Starting phenix.real_space_refine on Sun Jul 5 08:58:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x6f_38087/07_2026/8x6f_38087.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x6f_38087/07_2026/8x6f_38087.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x6f_38087/07_2026/8x6f_38087.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x6f_38087/07_2026/8x6f_38087.map" model { file = "/net/cci-nas-00/data/ceres_data/8x6f_38087/07_2026/8x6f_38087.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x6f_38087/07_2026/8x6f_38087.cif" } resolution = 3.7 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= 0.003 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 91 5.49 5 S 93 5.16 5 C 16683 2.51 5 N 4714 2.21 5 O 5401 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26982 Number of models: 1 Model: "" Number of chains: 9 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: "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: "E" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2195 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 9, 'TRANS': 261} Chain: "N" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1067 Classifications: {'DNA': 52} Link IDs: {'rna3p': 51} Chain: "T" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 797 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain breaks: 1 Time building chain proxies: 6.61, per 1000 atoms: 0.24 Number of scatterers: 26982 At special positions: 0 Unit cell: (151.13, 145.18, 138.04, 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 93 16.00 P 91 15.00 O 5401 8.00 N 4714 7.00 C 16683 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: 2.66 Conformation dependent library (CDL) restraints added in 1.2 seconds 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5904 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 45 sheets defined 44.2% alpha, 17.6% beta 35 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 3.52 Creating SS restraints... Processing helix chain 'A' and resid 31 through 47 removed outlier: 3.694A pdb=" N THR A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 84 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 removed outlier: 3.808A pdb=" N ASN A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 226 removed outlier: 4.063A pdb=" N ILE A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE A 224 " --> pdb=" O HIS A 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 47 removed outlier: 3.669A pdb=" N THR B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 83 Processing helix chain 'B' and resid 110 through 112 No H-bonds generated for 'chain 'B' and resid 110 through 112' Processing helix chain 'B' and resid 150 through 155 Processing helix chain 'B' and resid 205 through 226 removed outlier: 3.971A pdb=" N ILE B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE B 224 " --> pdb=" O HIS B 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 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 removed outlier: 3.735A pdb=" N GLY C 200 " --> pdb=" O LEU C 196 " (cutoff:3.500A) 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 259 Processing helix chain 'C' and resid 267 through 279 Processing helix chain 'C' and resid 280 through 285 removed outlier: 4.051A pdb=" N ARG C 284 " --> pdb=" O HIS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 325 removed outlier: 4.943A pdb=" N ASP C 320 " --> pdb=" O ASP C 316 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N VAL C 321 " --> pdb=" O GLU C 317 " (cutoff:3.500A) removed outlier: 3.616A 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 402 through 404 No H-bonds generated for 'chain 'C' and resid 402 through 404' Processing helix chain 'C' and resid 410 through 437 Processing helix chain 'C' and resid 443 through 448 removed outlier: 3.793A pdb=" N LEU C 447 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE C 448 " --> pdb=" O PRO C 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 443 through 448' Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 474 through 483 Processing helix chain 'C' and resid 499 through 504 removed outlier: 3.872A pdb=" N ARG C 503 " --> pdb=" O GLN C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 510 removed outlier: 3.521A 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: 3.761A 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: 4.098A pdb=" N ARG C 644 " --> pdb=" O ALA C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 670 removed outlier: 4.548A pdb=" N VAL C 664 " --> pdb=" O GLY C 660 " (cutoff:3.500A) removed outlier: 4.019A 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 817 through 821 Processing helix chain 'C' and resid 854 through 865 Processing helix chain 'C' and resid 940 through 944 Processing