma weight residual 220.00 71.07 148.93 1 3.50e+01 8.16e-04 1.45e+01 ... (remaining 16896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3714 0.062 - 0.125: 542 0.125 - 0.187: 24 0.187 - 0.250: 4 0.250 - 0.312: 1 Chirality restraints: 4285 Sorted by residual: chirality pdb=" CA PHE H 79 " pdb=" N PHE H 79 " pdb=" C PHE H 79 " pdb=" CB PHE H 79 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA PRO A 172 " pdb=" N PRO A 172 " pdb=" C PRO A 172 " pdb=" CB PRO A 172 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA VAL D 669 " pdb=" N VAL D 669 " pdb=" C VAL D 669 " pdb=" CB VAL D 669 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 4282 not shown) Planarity restraints: 4689 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 171 " 0.105 5.00e-02 4.00e+02 1.59e-01 4.03e+01 pdb=" N PRO A 172 " -0.274 5.00e-02 4.00e+02 pdb=" CA PRO A 172 " 0.089 5.00e-02 4.00e+02 pdb=" CD PRO A 172 " 0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET H 77 " -0.027 2.00e-02 2.50e+03 5.46e-02 2.98e+01 pdb=" C MET H 77 " 0.094 2.00e-02 2.50e+03 pdb=" O MET H 77 " -0.036 2.00e-02 2.50e+03 pdb=" N SER H 78 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT T 54 " -0.023 2.00e-02 2.50e+03 1.15e-02 3.28e+00 pdb=" N1 DT T 54 " 0.024 2.00e-02 2.50e+03 pdb=" C2 DT T 54 " 0.003 2.00e-02 2.50e+03 pdb=" O2 DT T 54 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DT T 54 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT T 54 " -0.005 2.00e-02 2.50e+03 pdb=" O4 DT T 54 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DT T 54 " -0.003 2.00e-02 2.50e+03 pdb=" C7 DT T 54 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DT T 54 " 0.002 2.00e-02 2.50e+03 ... (remaining 4686 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2466 2.74 - 3.28: 27327 3.28 - 3.82: 47058 3.82 - 4.36: 55865 4.36 - 4.90: 94223 Nonbonded interactions: 226939 Sorted by model distance: nonbonded pdb=" OD2 ASP C1101 " pdb=" OG SER C1127 " model vdw 2.200 3.040 nonbonded pdb=" OG1 THR H 103 " pdb=" OH TYR H 160 " model vdw 2.213 3.040 nonbonded pdb=" ND2 ASN B 155 " pdb=" OE1 GLU C 834 " model vdw 2.215 3.120 nonbonded pdb=" OD1 ASP C 784 " pdb=" OG1 THR C 787 " model vdw 2.226 3.040 nonbonded pdb=" O ASP C 51 " pdb=" NZ LYS C 263 " model vdw 2.234 3.120 ... (remaining 226934 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 7 through 227) selection = chain 'B' } 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=1.00 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 29.760 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 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 0.091 27891 Z= 0.242 Angle : 0.631 11.341 38020 Z= 0.421 Chirality : 0.044 0.312 4285 Planarity : 0.004 0.159 4689 Dihedral : 16.817 148.926 10885 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.68 % Favored : 98.26 % Rotamer: Outliers : 0.25 % Allowed : 10.12 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: 3214 helix: 1.46 (0.15), residues: 1259 sheet: 0.57 (0.26), residues: 413 loop : 0.71 (0.17), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 61 TYR 0.014 0.001 TYR C1098 PHE 0.022 0.001 PHE B 65 TRP 0.012 0.001 TRP C 765 HIS 0.005 0.001 HIS H 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.24 (27891) covalent geometry : angle 0.63112 / 0.42 (38020) hydrogen bonds : bond 0.14395 / 9.69 ( 1256) hydrogen bonds : angle 6.37236 / 4.65 ( 3465) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 614 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 PRO cc_start: 0.7972 (Cg_endo) cc_final: 0.7724 (Cg_exo) REVERT: A 10 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6272 (pt0) REVERT: A 29 GLU cc_start: 0.6828 (mm-30) cc_final: 0.6377 (mt-10) REVERT: A 54 LYS cc_start: 0.6201 (ttpp) cc_final: 0.5696 (mtpt) REVERT: A 103 ASP cc_start: 0.6105 (p0) cc_final: 0.5463 (p0) REVERT: A 119 GLU cc_start: 0.7273 (tt0) cc_final: 0.6932 (mt-10) REVERT: A 143 ASN cc_start: 0.5494 (p0) cc_final: 0.5264 (p0) REVERT: A 190 ASP cc_start: 0.7031 (m-30) cc_final: 0.6606 (p0) REVERT: B 26 GLU cc_start: 0.7735 (pt0) cc_final: 0.6705 (pm20) REVERT: B 90 TYR cc_start: 0.7838 (m-80) cc_final: 0.7479 (m-10) REVERT: B 115 ASP cc_start: 0.6268 (p0) cc_final: 0.5862 (p0) REVERT: B 119 GLU cc_start: 0.7441 (tt0) cc_final: 0.6903 (mt-10) REVERT: B 124 GLU cc_start: 0.7678 (pm20) cc_final: 0.7379 (pm20) REVERT: B 126 LYS cc_start: 0.8168 (tttt) cc_final: 0.7904 (tttm) REVERT: B 132 LYS cc_start: 0.7424 (ttmm) cc_final: 0.7088 (tttt) REVERT: B 204 ILE cc_start: 0.7382 (tt) cc_final: 0.6901 (tp) REVERT: B 208 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6589 (tp30) REVERT: C 13 LYS cc_start: 0.7698 (mttt) cc_final: 0.7485 (mttt) REVERT: C 35 LYS cc_start: 0.7068 (mttt) cc_final: 0.6745 (mttt) REVERT: C 38 GLU cc_start: 0.7700 (tt0) cc_final: 0.7274 (mm-30) REVERT: C 47 GLU cc_start: 0.8003 (tt0) cc_final: 0.7710 (tt0) REVERT: C 50 ARG cc_start: 0.6170 (tpp-160) cc_final: 0.5906 (tpp-160) REVERT: C 51 ASP cc_start: 0.6455 (m-30) cc_final: 0.6217 (m-30) REVERT: C 67 VAL cc_start: 0.7375 (t) cc_final: 0.7053 (m) REVERT: C 98 LEU cc_start: 0.6699 (tp) cc_final: 0.6288 (tp) REVERT: C 113 MET cc_start: 0.7573 (tpp) cc_final: 0.7311 (mmm) REVERT: C 165 ASN cc_start: 0.6572 (t0) cc_final: 0.6359 (t0) REVERT: C 266 ASP cc_start: 0.6345 (t0) cc_final: 0.5549 (m-30) REVERT: C 277 LYS cc_start: 0.5923 (tttt) cc_final: 0.5645 (ttpp) REVERT: C 458 LYS cc_start: 0.7238 (tttt) cc_final: 0.6896 (tttp) REVERT: C 500 MET cc_start: 0.2977 (tpt) cc_final: 0.2428 (mmm) REVERT: C 520 GLU cc_start: 0.5969 (mt-10) cc_final: 0.5532 (pt0) REVERT: C 535 ARG cc_start: 0.6632 (mtt180) cc_final: 0.6040 (mtm180) REVERT: C 577 ASN cc_start: 0.6664 (p0) cc_final: 0.6333 (p0) REVERT: C 585 ARG cc_start: 0.5925 (mtt180) cc_final: 0.5483 (mtt-85) REVERT: C 589 ASP cc_start: 0.6053 (m-30) cc_final: 0.5307 (t70) REVERT: C 638 MET cc_start: 0.5862 (mtt) cc_final: 0.5586 (mtt) REVERT: C 797 GLU cc_start: 0.6630 (pm20) cc_final: 0.6406 (pt0) REVERT: C 799 ARG cc_start: 0.7138 (ttm110) cc_final: 0.6720 (ttm-80) REVERT: C 814 ASN cc_start: 0.6655 (m-40) cc_final: 0.6315 (t0) REVERT: C 834 GLU cc_start: 0.8155 (tt0) cc_final: 0.7726 (pm20) REVERT: C 839 ASP cc_start: 0.6880 (m-30) cc_final: 0.6439 (m-30) REVERT: C 880 HIS cc_start: 0.6354 (p-80) cc_final: 0.5923 (t-90) REVERT: C 966 MET cc_start: 0.6629 (mtm) cc_final: 0.6404 (mtm) REVERT: C 1043 MET cc_start: 0.5365 (ptt) cc_final: 0.4188 (tmm) REVERT: C 1045 ASP cc_start: 0.6814 (m-30) cc_final: 0.5776 (t0) REVERT: C 1154 MET cc_start: 0.7290 (mtm) cc_final: 0.7038 (ttm) REVERT: D 10 MET cc_start: 0.7942 (ttm) cc_final: 0.7525 (ttt) REVERT: D 11 LYS cc_start: 0.7303 (tttt) cc_final: 0.6743 (tttm) REVERT: D 43 LYS cc_start: 0.7542 (tppt) cc_final: 0.7259 (tttm) REVERT: D 86 LYS cc_start: 0.6169 (tttt) cc_final: 0.5805 (mptt) REVERT: D 130 TYR cc_start: 0.8210 (m-80) cc_final: 0.7934 (m-80) REVERT: D 154 GLU cc_start: 0.5941 (mt-10) cc_final: 0.5693 (mt-10) REVERT: D 155 PHE cc_start: 0.6608 (t80) cc_final: 0.6366 (t80) REVERT: D 216 PHE cc_start: 0.7127 (m-80) cc_final: 0.6899 (m-80) REVERT: D 237 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7698 (mm-30) REVERT: D 351 LYS cc_start: 0.7756 (mmtt) cc_final: 0.6980 (mptt) REVERT: D 406 ARG cc_start: 0.7045 (ttm170) cc_final: 0.6601 (ttp-170) REVERT: D 432 GLU cc_start: 0.7349 (mm-30) cc_final: 0.6499 (mp0) REVERT: D 453 ASP cc_start: 0.8121 (m-30) cc_final: 0.7702 (m-30) REVERT: D 473 MET cc_start: 0.8862 (mtp) cc_final: 0.8581 (mtp) REVERT: D 486 LYS cc_start: 0.7706 (mttt) cc_final: 0.7271 (mmtt) REVERT: D 494 ASP cc_start: 0.7140 (t0) cc_final: 0.6886 (t0) REVERT: D 510 VAL cc_start: 0.8544 (m) cc_final: 0.8160 (p) REVERT: D 584 GLU cc_start: 0.7114 (tt0) cc_final: 0.6875 (tm-30) REVERT: D 592 ASN cc_start: 0.8341 (m-40) cc_final: 0.7882 (t0) REVERT: D 603 GLU cc_start: 0.7021 (tp30) cc_final: 0.6658 (tt0) REVERT: D 608 GLU cc_start: 0.7099 (tt0) cc_final: 0.6741 (tt0) REVERT: D 617 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7241 (mp0) REVERT: D 633 ASN cc_start: 0.7420 (t0) cc_final: 0.7092 (t0) REVERT: D 642 MET cc_start: 0.7708 (mtp) cc_final: 0.7285 (mmm) REVERT: D 789 LYS cc_start: 0.6233 (tttt) cc_final: 0.5930 (tttp) REVERT: D 933 GLU cc_start: 0.7204 (tm-30) cc_final: 0.6976 (tm-30) REVERT: D 1044 LEU cc_start: 0.6524 (tt) cc_final: 0.6102 (tt) REVERT: D 1053 LYS cc_start: 0.8049 (tttt) cc_final: 0.7566 (ttmm) REVERT: D 1054 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6753 (mm-30) REVERT: D 1065 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6576 (tt0) REVERT: D 1109 GLU cc_start: 0.6554 (tp30) cc_final: 0.5604 (tm-30) REVERT: D 1129 LYS cc_start: 0.7015 (tttt) cc_final: 0.6411 (tptp) REVERT: D 1163 LEU cc_start: 0.8174 (mt) cc_final: 0.7942 (mt) REVERT: D 1181 MET cc_start: 0.8296 (mmm) cc_final: 0.8068 (mmm) REVERT: D 1188 LYS cc_start: 0.7355 (mttt) cc_final: 0.6653 (mtpp) REVERT: E 14 LYS cc_start: 0.5243 (OUTLIER) cc_final: 0.4828 (pttp) REVERT: F 25 LYS cc_start: 0.6788 (mttm) cc_final: 0.6308 (mptt) REVERT: G 29 GLN cc_start: 0.7103 (mm-40) cc_final: 0.6180 (mm-40) REVERT: G 39 LYS cc_start: 0.7339 (ttpp) cc_final: 0.6562 (pttt) REVERT: G 50 LYS cc_start: 0.7910 (tptt) cc_final: 0.7494 (tptp) REVERT: H 33 ASP cc_start: 0.7521 (m-30) cc_final: 0.7213 (m-30) REVERT: H 52 LYS cc_start: 0.5478 (mttt) cc_final: 0.3881 (ttpp) REVERT: H 56 HIS cc_start: 0.7265 (p90) cc_final: 0.6691 (p90) REVERT: H 65 MET cc_start: 0.6394 (mmm) cc_final: 0.5912 (mmm) REVERT: H 81 ARG cc_start: 0.5936 (mtt180) cc_final: 0.5044 (mtp180) REVERT: H 144 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6362 (tt0) REVERT: H 166 ASP cc_start: 0.6017 (m-30) cc_final: 0.5630 (m-30) REVERT: H 201 GLU cc_start: 0.6267 (mm-30) cc_final: 0.5945 (mt-10) REVERT: H 237 MET cc_start: 0.7116 (tpt) cc_final: 0.6646 (tpt) REVERT: H 245 THR cc_start: 0.7164 (m) cc_final: 0.6902 (p) REVERT: H 251 GLN cc_start: 0.5860 (mt0) cc_final: 0.5636 (mt0) outliers start: 7 outliers final: 3 residues processed: 620 average time/residue: 0.2307 time to fit residues: 213.0841 Evaluate side-chains 367 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 363 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain C residue 870 GLU Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 43 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.0030 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 8.9990 overall best weight: 1.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN C 109 GLN C 445 GLN C 677 HIS C 683 HIS C 970 GLN D 385 ASN D 703 ASN D 897 ASN D1062 GLN D1101 HIS E 57 GLN G 42 ASN H 23 HIS ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 HIS ** H 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.170839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.132691 restraints weight = 32203.465| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.67 r_work: 0.3302 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27891 Z= 0.156 Angle : 0.579 16.644 38020 Z= 0.311 Chirality : 0.045 0.317 4285 Planarity : 0.005 0.171 4689 Dihedral : 16.773 149.790 4453 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.40 % Favored : 98.57 % Rotamer: Outliers : 1.60 % Allowed : 12.46 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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: 1.29 (0.15), residues: 3214 helix: 1.46 (0.14), residues: 1286 sheet: 0.50 (0.26), residues: 389 loop : 0.59 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 26 TYR 0.019 0.001 TYR C1098 PHE 0.019 0.002 PHE E 40 TRP 0.010 0.001 TRP A 199 HIS 0.006 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (27891) covalent geometry : angle 0.57877 / 0.31 (38020) hydrogen bonds : bond 0.04667 / 3.16 ( 1256) hydrogen bonds : angle 5.05380 / 3.69 ( 3465) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 389 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7278 (pt0) REVERT: A 54 LYS cc_start: 0.6775 (ttpp) cc_final: 0.6553 (mtpt) REVERT: A 103 ASP cc_start: 0.5939 (p0) cc_final: 0.5285 (p0) REVERT: A 106 GLU cc_start: 0.6614 (mp0) cc_final: 0.6274 (mt-10) REVERT: A 126 LYS cc_start: 0.6634 (tttt) cc_final: 0.6068 (pttt) REVERT: B 16 GLU cc_start: 0.6905 (mm-30) cc_final: 0.6163 (mm-30) REVERT: B 74 ASP cc_start: 0.7975 (p0) cc_final: 0.7625 (p0) REVERT: B 182 ASN cc_start: 0.7607 (t0) cc_final: 0.7324 (t0) REVERT: C 51 ASP cc_start: 0.6720 (m-30) cc_final: 0.6358 (m-30) REVERT: C 109 GLN cc_start: 0.4844 (tt0) cc_final: 0.4479 (tt0) REVERT: C 116 PHE cc_start: 0.7324 (t80) cc_final: 0.7111 (t80) REVERT: C 148 GLU cc_start: 0.4913 (tt0) cc_final: 0.4444 (tt0) REVERT: C 163 ILE cc_start: 0.7040 (mt) cc_final: 0.6732 (tt) REVERT: C 165 ASN cc_start: 0.6746 (t0) cc_final: 0.6436 (t0) REVERT: C 178 ASP cc_start: 0.5794 (m-30) cc_final: 0.5387 (t70) REVERT: C 263 LYS cc_start: 0.7598 (mmmt) cc_final: 0.6182 (mmmt) REVERT: C 500 MET cc_start: 0.4105 (tpt) cc_final: 0.3716 (mmm) REVERT: C 607 MET cc_start: 0.7848 (mmp) cc_final: 0.7524 (mmt) REVERT: C 638 MET cc_start: 0.7827 (mtt) cc_final: 0.7544 (mtt) REVERT: C 677 HIS cc_start: 0.8598 (m90) cc_final: 0.8213 (m90) REVERT: C 799 ARG cc_start: 0.7814 (ttm110) cc_final: 0.7399 (ttm-80) REVERT: C 814 ASN cc_start: 0.6574 (m-40) cc_final: 0.6296 (t0) REVERT: C 839 ASP cc_start: 0.7697 (m-30) cc_final: 0.7463 (m-30) REVERT: C 1045 ASP cc_start: 0.6891 (m-30) cc_final: 0.6346 (t0) REVERT: D 10 MET cc_start: 0.8099 (ttm) cc_final: 0.7885 (ttt) REVERT: D 11 LYS cc_start: 0.8345 (tttt) cc_final: 0.7903 (tttm) REVERT: D 260 ARG cc_start: 0.8339 (ttm170) cc_final: 0.8078 (ttm-80) REVERT: D 303 ARG cc_start: 0.7329 (mmt180) cc_final: 0.6932 (tpt90) REVERT: D 351 LYS cc_start: 0.8365 (mmtt) cc_final: 0.8100 (mptt) REVERT: D 432 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7023 (mp0) REVERT: D 494 ASP cc_start: 0.8119 (t0) cc_final: 0.7903 (t0) REVERT: D 510 VAL cc_start: 0.9037 (m) cc_final: 0.8619 (p) REVERT: D 668 VAL cc_start: 0.7554 (p) cc_final: 0.7338 (p) REVERT: D 690 GLN cc_start: 0.5046 (OUTLIER) cc_final: 0.4786 (tm-30) REVERT: D 708 ILE cc_start: 0.6080 (mt) cc_final: 0.5852 (mm) REVERT: D 789 LYS cc_start: 0.7324 (tttt) cc_final: 0.7056 (ttmm) REVERT: D 835 GLU cc_start: 0.6489 (tp30) cc_final: 0.6165 (pt0) REVERT: D 1053 LYS cc_start: 0.8429 (tttt) cc_final: 0.7946 (ttmm) REVERT: D 1054 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7565 (mm-30) REVERT: D 1109 GLU cc_start: 0.6277 (tp30) cc_final: 0.5405 (tm-30) REVERT: D 1129 LYS cc_start: 0.7840 (tttt) cc_final: 0.7637 (tptp) REVERT: D 1181 MET cc_start: 0.9009 (mmm) cc_final: 0.8703 (mmm) REVERT: D 1188 LYS cc_start: 0.8042 (mttt) cc_final: 0.7662 (mtpp) REVERT: E 57 GLN cc_start: 0.3471 (OUTLIER) cc_final: 0.2766 (mm110) REVERT: F 25 LYS cc_start: 0.8346 (mttm) cc_final: 0.7778 (mmtt) REVERT: F 31 ASP cc_start: 0.7742 (t70) cc_final: 0.7467 (t70) REVERT: G 29 GLN cc_start: 0.7119 (mm-40) cc_final: 0.6519 (mm-40) REVERT: G 50 LYS cc_start: 0.8022 (tptt) cc_final: 0.7596 (tptp) REVERT: H 52 LYS cc_start: 0.6452 (mttt) cc_final: 0.4808 (ttpp) REVERT: H 56 HIS cc_start: 0.7260 (p90) cc_final: 0.7011 (p90) REVERT: H 144 GLU cc_start: 0.7011 (mt-10) cc_final: 0.6667 (tt0) REVERT: H 237 MET cc_start: 0.7402 (tpt) cc_final: 0.7199 (tpt) outliers start: 45 outliers final: 22 residues processed: 421 average time/residue: 0.2007 time to fit residues: 130.6211 Evaluate side-chains 344 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 320 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 852 GLU Chi-restraints excluded: chain C residue 859 LEU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 920 HIS Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1103 THR Chi-restraints excluded: chain C residue 1132 MET Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 690 GLN Chi-restraints excluded: chain D residue 730 ILE Chi-restraints excluded: chain D residue 1049 SER Chi-restraints excluded: chain E residue 57 GLN Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain H residue 204 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 322 optimal weight: 40.0000 chunk 273 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 237 optimal weight: 6.9990 chunk 276 optimal weight: 10.0000 chunk 196 optimal weight: 9.