helix chain 'C' and resid 960 through 966 removed outlier: 4.344A pdb=" N SER C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) removed outlier: 3.654A 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 1008 Processing helix chain 'C' and resid 1076 through 1086 Processing helix chain 'C' and resid 1088 through 1097 removed outlier: 3.564A pdb=" N LEU C1092 " --> pdb=" O ALA C1088 " (cutoff:3.500A) Processing helix chain 'C' and resid 1102 through 1116 removed outlier: 4.025A pdb=" N VAL C1107 " --> pdb=" O THR C1103 " (cutoff:3.500A) Processing helix chain 'C' and resid 1125 through 1138 removed outlier: 3.567A pdb=" N ARG C1129 " --> pdb=" O PRO C1125 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 7 removed outlier: 3.540A pdb=" N ASN D 6 " --> pdb=" O ASP D 3 " (cutoff:3.500A) 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: 3.893A 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 108 Processing helix chain 'D' and resid 112 through 118 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 151 through 162 Processing helix chain 'D' and resid 171 through 182 removed outlier: 3.734A 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 removed outlier: 3.514A pdb=" N GLY D 220 " --> pdb=" O PHE D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 225 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: 3.840A 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: 3.687A 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 392 Processing helix chain 'D' and resid 394 through 405 removed outlier: 4.179A pdb=" N TRP D 398 " --> pdb=" O ASP D 394 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASP D 399 " --> pdb=" O ASP D 395 " (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 474 through 478 Processing helix chain 'D' and resid 493 through 503 Processing helix chain 'D' and resid 518 through 529 Processing helix chain 'D' and resid 542 through 545 Processing helix chain 'D' and resid 552 through 555 Processing helix chain 'D' and resid 562 through 570 removed outlier: 3.842A pdb=" N ILE D 570 " --> pdb=" O ILE D 566 " (cutoff:3.500A) 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 604 through 613 removed outlier: 3.705A pdb=" N GLU D 608 " --> pdb=" O GLY D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 635 Processing helix chain 'D' and resid 636 through 659 removed outlier: 3.619A pdb=" N GLY D 659 " --> pdb=" O SER D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 667 Processing helix chain 'D' and resid 670 through 672 No H-bonds generated for 'chain 'D' and resid 670 through 672' Processing helix chain 'D' and resid 673 through 693 Processing helix chain 'D' and resid 697 through 724 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: 3.804A pdb=" N HIS D 785 " --> pdb=" O PHE D 781 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY D 786 " --> pdb=" O ILE D 782 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA D 799 " --> pdb=" O ALA D 795 " (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 903 through 908 Processing helix chain 'D' and resid 922 through 938 Proline residue: D 934 - end of helix removed outlier: 4.251A pdb=" N GLN D 937 " --> pdb=" O GLU D 933 " (cutoff:3.500A) Processing helix chain 'D' and resid 955 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 removed outlier: 3.648A pdb=" N GLY D1043 " --> pdb=" O LEU D1039 " (cutoff:3.500A) Processing helix chain 'D' and resid 1043 through 1062 removed outlier: 4.035A pdb=" N GLN D1062 " --> pdb=" O VAL D1058 " (cutoff:3.500A) Processing helix chain 'D' and resid 1067 through 1079 removed outlier: 4.357A 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: 3.713A pdb=" N ALA D1140 " --> pdb=" O SER D1136 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN D1144 " --> pdb=" O ALA D1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 1145 through 1157 Processing helix chain 'D' and resid 1164 through 1171 removed outlier: 3.715A 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 'F' and resid 5 through 13 removed outlier: 3.640A pdb=" N GLN F 12 " --> pdb=" O GLN F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 33 Processing helix chain 'F' and resid 34 through 37 removed outlier: 3.981A 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 58 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 30 through 39 Processing helix chain 'G' and resid 40 through 42 No H-bonds generated for 'chain 'G' and resid 40 through 42' Processing helix chain 'G' and resid 53 through 63 Processing helix chain 'E' and resid 98 through 107 Processing helix chain 'E' and resid 113 through 126 Processing helix chain 'E' and resid 128 through 151 removed outlier: 4.592A pdb=" N ARG E 141 " --> pdb=" O GLU E 137 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG E 149 " --> pdb=" O SER E 145 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR E 150 " --> pdb=" O ILE E 146 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 175 Processing helix chain 'E' and resid 182 through 203 removed outlier: 3.723A pdb=" N TYR E 186 " --> pdb=" O LYS E 182 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TRP E 189 " --> pdb=" O THR E 185 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TRP E 190 " --> pdb=" O TYR E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 231 Processing helix chain 'E' and resid 235 through 244 Processing helix chain 'E' and resid 246 through 258 removed outlier: 3.576A pdb=" N GLN E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 278 Processing helix chain 'E' and resid 286 through 305 Processing helix chain 'E' and resid 308 through 320 Processing helix chain 'E' and resid 328 through 337 Processing helix chain 'E' and resid 339 through 356 removed outlier: 3.649A pdb=" N ILE E 343 " --> pdb=" O THR E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 365 removed outlier: 4.825A pdb=" N ARG E 362 " --> pdb=" O SER E 358 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU E 363 " --> pdb=" O ARG E 359 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP E 365 " --> pdb=" O LYS E 361 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 14 removed outlier: 6.828A pdb=" N LYS A 22 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE A 14 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N PHE A 20 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LYS A 22 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL A 198 " --> pdb=" O LYS A 22 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N VAL A 24 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LEU A 196 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU A 26 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU A 194 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N SER A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.279A 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: 3.511A pdb=" N VAL A 141 " --> pdb=" O TYR A 55 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR A 55 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ASN A 143 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N VAL A 53 " --> pdb=" O ASN A 143 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY A 145 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 5.212A 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: 6.542A pdb=" N LYS B 22 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE B 14 " --> pdb=" O PHE B 20 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N PHE B 20 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N PHE B 20 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N THR B 200 " --> pdb=" O PHE B 20 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LYS B 22 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL B 198 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL B 24 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU B 196 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLU B 26 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU B 194 " --> pdb=" O GLU B 26 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N SER B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 185 " --> pdb=" O SER B 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 95 through 101 removed outlier: 3.596A pdb=" N TYR B 55 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN B 143 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N VAL B 53 " --> pdb=" O ASN B 143 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLY B 145 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 5.037A 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: 6.545A pdb=" N GLY B 105 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR B 129 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 6.800A 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: 7.404A pdb=" N ALA C 988 " --> pdb=" O LYS C 13 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ARG C 15 " --> pdb=" O ALA C 988 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 55 through 56 removed outlier: 5.292A pdb=" N LEU C 64 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE C 99 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N PHE C 66 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG C 97 " --> pdb=" O PHE C 66 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP C 68 " --> pdb=" O LYS C 95 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ALA C 90 " --> pdb=" O ASP C 115 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASP C 115 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU C 92 " --> pdb=" O MET C 113 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE C 100 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 3.656A 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: 3.638A pdb=" N SER C 136 " --> pdb=" O ARG C 484 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N SER C 529 " --> pdb=" O CYS C 514 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 144 through 150 removed outlier: 6.420A pdb=" N TYR C 158 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 4.224A 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: 3.792A 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: 6.992A 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: 3.997A 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: 5.383A 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 573 through 574 Processing sheet with id=AC4, first strand: chain 'C' and resid 673 through 674 removed outlier: 6.520A pdb=" N ILE C 673 " --> pdb=" O LEU C 741 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 700 through 710 removed outlier: 5.080A pdb=" N ARG C 693 " --> pdb=" O GLY C 704 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU C 706 " --> pdb=" O VAL C 691 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL C 691 " --> pdb=" O LEU C 706 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG C 708 " --> pdb=" O ILE C 689 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE C 689 " --> pdb=" O ARG C 708 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N GLU C 688 " --> pdb=" O VAL C 684 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N VAL C 684 " --> pdb=" O GLU C 688 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU C 690 " --> pdb=" O GLU C 682 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 715 through 716 Processing sheet with id=AC7, first strand: chain 'C' and resid 747 through 748 Processing sheet with id=AC8, first strand: chain 'C' and resid 756 through 762 removed outlier: 8.926A pdb=" N ILE C 955 " --> pdb=" O ASN C 757 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL C 759 " --> pdb=" O ILE C 955 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU C 957 " --> pdb=" O VAL C 759 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLY C 761 " --> pdb=" O LEU C 957 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET C 956 " --> pdb=" O ILE C 775 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE C 775 " --> pdb=" O MET C 956 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL C 774 " --> pdb=" O LYS C 937 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N VAL C 939 " --> pdb=" O VAL C 774 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N MET C 776 " --> pdb=" O VAL C 939 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 788 through 799 removed outlier: 5.913A pdb=" N SER C 788 " --> pdb=" O LYS C 916 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS C 916 " --> pdb=" O SER C 788 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N HIS C 790 " --> pdb=" O VAL C 914 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL C 914 " --> pdb=" O HIS C 790 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLU C 792 " --> pdb=" O TYR C 912 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N TYR C 912 " --> pdb=" O GLU C 792 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TYR C 794 " --> pdb=" O ARG C 910 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG C 910 " --> pdb=" O TYR C 794 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N SER C 796 " --> pdb=" O LEU C 908 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU C 908 " --> pdb=" O SER C 796 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA C 798 " --> pdb=" O ASN C 906 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ASN C 906 " --> pdb=" O ASN C 893 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ASN C 893 " --> pdb=" O ASN C 906 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU C 908 " --> pdb=" O VAL C 891 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL C 891 " --> pdb=" O LEU C 908 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ARG C 910 " --> pdb=" O VAL C 889 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL C 889 " --> pdb=" O ARG C 910 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TYR C 912 " --> pdb=" O LEU C 887 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 807 through 808 Processing sheet with id=AD2, first strand: chain 'C' and resid 840 through 842 removed outlier: 6.710A pdb=" N LEU C 876 " --> pdb=" O LEU C 841 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1049 through 1051 Processing sheet with id=AD4, first strand: chain 'C' and resid 1049 through 1051 removed outlier: 7.789A pdb=" N ILE D 436 " --> pdb=" O ARG D 341 