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 280 HIS C 472 GLN C 724 ASN D 675 GLN ** D 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 897 ASN ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.164539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.126304 restraints weight = 32777.415| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.78 r_work: 0.3198 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 27891 Z= 0.257 Angle : 0.661 18.747 38020 Z= 0.352 Chirality : 0.049 0.312 4285 Planarity : 0.006 0.173 4689 Dihedral : 16.834 146.870 4443 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.02 % Favored : 97.95 % Rotamer: Outliers : 3.12 % Allowed : 13.25 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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: 0.70 (0.14), residues: 3214 helix: 0.96 (0.14), residues: 1280 sheet: 0.30 (0.26), residues: 392 loop : 0.23 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 166 TYR 0.029 0.002 TYR C1098 PHE 0.023 0.002 PHE G 47 TRP 0.013 0.002 TRP A 199 HIS 0.008 0.002 HIS B 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00614 / 0.26 (27891) covalent geometry : angle 0.66126 / 0.35 (38020) hydrogen bonds : bond 0.05224 / 3.53 ( 1256) hydrogen bonds : angle 5.06817 / 3.66 ( 3465) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 338 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7371 (pt0) REVERT: A 54 LYS cc_start: 0.7119 (OUTLIER) cc_final: 0.6849 (mtpt) REVERT: A 103 ASP cc_start: 0.6248 (p0) cc_final: 0.5554 (p0) REVERT: A 106 GLU cc_start: 0.6643 (mp0) cc_final: 0.6368 (mt-10) REVERT: A 126 LYS cc_start: 0.6581 (tttt) cc_final: 0.6132 (pttp) REVERT: C 47 GLU cc_start: 0.8140 (tt0) cc_final: 0.7882 (tt0) REVERT: C 51 ASP cc_start: 0.6607 (m-30) cc_final: 0.6213 (m-30) REVERT: C 109 GLN cc_start: 0.5075 (tt0) cc_final: 0.4754 (tt0) REVERT: C 116 PHE cc_start: 0.7451 (t80) cc_final: 0.7139 (t80) REVERT: C 148 GLU cc_start: 0.5303 (tt0) cc_final: 0.4988 (tt0) REVERT: C 178 ASP cc_start: 0.5802 (m-30) cc_final: 0.5379 (t70) REVERT: C 263 LYS cc_start: 0.7504 (mmmt) cc_final: 0.6236 (mmmt) REVERT: C 266 ASP cc_start: 0.7047 (m-30) cc_final: 0.5866 (p0) REVERT: C 500 MET cc_start: 0.3985 (tpt) cc_final: 0.3709 (mmm) REVERT: C 579 LYS cc_start: 0.6791 (mtpt) cc_final: 0.6454 (mmtm) REVERT: C 638 MET cc_start: 0.7953 (mtt) cc_final: 0.7729 (mtt) REVERT: C 814 ASN cc_start: 0.6835 (m-40) cc_final: 0.6590 (t0) REVERT: C 978 MET cc_start: 0.9202 (tpt) cc_final: 0.8915 (tpt) REVERT: C 1045 ASP cc_start: 0.6884 (m-30) cc_final: 0.6290 (t0) REVERT: D 10 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7945 (ttt) REVERT: D 11 LYS cc_start: 0.8373 (tttt) cc_final: 0.7954 (tttm) REVERT: D 260 ARG cc_start: 0.8415 (ttm170) cc_final: 0.7896 (mtp85) REVERT: D 351 LYS cc_start: 0.8580 (mmtt) cc_final: 0.8250 (mptt) REVERT: D 432 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7260 (mp0) REVERT: D 451 ASP cc_start: 0.8191 (p0) cc_final: 0.7784 (p0) REVERT: D 507 LYS cc_start: 0.8830 (mmmt) cc_final: 0.8354 (mmmt) REVERT: D 789 LYS cc_start: 0.7507 (tttt) cc_final: 0.7162 (ttmm) REVERT: D 835 GLU cc_start: 0.6591 (tp30) cc_final: 0.6162 (pt0) REVERT: D 1053 LYS cc_start: 0.8426 (tttt) cc_final: 0.7868 (ttmm) REVERT: D 1129 LYS cc_start: 0.8097 (tttt) cc_final: 0.7807 (tptp) REVERT: D 1181 MET cc_start: 0.9119 (mmm) cc_final: 0.8849 (mmm) REVERT: D 1188 LYS cc_start: 0.8204 (mttt) cc_final: 0.7731 (mtpp) REVERT: E 62 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6679 (mp) REVERT: F 25 LYS cc_start: 0.8398 (mttm) cc_final: 0.7845 (mmtt) REVERT: F 32 GLU cc_start: 0.7165 (tt0) cc_final: 0.6718 (tt0) REVERT: G 27 GLU cc_start: 0.7956 (tp30) cc_final: 0.7664 (tp30) REVERT: G 29 GLN cc_start: 0.7381 (mm-40) cc_final: 0.7161 (mp10) REVERT: G 50 LYS cc_start: 0.8126 (tptt) cc_final: 0.7900 (tmtt) REVERT: H 52 LYS cc_start: 0.6880 (mttt) cc_final: 0.4740 (ttpp) REVERT: H 56 HIS cc_start: 0.7280 (p90) cc_final: 0.6887 (p90) REVERT: H 144 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6870 (tt0) REVERT: H 195 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7604 (mt-10) REVERT: H 198 MET cc_start: 0.8182 (mtp) cc_final: 0.7649 (mtt) REVERT: H 202 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.7175 (tptt) REVERT: H 237 MET cc_start: 0.7543 (tpt) cc_final: 0.7242 (tpt) REVERT: H 239 VAL cc_start: 0.7308 (t) cc_final: 0.7079 (t) outliers start: 88 outliers final: 45 residues processed: 405 average time/residue: 0.1960 time to fit residues: 124.4396 Evaluate side-chains 345 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 296 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 529 SER Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 852 GLU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1132 MET Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 552 GLU Chi-restraints excluded: chain D residue 730 ILE Chi-restraints excluded: chain D residue 864 ILE Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1099 ASP Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain H residue 202 LYS Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain H residue 245 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 201 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 275 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 280 HIS C 575 GLN C 598 ASN C1042 HIS D 218 ASN D 703 ASN ** D 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 785 HIS ** H 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.168916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.131384 restraints weight = 32378.031| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.65 r_work: 0.3242 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27891 Z= 0.126 Angle : 0.542 19.271 38020 Z= 0.289 Chirality : 0.044 0.294 4285 Planarity : 0.005 0.174 4689 Dihedral : 16.727 145.077 4443 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.43 % Favored : 98.54 % Rotamer: Outliers : 1.81 % Allowed : 15.55 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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: 1.03 (0.15), residues: 3214 helix: 1.33 (0.14), residues: 1270 sheet: 0.37 (0.26), residues: 382 loop : 0.36 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 644 TYR 0.020 0.001 TYR A 178 PHE 0.021 0.001 PHE D 155 TRP 0.011 0.001 TRP C 765 HIS 0.005 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (27891) covalent geometry : angle 0.54197 / 0.29 (38020) hydrogen bonds : bond 0.04161 / 2.83 ( 1256) hydrogen bonds : angle 4.79357 / 3.48 ( 3465) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 325 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7263 (pt0) REVERT: A 103 ASP cc_start: 0.6342 (p0) cc_final: 0.5598 (p0) REVERT: A 126 LYS cc_start: 0.6567 (tttt) cc_final: 0.6061 (pttp) REVERT: B 80 MET cc_start: 0.8361 (mmt) cc_final: 0.8159 (mmt) REVERT: B 124 GLU cc_start: 0.7682 (pm20) cc_final: 0.7316 (pm20) REVERT: B 140 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8198 (mt) REVERT: C 47 GLU cc_start: 0.8027 (tt0) cc_final: 0.7739 (tt0) REVERT: C 51 ASP cc_start: 0.6537 (m-30) cc_final: 0.6108 (m-30) REVERT: C 109 GLN cc_start: 0.5310 (tt0) cc_final: 0.5012 (tt0) REVERT: C 116 PHE cc_start: 0.7279 (t80) cc_final: 0.7002 (t80) REVERT: C 148 GLU cc_start: 0.5351 (tt0) cc_final: 0.5031 (tt0) REVERT: C 178 ASP cc_start: 0.5741 (m-30) cc_final: 0.5329 (t70) REVERT: C 263 LYS cc_start: 0.7518 (mmmt) cc_final: 0.6060 (mmmt) REVERT: C 266 ASP cc_start: 0.6885 (m-30) cc_final: 0.5727 (p0) REVERT: C 500 MET cc_start: 0.3977 (tpt) cc_final: 0.3199 (mmm) REVERT: C 504 ASP cc_start: 0.8048 (m-30) cc_final: 0.7644 (m-30) REVERT: C 579 LYS cc_start: 0.6762 (mtpt) cc_final: 0.6453 (mmtm) REVERT: C 638 MET cc_start: 0.7740 (mtt) cc_final: 0.7517 (mtt) REVERT: C 752 MET cc_start: 0.8230 (tpp) cc_final: 0.7885 (tpp) REVERT: C 793 GLU cc_start: 0.7368 (pt0) cc_final: 0.7025 (pt0) REVERT: C 814 ASN cc_start: 0.6732 (m-40) cc_final: 0.6418 (t0) REVERT: C 839 ASP cc_start: 0.7882 (m-30) cc_final: 0.7654 (m-30) REVERT: C 1045 ASP cc_start: 0.6869 (m-30) cc_final: 0.6336 (t0) REVERT: C 1145 MET cc_start: 0.8037 (mmm) cc_final: 0.7821 (mmt) REVERT: D 11 LYS cc_start: 0.8337 (tttt) cc_final: 0.7932 (tttm) REVERT: D 73 MET cc_start: -0.0607 (mpp) cc_final: -0.1177 (mpp) REVERT: D 260 ARG cc_start: 0.8389 (ttm170) cc_final: 0.7930 (mtp85) REVERT: D 303 ARG cc_start: 0.8046 (tpt170) cc_final: 0.7554 (tpt90) REVERT: D 351 LYS cc_start: 0.8467 (mmtt) cc_final: 0.8148 (mptt) REVERT: D 432 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7149 (mp0) REVERT: D 789 LYS cc_start: 0.7561 (tttt) cc_final: 0.7222 (ttmm) REVERT: D 1053 LYS cc_start: 0.8396 (tttt) cc_final: 0.7860 (ttmm) REVERT: D 1129 LYS cc_start: 0.7981 (tttt) cc_final: 0.7764 (tptp) REVERT: D 1181 MET cc_start: 0.9043 (mmm) cc_final: 0.8772 (mmm) REVERT: D 1188 LYS cc_start: 0.8072 (mttt) cc_final: 0.7648 (mtpp) REVERT: F 25 LYS cc_start: 0.8313 (mttm) cc_final: 0.8061 (mttt) REVERT: F 31 ASP cc_start: 0.7730 (t70) cc_final: 0.7362 (t70) REVERT: F 32 GLU cc_start: 0.7278 (tt0) cc_final: 0.6852 (tt0) REVERT: G 29 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6882 (mm-40) REVERT: G 50 LYS cc_start: 0.8099 (tptt) cc_final: 0.7730 (tptp) REVERT: H 52 LYS cc_start: 0.6754 (mttt) cc_final: 0.4820 (ttpp) REVERT: H 56 HIS cc_start: 0.7166 (p90) cc_final: 0.6760 (p90) REVERT: H 144 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7068 (tt0) REVERT: H 195 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7456 (mt-10) REVERT: H 198 MET cc_start: 0.8186 (mtp) cc_final: 0.7578 (mtt) REVERT: H 202 LYS cc_start: 0.7288 (OUTLIER) cc_final: 0.7085 (tptt) REVERT: H 237 MET cc_start: 0.7478 (tpt) cc_final: 0.7260 (tpt) REVERT: H 239 VAL cc_start: 0.7391 (t) cc_final: 0.7132 (t) outliers start: 51 outliers final: 32 residues processed: 366 average time/residue: 0.2052 time to fit residues: 117.1601 Evaluate side-chains 325 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 291 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 797 GLU Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 852 GLU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1132 MET Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 824 THR Chi-restraints excluded: chain D residue 864 ILE Chi-restraints excluded: chain D residue 1139 SER Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain H residue 202 LYS Chi-restraints excluded: chain H residue 204 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 14 optimal weight: 10.0000 chunk 316 optimal weight: 8.9990 chunk 291 optimal weight: 8.9990 chunk 136 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 202 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 ASN C 598 ASN D 218 ASN ** D 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1101 HIS ** H 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.168632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.130717 restraints weight = 32377.975| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.64 r_work: 0.3242 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27891 Z= 0.136 Angle : 0.529 19.492 38020 Z= 0.281 Chirality : 0.044 0.296 4285 Planarity : 0.005 0.175 4689 Dihedral : 16.634 143.325 4443 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.80 % Favored : 98.16 % Rotamer: Outliers : 2.38 % Allowed : 15.98 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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: 1.09 (0.15), residues: 3214 helix: 1.46 (0.14), residues: 1264 sheet: 0.37 (0.26), residues: 390 loop : 0.34 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 644 TYR 0.021 0.001 TYR A 178 PHE 0.020 0.001 PHE D 155 TRP 0.012 0.001 TRP C 765 HIS 0.010 0.001 HIS D1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (27891) covalent geometry : angle 0.52946 / 0.28 (38020) hydrogen bonds : bond 0.04035 / 2.73 ( 1256) hydrogen bonds : angle 4.68762 / 3.40 ( 3465) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 315 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7308 (pt0) REVERT: A 103 ASP cc_start: 0.6435 (p0) cc_final: 0.5660 (p0) REVERT: A 126 LYS cc_start: 0.6624 (tttt) cc_final: 0.6073 (pttp) REVERT: A 174 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7491 (mm-30) REVERT: B 140 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8137 (mt) REVERT: C 51 ASP cc_start: 0.6428 (m-30) cc_final: 0.6007 (m-30) REVERT: C 75 LYS cc_start: 0.6546 (mtmt) cc_final: 0.6321 (mttt) REVERT: C 178 ASP cc_start: 0.5776 (m-30) cc_final: 0.5368 (t70) REVERT: C 263 LYS cc_start: 0.7571 (mmmt) cc_final: 0.6209 (mmmt) REVERT: C 266 ASP cc_start: 0.6986 (m-30) cc_final: 0.5769 (p0) REVERT: C 500 MET cc_start: 0.4056 (tpt) cc_final: 0.3262 (mmm) REVERT: C 504 ASP cc_start: 0.8161 (m-30) cc_final: 0.7705 (m-30) REVERT: C 579 LYS cc_start: 0.6770 (mtpt) cc_final: 0.6449 (mmtm) REVERT: C 638 MET cc_start: 0.7739 (mtt) cc_final: 0.7488 (mtt) REVERT: C 793 GLU cc_start: 0.7343 (pt0) cc_final: 0.7002 (pt0) REVERT: C 814 ASN cc_start: 0.6839 (m-40) cc_final: 0.6401 (t0) REVERT: C 1045 ASP cc_start: 0.6913 (m-30) cc_final: 0.6415 (t0) REVERT: D 11 LYS cc_start: 0.8315 (tttt) cc_final: 0.7961 (tttm) REVERT: D 73 MET cc_start: -0.0623 (mpp) cc_final: -0.1084 (mpp) REVERT: D 260 ARG cc_start: 0.8320 (ttm170) cc_final: 0.7918 (mtp85) REVERT: D 303 ARG cc_start: 0.8053 (tpt170) cc_final: 0.7593 (tpt90) REVERT: D 351 LYS cc_start: 0.8462 (mmtt) cc_final: 0.8136 (mptt) REVERT: D 432 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7215 (mp0) REVERT: D 789 LYS cc_start: 0.7382 (tttt) cc_final: 0.7106 (ttmm) REVERT: D 1053 LYS cc_start: 0.8422 (tttt) cc_final: 0.7907 (ttmm) REVERT: D 1129 LYS cc_start: 0.7958 (tttt) cc_final: 0.7727 (tptp) REVERT: D 1181 MET cc_start: 0.9054 (mmm) cc_final: 0.8772 (mmm) REVERT: D 1188 LYS cc_start: 0.7980 (mttt) cc_final: 0.7626 (mtpp) REVERT: F 25 LYS cc_start: 0.8285 (mttm) cc_final: 0.8012 (mttt) REVERT: F 32 GLU cc_start: 0.7200 (tt0) cc_final: 0.6783 (tt0) REVERT: G 29 GLN cc_start: 0.7188 (mm-40) cc_final: 0.6964 (mp10) REVERT: G 50 LYS cc_start: 0.8027 (tptt) cc_final: 0.7643 (tptp) REVERT: H 52 LYS cc_start: 0.6795 (mttt) cc_final: 0.4814 (ttpt) REVERT: H 56 HIS cc_start: 0.7156 (p90) cc_final: 0.6766 (p90) REVERT: H 144 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7022 (tt0) REVERT: H 195 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7457 (mt-10) REVERT: H 198 MET cc_start: 0.8184 (mtp) cc_final: 0.7567 (mtt) REVERT: H 202 LYS cc_start: 0.7261 (OUTLIER) cc_final: 0.7047 (tptt) REVERT: H 237 MET cc_start: 0.7645 (tpt) cc_final: 0.7377 (tpt) REVERT: H 239 VAL cc_start: 0.7401 (t) cc_final: 0.7120 (t) outliers start: 67 outliers final: 45 residues processed: 373 average time/residue: 0.2062 time to fit residues: 120.5720 Evaluate side-chains 344 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 297 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 529 SER Chi-restraints excluded: chain C residue 797 GLU Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 852 GLU Chi-restraints excluded: chain C residue 859 LEU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 965 ARG Chi-restraints excluded: chain C residue 1132 MET Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 730 ILE Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 824 THR Chi-restraints excluded: chain D residue 864 ILE Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1139 SER Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 202 LYS Chi-restraints excluded: chain H residue 204 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 246 optimal weight: 7.9990 chunk 93 optimal weight: 30.0000 chunk 35 optimal weight: 9.9990 chunk 278 optimal weight: 9.9990 chunk 108 optimal weight: 0.6980 chunk 214 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 chunk 300 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 109 GLN C 598 ASN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 ASN ** D 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1101 HIS ** H 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.168765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.130987 restraints weight = 32347.751| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.65 r_work: 0.3281 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27891 Z= 0.135 Angle : 0.530 22.925 38020 Z= 0.279 Chirality : 0.044 0.268 4285 Planarity : 0.005 0.184 4689 Dihedral : 16.571 141.934 4443 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.74 % Favored : 98.23 % Rotamer: Outliers : 2.49 % Allowed : 16.58 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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: 1.10 (0.15), residues: 3214 helix: 1.47 (0.14), residues: 1276 sheet: 0.34 (0.26), residues: 402 loop : 0.34 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 752 TYR 0.021 0.001 TYR A 178 PHE 0.019 0.001 PHE D 155 TRP 0.011 0.001 TRP C 765 HIS 0.007 0.001 HIS D1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (27891) covalent geometry : angle 0.53039 / 0.28 (38020) hydrogen bonds : bond 0.03923 / 2.65 ( 1256) hydrogen bonds : angle 4.63402 / 3.37 ( 3465) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 301 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7230 (pt0) REVERT: A 103 ASP cc_start: 0.6301 (p0) cc_final: 0.5556 (p0) REVERT: A 126 LYS cc_start: 0.6637 (tttt) cc_final: 0.6065 (pttp) REVERT: A 174 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7508 (mm-30) REVERT: B 140 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8146 (mt) REVERT: B 146 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7902 (mtp85) REVERT: C 51 ASP cc_start: 0.6387 (m-30) cc_final: 0.5971 (m-30) REVERT: C 75 LYS cc_start: 0.6545 (mtmt) cc_final: 0.6336 (mttt) REVERT: C 178 ASP cc_start: 0.5826 (m-30) cc_final: 0.5402 (t70) REVERT: C 263 LYS cc_start: 0.7377 (mmmt) cc_final: 0.6269 (mmmt) REVERT: C 266 ASP cc_start: 0.6931 (m-30) cc_final: 0.5889 (p0) REVERT: C 500 MET cc_start: 0.4133 (tpt) cc_final: 0.3333 (mmm) REVERT: C 504 ASP cc_start: 0.8228 (m-30) cc_final: 0.7736 (m-30) REVERT: C 579 LYS cc_start: 0.6778 (mtpt) cc_final: 0.6476 (mmtm) REVERT: C 607 MET cc_start: 0.7836 (mmp) cc_final: 0.7600 (mmt) REVERT: C 638 MET cc_start: 0.7615 (mtt) cc_final: 0.7374 (mtt) REVERT: C 793 GLU cc_start: 0.7309 (pt0) cc_final: 0.6993 (pt0) REVERT: C 814 ASN cc_start: 0.6608 (m-40) cc_final: 0.6236 (t0) REVERT: C 925 MET cc_start: 0.7718 (mmm) cc_final: 0.7318 (mtt) REVERT: C 999 ASP cc_start: 0.7402 (m-30) cc_final: 0.7120 (m-30) REVERT: C 1045 ASP cc_start: 0.6844 (m-30) cc_final: 0.6376 (t0) REVERT: D 11 LYS cc_start: 0.8268 (tttt) cc_final: 0.7861 (tttt) REVERT: D 73 MET cc_start: -0.0339 (mpp) cc_final: -0.0859 (mpp) REVERT: D 119 ASP cc_start: 0.6561 (t70) cc_final: 0.6350 (t0) REVERT: D 138 ASP cc_start: 0.7042 (OUTLIER) cc_final: 0.6643 (m-30) REVERT: D 260 ARG cc_start: 0.8289 (ttm170) cc_final: 0.7875 (mtp85) REVERT: D 303 ARG cc_start: 0.8045 (tpt170) cc_final: 0.7597 (tpt90) REVERT: D 351 LYS cc_start: 0.8440 (mmtt) cc_final: 0.8126 (mptt) REVERT: D 432 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7287 (mp0) REVERT: D 693 ARG cc_start: 0.4647 (OUTLIER) cc_final: 0.3310 (ttp-170) REVERT: D 754 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6614 (pp) REVERT: D 789 LYS cc_start: 0.7371 (tttt) cc_final: 0.7113 (ttmm) REVERT: D 835 GLU cc_start: 0.6565 (tp30) cc_final: 0.6279 (pt0) REVERT: D 1053 LYS cc_start: 0.8423 (tttt) cc_final: 0.7886 (ttmm) REVERT: D 1109 GLU cc_start: 0.6029 (tp30) cc_final: 0.5588 (tm-30) REVERT: D 1129 LYS cc_start: 0.7913 (tttt) cc_final: 0.7697 (tptp) REVERT: D 1181 MET cc_start: 0.9037 (mmm) cc_final: 0.8782 (mmm) REVERT: D 1188 LYS cc_start: 0.8061 (mttt) cc_final: 0.7687 (mtpp) REVERT: E 62 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6679 (mp) REVERT: F 25 LYS cc_start: 0.8273 (mttm) cc_final: 0.7998 (mttt) REVERT: F 32 GLU cc_start: 0.7242 (tt0) cc_final: 0.6854 (tt0) REVERT: G 29 GLN cc_start: 0.7322 (mm-40) cc_final: 0.7080 (mp10) REVERT: H 52 LYS cc_start: 0.6859 (mttt) cc_final: 0.4839 (ttpt) REVERT: H 56 HIS cc_start: 0.7133 (p90) cc_final: 0.6757 (p90) REVERT: H 144 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7067 (tt0) REVERT: H 195 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7461 (mt-10) REVERT: H 198 MET cc_start: 0.8163 (mtp) cc_final: 0.7570 (mtt) REVERT: H 202 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.7050 (tptt) REVERT: H 206 ILE cc_start: 0.7326 (mm) cc_final: 0.7106 (tt) REVERT: H 237 MET cc_start: 0.7653 (tpt) cc_final: 0.7354 (tpt) REVERT: H 239 VAL cc_start: 0.7339 (t) cc_final: 0.7086 (t) REVERT: H 251 GLN cc_start: 0.5820 (mt0) cc_final: 0.5348 (pt0) outliers start: 70 outliers final: 50 residues processed: 361 average time/residue: 0.2079 time to fit residues: 117.1247 Evaluate side-chains 341 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 284 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 401 ASP Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 797 GLU Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 852 GLU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 965 ARG Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1103 THR Chi-restraints excluded: chain C residue 1132 MET Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 693 ARG Chi-restraints excluded: chain D residue 730 ILE Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 824 THR Chi-restraints excluded: chain D residue 864 ILE Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1139 SER Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 25 ASN Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 202 LYS Chi-restraints excluded: chain H residue 204 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 32 optimal weight: 9.9990 chunk 171 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 chunk 322 optimal weight: 40.0000 chunk 239 optimal weight: 8.9990 chunk 264 optimal weight: 9.9990 chunk 232 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 253 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 188 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 598 ASN D 218 ASN ** D 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1101 HIS ** H 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.167045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.129409 restraints weight = 32376.177| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.65 r_work: 0.3220 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27891 Z= 0.181 Angle : 0.566 23.266 38020 Z= 0.296 Chirality : 0.045 0.281 4285 Planarity : 0.005 0.186 4689 Dihedral : 16.567 141.284 4443 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.12 % Favored : 97.85 % Rotamer: Outliers : 2.91 % Allowed : 16.44 