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL D 343 " --> pdb=" O ILE D 436 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU D 438 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ALA D 345 " --> pdb=" O LEU D 438 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1074 through 1075 removed outlier: 3.705A pdb=" N LYS D 334 " --> pdb=" O PHE C1075 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1143 through 1145 Processing sheet with id=AD7, first strand: chain 'D' and resid 24 through 27 removed outlier: 7.623A pdb=" N HIS D 94 " --> pdb=" O PHE D 25 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU D 27 " --> pdb=" O HIS D 94 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLU D 96 " --> pdb=" O GLU D 27 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N LEU D 97 " --> pdb=" O PRO D 232 " (cutoff:3.500A) removed outlier: 10.932A pdb=" N ALA D 99 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL D 230 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 149 through 150 removed outlier: 6.999A pdb=" N VAL D 167 " --> pdb=" O VAL D 137 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 241 through 243 removed outlier: 6.683A pdb=" N PHE D 249 " --> pdb=" O VAL E 261 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 515 through 516 Processing sheet with id=AE2, first strand: chain 'D' and resid 816 through 817 removed outlier: 5.894A pdb=" N ILE D 816 " --> pdb=" O VAL D 902 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'D' and resid 828 through 830 Processing sheet with id=AE4, first strand: chain 'D' and resid 833 through 835 removed outlier: 6.668A pdb=" N ILE D 833 " --> pdb=" O ILE D 840 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 856 through 857 removed outlier: 6.902A pdb=" N ILE D 856 " --> pdb=" O ILE D 865 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1003 through 1008 removed outlier: 6.630A pdb=" N LYS D 998 " --> pdb=" O VAL D 982 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL D 982 " --> pdb=" O LYS D 998 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1097 through 1099 removed outlier: 5.553A pdb=" N VAL D1082 " --> pdb=" O VAL D1123 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL D1123 " --> pdb=" O VAL D1082 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ILE D1084 " --> pdb=" O LYS D1121 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS D1121 " --> pdb=" O ILE D1084 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1189 through 1191 Processing sheet with id=AE9, first strand: chain 'G' and resid 44 through 50 removed outlier: 6.220A pdb=" N PHE G 7 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE G 48 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS G 5 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N GLU G 69 " --> pdb=" O SER G 23 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N TYR G 25 " --> pdb=" O GLU G 69 " (cutoff:3.500A) 1126 hydrogen bonds defined for protein. 3147 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 7.54 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4552 1.32 - 1.44: 7090 1.44 - 1.56: 15623 1.56 - 1.69: 179 1.69 - 1.81: 170 Bond restraints: 27614 Sorted by residual: bond pdb=" C3' DT T 43 " pdb=" C2' DT T 43 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.50e+01 bond pdb=" C1' DC N 60 " pdb=" N1 DC N 60 " ideal model delta sigma weight residual 1.468 1.522 -0.054 1.40e-02 5.10e+03 1.49e+01 bond pdb=" N ILE B 164 " pdb=" CA ILE B 164 " ideal model delta sigma weight residual 1.460 1.487 -0.027 7.30e-03 1.88e+04 1.36e+01 bond pdb=" C PRO A 172 " pdb=" O PRO A 172 " ideal model delta sigma weight residual 1.237 1.191 0.046 1.26e-02 6.30e+03 1.35e+01 bond pdb=" C3' DG T 52 " pdb=" C2' DG T 52 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 ... (remaining 27609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 36551 2.04 - 4.08: 1073 4.08 - 6.12: 59 6.12 - 8.16: 8 8.16 - 10.20: 3 Bond angle restraints: 37694 Sorted by residual: angle pdb=" C PHE G 47 " pdb=" CA PHE G 47 " pdb=" CB PHE G 47 " ideal model delta sigma weight residual 110.14 100.67 9.47 1.54e+00 4.22e-01 3.78e+01 angle pdb=" N PRO D 671 " pdb=" CA PRO D 671 " pdb=" C PRO D 671 " ideal model delta sigma weight residual 113.53 105.61 7.92 1.39e+00 5.18e-01 3.25e+01 angle pdb=" C THR C 544 " pdb=" CA THR C 544 " pdb=" CB THR C 544 " ideal model delta sigma weight residual 109.15 117.01 -7.86 1.60e+00 3.91e-01 2.41e+01 angle pdb=" N THR C 874 " pdb=" CA THR C 874 " pdb=" C THR C 874 " ideal model delta sigma weight residual 113.50 105.80 7.70 1.65e+00 3.67e-01 2.18e+01 angle pdb=" O4' DA N 72 " pdb=" C4' DA N 72 " pdb=" C3' DA N 72 " ideal model delta sigma weight residual 106.00 103.23 2.77 6.00e-01 2.78e+00 2.13e+01 ... (remaining 