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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: 0.95 (0.15), residues: 3214 helix: 1.31 (0.14), residues: 1284 sheet: 0.36 (0.26), residues: 388 loop : 0.24 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 752 TYR 0.022 0.002 TYR C1098 PHE 0.021 0.002 PHE D 654 TRP 0.015 0.001 TRP C 765 HIS 0.007 0.001 HIS D1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (27891) covalent geometry : angle 0.56569 / 0.30 (38020) hydrogen bonds : bond 0.04178 / 2.82 ( 1256) hydrogen bonds : angle 4.68989 / 3.40 ( 3465) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 295 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7211 (pt0) REVERT: A 103 ASP cc_start: 0.6335 (p0) cc_final: 0.5459 (p0) REVERT: A 174 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7503 (mm-30) REVERT: B 140 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8188 (mt) REVERT: B 146 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7792 (mtp85) REVERT: C 51 ASP cc_start: 0.6316 (m-30) cc_final: 0.5905 (m-30) REVERT: C 178 ASP cc_start: 0.5823 (m-30) cc_final: 0.5358 (t70) REVERT: C 263 LYS cc_start: 0.7365 (mmmt) cc_final: 0.6256 (mmmt) REVERT: C 500 MET cc_start: 0.4160 (tpt) cc_final: 0.3325 (mmm) REVERT: C 504 ASP cc_start: 0.8134 (m-30) cc_final: 0.7597 (m-30) REVERT: C 579 LYS cc_start: 0.6781 (mtpt) cc_final: 0.6468 (mmtm) REVERT: C 607 MET cc_start: 0.7846 (mmp) cc_final: 0.7598 (mmt) REVERT: C 638 MET cc_start: 0.7599 (mtt) cc_final: 0.7372 (mtt) REVERT: C 793 GLU cc_start: 0.7316 (pt0) cc_final: 0.6976 (pt0) REVERT: C 814 ASN cc_start: 0.6523 (m-40) cc_final: 0.6080 (t0) REVERT: C 1045 ASP cc_start: 0.6887 (m-30) cc_final: 0.6377 (t0) REVERT: D 11 LYS cc_start: 0.8274 (tttt) cc_final: 0.7926 (tttm) REVERT: D 138 ASP cc_start: 0.7064 (OUTLIER) cc_final: 0.6662 (m-30) REVERT: D 260 ARG cc_start: 0.8322 (ttm170) cc_final: 0.7898 (mtp85) REVERT: D 303 ARG cc_start: 0.8038 (tpt170) cc_final: 0.7573 (tpt90) REVERT: D 351 LYS cc_start: 0.8521 (mmtt) cc_final: 0.8146 (mptt) REVERT: D 432 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7220 (mp0) REVERT: D 693 ARG cc_start: 0.4679 (OUTLIER) cc_final: 0.3568 (ptm160) REVERT: D 754 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6555 (pp) REVERT: D 789 LYS cc_start: 0.7377 (tttt) cc_final: 0.7117 (ttmm) REVERT: D 835 GLU cc_start: 0.6416 (tp30) cc_final: 0.6177 (pt0) REVERT: D 1053 LYS cc_start: 0.8433 (tttt) cc_final: 0.7830 (ttmm) REVERT: D 1109 GLU cc_start: 0.6104 (tp30) cc_final: 0.5636 (tm-30) REVERT: D 1129 LYS cc_start: 0.7890 (tttt) cc_final: 0.7667 (tptp) REVERT: D 1181 MET cc_start: 0.9066 (mmm) cc_final: 0.8822 (mmm) REVERT: E 62 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6532 (mp) REVERT: F 25 LYS cc_start: 0.8260 (mttm) cc_final: 0.7804 (mptt) REVERT: F 32 GLU cc_start: 0.7179 (tt0) cc_final: 0.6827 (tt0) REVERT: G 27 GLU cc_start: 0.7876 (tp30) cc_final: 0.7560 (tp30) REVERT: G 29 GLN cc_start: 0.7408 (mm-40) cc_final: 0.7150 (mp10) REVERT: H 52 LYS cc_start: 0.6901 (mttt) cc_final: 0.4834 (ttpt) REVERT: H 56 HIS cc_start: 0.7154 (p90) cc_final: 0.6761 (p90) REVERT: H 144 GLU cc_start: 0.7529 (mt-10) cc_final: 0.6939 (tt0) REVERT: H 195 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7567 (mt-10) REVERT: H 198 MET cc_start: 0.8177 (mtp) cc_final: 0.7552 (mtt) REVERT: H 237 MET cc_start: 0.7654 (tpt) cc_final: 0.7383 (tpt) REVERT: H 239 VAL cc_start: 0.7364 (t) cc_final: 0.7111 (t) outliers start: 82 outliers final: 66 residues processed: 366 average time/residue: 0.2078 time to fit residues: 118.1871 Evaluate side-chains 355 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 283 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 23 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 401 ASP Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 529 SER Chi-restraints excluded: chain C residue 797 GLU Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 852 GLU Chi-restraints excluded: chain C residue 859 LEU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 964 SER Chi-restraints excluded: chain C residue 965 ARG Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1103 THR Chi-restraints excluded: chain C residue 1132 MET Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 693 ARG Chi-restraints excluded: chain D residue 730 ILE Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 824 THR Chi-restraints excluded: chain D residue 864 ILE Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1124 LEU Chi-restraints excluded: chain D residue 1139 SER Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 202 LYS Chi-restraints excluded: chain H residue 204 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 2 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 295 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 269 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 289 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 465 GLN C 598 ASN D 218 ASN ** D 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 785 HIS D1101 HIS ** H 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.167630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.129707 restraints weight = 32428.154| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.67 r_work: 0.3222 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27891 Z= 0.154 Angle : 0.539 18.286 38020 Z= 0.285 Chirality : 0.044 0.250 4285 Planarity : 0.005 0.171 4689 Dihedral : 16.522 139.722 4443 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.96 % Favored : 98.01 % Rotamer: Outliers : 2.73 % Allowed : 16.94 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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: 0.98 (0.15), residues: 3214 helix: 1.37 (0.14), residues: 1277 sheet: 0.36 (0.26), residues: 388 loop : 0.24 (0.16), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 113 TYR 0.021 0.001 TYR A 178 PHE 0.019 0.002 PHE D 155 TRP 0.012 0.001 TRP C 765 HIS 0.007 0.001 HIS D1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (27891) covalent geometry : angle 0.53905 / 0.28 (38020) hydrogen bonds : bond 0.03994 / 2.70 ( 1256) hydrogen bonds : angle 4.64701 / 3.37 ( 3465) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 303 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7178 (pt0) REVERT: A 103 ASP cc_start: 0.6432 (p0) cc_final: 0.5553 (p0) REVERT: A 126 LYS cc_start: 0.6732 (tttm) cc_final: 0.6246 (pttp) REVERT: A 174 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7487 (mm-30) REVERT: B 140 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8153 (mt) REVERT: B 146 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7757 (mtp85) REVERT: C 178 ASP cc_start: 0.5683 (m-30) cc_final: 0.5273 (t70) REVERT: C 263 LYS cc_start: 0.7524 (mmmt) cc_final: 0.6377 (mmmt) REVERT: C 419 PHE cc_start: 0.7774 (OUTLIER) cc_final: 0.7375 (m-10) REVERT: C 500 MET cc_start: 0.4403 (tpt) cc_final: 0.3583 (mmm) REVERT: C 504 ASP cc_start: 0.8131 (m-30) cc_final: 0.7597 (m-30) REVERT: C 607 MET cc_start: 0.7770 (mmp) cc_final: 0.7539 (mmt) REVERT: C 638 MET cc_start: 0.7572 (mtt) cc_final: 0.7324 (mtt) REVERT: C 793 GLU cc_start: 0.7334 (pt0) cc_final: 0.6999 (pt0) REVERT: C 814 ASN cc_start: 0.6624 (m-40) cc_final: 0.5946 (t0) REVERT: C 925 MET cc_start: 0.7916 (mmm) cc_final: 0.7442 (mtt) REVERT: C 1043 MET cc_start: 0.5119 (ptt) cc_final: 0.4903 (ptt) REVERT: C 1045 ASP cc_start: 0.6964 (m-30) cc_final: 0.6443 (t0) REVERT: D 11 LYS cc_start: 0.8277 (tttt) cc_final: 0.7935 (tttm) REVERT: D 138 ASP cc_start: 0.7068 (OUTLIER) cc_final: 0.6685 (m-30) REVERT: D 260 ARG cc_start: 0.8308 (ttm170) cc_final: 0.7896 (mtp85) REVERT: D 303 ARG cc_start: 0.8054 (tpt170) cc_final: 0.7591 (tpt90) REVERT: D 351 LYS cc_start: 0.8519 (mmtt) cc_final: 0.8143 (mptt) REVERT: D 388 SER cc_start: 0.8190 (m) cc_final: 0.7879 (t) REVERT: D 432 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7066 (mp0) REVERT: D 693 ARG cc_start: 0.4704 (OUTLIER) cc_final: 0.3553 (ptm160) REVERT: D 754 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6542 (pp) REVERT: D 789 LYS cc_start: 0.7388 (tttt) cc_final: 0.7071 (ttmm) REVERT: D 835 GLU cc_start: 0.6606 (tp30) cc_final: 0.6204 (pt0) REVERT: D 1053 LYS cc_start: 0.8525 (tttt) cc_final: 0.7908 (ttmm) REVERT: D 1109 GLU cc_start: 0.6022 (tp30) cc_final: 0.5574 (tm-30) REVERT: D 1129 LYS cc_start: 0.7950 (tttt) cc_final: 0.7687 (tptp) REVERT: D 1181 MET cc_start: 0.9054 (mmm) cc_final: 0.8806 (mmm) REVERT: E 62 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6605 (mp) REVERT: F 25 LYS cc_start: 0.8234 (mttm) cc_final: 0.7960 (mttt) REVERT: F 32 GLU cc_start: 0.7110 (tt0) cc_final: 0.6714 (tt0) REVERT: G 27 GLU cc_start: 0.7858 (tp30) cc_final: 0.7582 (tp30) REVERT: G 29 GLN cc_start: 0.7439 (mm-40) cc_final: 0.7188 (mp10) REVERT: H 52 LYS cc_start: 0.6833 (mttt) cc_final: 0.4702 (ttpt) REVERT: H 56 HIS cc_start: 0.7170 (p90) cc_final: 0.6789 (p90) REVERT: H 144 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7007 (tt0) REVERT: H 195 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7555 (mt-10) REVERT: H 198 MET cc_start: 0.8177 (mtp) cc_final: 0.7558 (mtt) REVERT: H 237 MET cc_start: 0.7640 (tpt) cc_final: 0.7395 (tpt) REVERT: H 239 VAL cc_start: 0.7201 (t) cc_final: 0.6973 (t) outliers start: 77 outliers final: 60 residues processed: 369 average time/residue: 0.2062 time to fit residues: 118.4256 Evaluate side-chains 360 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 293 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 23 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 401 ASP Chi-restraints excluded: chain C residue 419 PHE Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 529 SER Chi-restraints excluded: chain C residue 797 GLU Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 852 GLU Chi-restraints excluded: chain C residue 859 LEU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 964 SER Chi-restraints excluded: chain C residue 965 ARG Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1103 THR Chi-restraints excluded: chain C residue 1132 MET Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 216 PHE Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 693 ARG Chi-restraints excluded: chain D residue 730 ILE Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 824 THR Chi-restraints excluded: chain D residue 864 ILE Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 25 ASN Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 202 LYS Chi-restraints excluded: chain H residue 204 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 40 optimal weight: 10.0000 chunk 265 optimal weight: 9.9990 chunk 294 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 312 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 chunk 296 optimal weight: 8.9990 chunk 306 optimal weight: 8.9990 chunk 286 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 ASN C 465 GLN D 218 ASN ** D 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1101 HIS ** H 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.164228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.126123 restraints weight = 32652.062| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.70 r_work: 0.3227 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 27891 Z= 0.279 Angle : 0.659 26.170 38020 Z= 0.344 Chirality : 0.049 0.264 4285 Planarity : 0.006 0.194 4689 Dihedral : 16.640 140.432 4443 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.11 % Rotamer: Outliers : 2.88 % Allowed : 17.26 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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: 0.48 (0.14), residues: 3214 helix: 0.94 (0.14), residues: 1272 sheet: 0.16 (0.26), residues: 390 loop : -0.05 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 752 TYR 0.028 0.002 TYR C1098 PHE 0.026 0.003 PHE D 654 TRP 0.015 0.002 TRP C 765 HIS 0.007 0.002 HIS D1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.28 (27891) covalent geometry : angle 0.65947 / 0.34 (38020) hydrogen bonds : bond 0.04830 / 3.26 ( 1256) hydrogen bonds : angle 4.93500 / 3.56 ( 3465) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 301 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7333 (pt0) REVERT: A 103 ASP cc_start: 0.6489 (p0) cc_final: 0.5522 (p0) REVERT: A 174 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7566 (mm-30) REVERT: B 74 ASP cc_start: 0.8493 (p0) cc_final: 0.8249 (p0) REVERT: B 140 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8301 (mt) REVERT: B 146 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7784 (mtp85) REVERT: C 178 ASP cc_start: 0.5590 (m-30) cc_final: 0.5357 (t0) REVERT: C 263 LYS cc_start: 0.7203 (mmmt) cc_final: 0.6490 (mmmt) REVERT: C 317 GLU cc_start: 0.3610 (mt-10) cc_final: 0.3374 (tt0) REVERT: C 500 MET cc_start: 0.4759 (tpt) cc_final: 0.4057 (mmm) REVERT: C 504 ASP cc_start: 0.8182 (m-30) cc_final: 0.7673 (m-30) REVERT: C 607 MET cc_start: 0.7732 (mmp) cc_final: 0.7515 (mmt) REVERT: C 638 MET cc_start: 0.7653 (mtt) cc_final: 0.7420 (mtt) REVERT: C 793 GLU cc_start: 0.7604 (pt0) cc_final: 0.7279 (pt0) REVERT: C 814 ASN cc_start: 0.6708 (m-40) cc_final: 0.5858 (t0) REVERT: C 852 GLU cc_start: 0.3665 (OUTLIER) cc_final: 0.3013 (pm20) REVERT: C 1043 MET cc_start: 0.5549 (ptt) cc_final: 0.5284 (ptt) REVERT: C 1045 ASP cc_start: 0.6994 (m-30) cc_final: 0.6486 (t0) REVERT: C 1117 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8213 (mt-10) REVERT: D 56 LYS cc_start: 0.8286 (tptp) cc_final: 0.7395 (ptpp) REVERT: D 138 ASP cc_start: 0.7279 (OUTLIER) cc_final: 0.6883 (m-30) REVERT: D 162 TYR cc_start: 0.6027 (m-80) cc_final: 0.5764 (m-80) REVERT: D 260 ARG cc_start: 0.8394 (ttm170) cc_final: 0.7979 (mtp85) REVERT: D 303 ARG cc_start: 0.8086 (tpt170) cc_final: 0.7325 (tpp80) REVERT: D 351 LYS cc_start: 0.8629 (mmtt) cc_final: 0.8256 (mptt) REVERT: D 432 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7325 (mp0) REVERT: D 693 ARG cc_start: 0.4927 (OUTLIER) cc_final: 0.3933 (ptm160) REVERT: D 754 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6654 (pp) REVERT: D 789 LYS cc_start: 0.7520 (tttt) cc_final: 0.7185 (ttmm) REVERT: D 835 GLU cc_start: 0.6523 (tp30) cc_final: 0.6290 (pt0) REVERT: D 957 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7221 (mt) REVERT: D 1053 LYS cc_start: 0.8425 (tttt) cc_final: 0.7792 (ttmm) REVERT: D 1129 LYS cc_start: 0.8004 (tttt) cc_final: 0.7759 (tptp) REVERT: D 1181 MET cc_start: 0.9119 (mmm) cc_final: 0.8878 (mmm) REVERT: F 25 LYS cc_start: 0.8275 (mttm) cc_final: 0.7984 (mttt) REVERT: F 32 GLU cc_start: 0.7311 (tt0) cc_final: 0.6944 (tt0) REVERT: G 10 HIS cc_start: 0.8745 (OUTLIER) cc_final: 0.8128 (m-70) REVERT: G 27 GLU cc_start: 0.7970 (tp30) cc_final: 0.7719 (tp30) REVERT: H 52 LYS cc_start: 0.7048 (mttt) cc_final: 0.4777 (ttpt) REVERT: H 56 HIS cc_start: 0.7229 (p90) cc_final: 0.6833 (p90) REVERT: H 144 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7057 (tt0) REVERT: H 195 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7579 (mt-10) REVERT: H 198 MET cc_start: 0.8207 (mtp) cc_final: 0.7652 (mtt) REVERT: H 206 ILE cc_start: 0.7358 (mm) cc_final: 0.7102 (tt) REVERT: H 237 MET cc_start: 0.7755 (tpt) cc_final: 0.7528 (tpt) REVERT: H 239 VAL cc_start: 0.7125 (t) cc_final: 0.6875 (t) outliers start: 81 outliers final: 57 residues processed: 373 average time/residue: 0.2090 time to fit residues: 121.1485 Evaluate side-chains 354 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 289 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 23 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 401 ASP Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 529 SER Chi-restraints excluded: chain C residue 797 GLU Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 852 GLU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 965 ARG Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1132 MET Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 693 ARG Chi-restraints excluded: chain D residue 730 ILE Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 824 THR Chi-restraints excluded: chain D residue 864 ILE Chi-restraints excluded: chain D residue 957 LEU Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain G residue 10 HIS Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 202 LYS Chi-restraints excluded: chain H residue 204 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 311 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 318 optimal weight: 0.4980 chunk 312 optimal weight: 8.9990 chunk 247 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 250 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 ASN C 465 GLN C 907 GLN D 218 ASN D 282 GLN ** D 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 744 ASN D 785 HIS D1101 HIS ** H 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.168039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.129957 restraints weight = 32366.060| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.65 r_work: 0.3236 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27891 Z= 0.122 Angle : 0.539 22.807 38020 Z= 0.284 Chirality : 0.044 0.254 4285 Planarity : 0.005 0.185 4689 Dihedral : 16.515 137.162 4443 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.77 % Favored : 98.20 % Rotamer: Outliers : 1.95 % Allowed : 17.79 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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: 0.88 (0.15), residues: 3214 helix: 1.36 (0.14), residues: 1277 sheet: 0.26 (0.26), residues: 394 loop : 0.13 (0.16), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 644 TYR 0.022 0.001 TYR A 178 PHE 0.022 0.001 PHE D 155 TRP 0.014 0.001 TRP C 765 HIS 0.007 0.001 HIS D1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (27891) covalent geometry : angle 0.53946 / 0.28 (38020) hydrogen bonds : bond 0.03852 / 2.61 ( 1256) hydrogen bonds : angle 4.66717 / 3.39 ( 3465) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 316 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7109 (pt0) REVERT: A 103 ASP cc_start: 0.6364 (p0) cc_final: 0.5447 (p0) REVERT: A 174 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7445 (mm-30) REVERT: B 140 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8140 (mt) REVERT: C 178 ASP cc_start: 0.5691 (m-30) cc_final: 0.5489 (t0) REVERT: C 263 LYS cc_start: 0.7221 (mmmt) cc_final: 0.6227 (mmmt) REVERT: C 500 MET cc_start: 0.4530 (tpt) cc_final: 0.3698 (mmm) REVERT: C 504 ASP cc_start: 0.8052 (m-30) cc_final: 0.7539 (m-30) REVERT: C 579 LYS cc_start: 0.6798 (mtpt) cc_final: 0.6524 (mmtt) REVERT: C 638 MET cc_start: 0.7573 (mtt) cc_final: 0.7311 (mtt) REVERT: C 793 GLU cc_start: 0.7386 (pt0) cc_final: 0.7062 (pt0) REVERT: C 814 ASN cc_start: 0.6507 (m-40) cc_final: 0.6046 (t0) REVERT: C 852 GLU cc_start: 0.3388 (OUTLIER) cc_final: 0.2796 (pm20) REVERT: C 925 MET cc_start: 0.8012 (mmm) cc_final: 0.7462 (mtt) REVERT: C 1043 MET cc_start: 0.5207 (ptt) cc_final: 0.4962 (ptt) REVERT: C 1045 ASP cc_start: 0.6917 (m-30) cc_final: 0.6448 (t0) REVERT: D 138 ASP cc_start: 0.7147 (OUTLIER) cc_final: 0.6896 (m-30) REVERT: D 162 TYR cc_start: 0.6004 (m-80) cc_final: 0.5731 (m-80) REVERT: D 260 ARG cc_start: 0.8228 (ttm170) cc_final: 0.7858 (mtp85) REVERT: D 303 ARG cc_start: 0.8016 (tpt170) cc_final: 0.7237 (tpp80) REVERT: D 351 LYS cc_start: 0.8526 (mmtt) cc_final: 0.8146 (mptt) REVERT: D 432 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7049 (mp0) REVERT: D 693 ARG cc_start: 0.4696 (OUTLIER) cc_final: 0.3650 (ptm160) REVERT: D 754 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6589 (pp) REVERT: D 789 LYS cc_start: 0.7405 (tttt) cc_final: 0.7092 (ttmm) REVERT: D 835 GLU cc_start: 0.6541 (tp30) cc_final: 0.6237 (pt0) REVERT: D 957 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7037 (mt) REVERT: D 1053 LYS cc_start: 0.8529 (tttt) cc_final: 0.7950 (ttmm) REVERT: D 1109 GLU cc_start: 0.5891 (tp30) cc_final: 0.5461 (tm-30) REVERT: D 1129 LYS cc_start: 0.7966 (tttt) cc_final: 0.7696 (tptp) REVERT: D 1181 MET cc_start: 0.9028 (mmm) cc_final: 0.8786 (mmm) REVERT: F 25 LYS cc_start: 0.8089 (mttm) cc_final: 0.7811 (mttt) REVERT: F 31 ASP cc_start: 0.7696 (t70) cc_final: 0.7397 (t70) REVERT: F 32 GLU cc_start: 0.7183 (tt0) cc_final: 0.6769 (tt0) REVERT: G 27 GLU cc_start: 0.7908 (tp30) cc_final: 0.7642 (tp30) REVERT: H 52 LYS cc_start: 0.6931 (mttt) cc_final: 0.4759 (ttpt) REVERT: H 56 HIS cc_start: 0.7157 (p90) cc_final: 0.6764 (p90) REVERT: H 144 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7031 (tt0) REVERT: H 164 SER cc_start: 0.7799 (t) cc_final: 0.7587 (m) REVERT: H 195 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7550 (mt-10) REVERT: H 198 MET cc_start: 0.8162 (mtp) cc_final: 0.7543 (mtt) REVERT: H 202 LYS cc_start: 0.7324 (OUTLIER) cc_final: 0.7019 (ttmt) REVERT: H 239 VAL cc_start: 0.6994 (t) cc_final: 0.6767 (t) REVERT: H 252 GLU cc_start: 0.6437 (pt0) cc_final: 0.6043 (pt0) outliers start: 55 outliers final: 44 residues processed: 363 average time/residue: 0.2074 time to fit residues: 117.2396 Evaluate side-chains 355 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 304 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 23 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 401 ASP Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 529 SER Chi-restraints excluded: chain C residue 797 GLU Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 852 GLU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 965 ARG Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1132 MET Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 693 ARG Chi-restraints excluded: chain D residue 730 ILE Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 957 LEU Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 202 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 210 optimal weight: 0.9990 chunk 208 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 310 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 327 optimal weight: 50.0000 chunk 143 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 465 GLN C 598 ASN D 218 ASN ** D 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 785 HIS D1101 HIS ** H 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.167225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.128855 restraints weight = 32439.974| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.64 r_work: 0.3297 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27891 Z= 0.149 Angle : 0.552 24.787 38020 Z= 0.288 Chirality : 0.044 0.245 4285 Planarity : 0.005 0.191 4689 Dihedral : 16.490 137.490 4443 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.46 % Favored : 97.51 % Rotamer: Outliers : 2.02 % Allowed : 18.08 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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: 0.95 (0.15), residues: 3214 helix: 1.41 (0.14), residues: 1271 sheet: 0.41 (0.27), residues: 374 loop : 0.15 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 644 TYR 0.048 0.002 TYR D1050 PHE 0.020 0.002 PHE D 155 TRP 0.015 0.001 TRP C 765 HIS 0.007 0.001 HIS D1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (27891) covalent geometry : angle 0.55179 / 0.29 (38020) hydrogen bonds : bond 0.03958 / 2.67 ( 1256) hydrogen bonds : angle 4.65110 / 3.37 ( 3465) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7350.51 seconds wall clock time: 126 minutes 43.24 seconds (7603.24 seconds total)