37689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.29: 15921 34.29 - 68.58: 779 68.58 - 102.88: 37 102.88 - 137.17: 3 137.17 - 171.46: 2 Dihedral angle restraints: 16742 sinusoidal: 7575 harmonic: 9167 Sorted by residual: dihedral pdb=" C4' DT N 51 " pdb=" C3' DT N 51 " pdb=" O3' DT N 51 " pdb=" P DA N 52 " ideal model delta sinusoidal sigma weight residual 220.00 48.54 171.46 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C PHE G 47 " pdb=" N PHE G 47 " pdb=" CA PHE G 47 " pdb=" CB PHE G 47 " ideal model delta harmonic sigma weight residual -122.60 -112.73 -9.87 0 2.50e+00 1.60e-01 1.56e+01 dihedral pdb=" C4' DT T 47 " pdb=" C3' DT T 47 " pdb=" O3' DT T 47 " pdb=" P DT T 48 " ideal model delta sinusoidal sigma weight residual 220.00 74.89 145.11 1 3.50e+01 8.16e-04 1.43e+01 ... (remaining 16739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3469 0.059 - 0.119: 667 0.119 - 0.178: 92 0.178 - 0.237: 23 0.237 - 0.296: 7 Chirality restraints: 4258 Sorted by residual: 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 2.74 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA LEU G 51 " pdb=" N LEU G 51 " pdb=" C LEU G 51 " pdb=" CB LEU G 51 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA VAL E 338 " pdb=" N VAL E 338 " pdb=" C VAL E 338 " pdb=" CB VAL E 338 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 4255 not shown) Planarity restraints: 4616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 873 " -0.013 2.00e-02 2.50e+03 2.70e-02 7.28e+00 pdb=" C ASP C 873 " 0.047 2.00e-02 2.50e+03 pdb=" O ASP C 873 " -0.018 2.00e-02 2.50e+03 pdb=" N THR C 874 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA T 62 " 0.014 2.00e-02 2.50e+03 1.56e-02 6.67e+00 pdb=" N9 DA T 62 " -0.007 2.00e-02 2.50e+03 pdb=" C8 DA T 62 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA T 62 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA T 62 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA T 62 " -0.006 2.00e-02 2.50e+03 pdb=" N6 DA T 62 " 0.001 2.00e-02 2.50e+03 pdb=" N1 DA T 62 " 0.035 2.00e-02 2.50e+03 pdb=" C2 DA T 62 " -0.033 2.00e-02 2.50e+03 pdb=" N3 DA T 62 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA T 62 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 376 " -0.038 5.00e-02 4.00e+02 5.80e-02 5.37e+00 pdb=" N PRO C 377 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 377 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 377 " -0.032 5.00e-02 4.00e+02 ... (remaining 4613 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3028 2.75 - 3.29: 27474 3.29 - 3.82: 46759 3.82 - 4.36: 54631 4.36 - 4.90: 91051 Nonbonded interactions: 222943 Sorted by model distance: nonbonded pdb=" N2 DG N 67 " pdb=" O2 DT T 20 " model vdw 2.210 3.120 nonbonded pdb=" O LEU C 41 " pdb=" OH TYR C 69 " model vdw 2.210 3.040 nonbonded pdb=" O PHE D 781 " pdb=" OG1 THR D 784 " model vdw 2.218 3.040 nonbonded pdb=" OG1 THR B 156 " pdb=" OD1 ASP B 158 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR G 25 " pdb=" OE1 GLU G 59 " model vdw 2.237 3.040 ... (remaining 222938 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 group one per residue 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: 0.750 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: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 30.980 Find NCS groups from input model: 0.340 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: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 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 : 0.005 0.054 27614 Z= 0.344 Angle : 0.717 10.197 37694 Z= 0.506 Chirality : 0.050 0.296 4258 Planarity : 0.004 0.063 4616 Dihedral : 17.828 171.461 10838 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.69 % Allowed : 12.27 % Favored : 87.04 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.15), residues: 3159 helix: 1.32 (0.15), residues: 1209 sheet: 0.44 (0.25), residues: 422 loop : 0.31 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 951 TYR 0.033 0.001 TYR G 58 PHE 0.022 0.001 PHE G 47 TRP 0.012 0.001 TRP D 105 HIS 0.005 0.001 HIS C1049 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.34 (27614) covalent geometry : angle 0.71705 / 0.51 (37694) hydrogen bonds : bond 0.14039 / 9.35 ( 1201) hydrogen bonds : angle 6.32339 / 4.36 ( 3309) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 654 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8092 (mt) REVERT: A 61 VAL cc_start: 0.6819 (t) cc_final: 0.6599 (t) REVERT: A 113 THR cc_start: 0.7595 (m) cc_final: 0.7375 (p) REVERT: A 124 GLU cc_start: 0.7664 (pm20) cc_final: 0.7458 (pm20) REVERT: B 55 TYR cc_start: 0.8200 (p90) cc_final: 0.7931 (p90) REVERT: B 100 ASP cc_start: 0.7193 (t0) cc_final: 0.6598 (p0) REVERT: B 193 LYS cc_start: 0.7705 (tttt) cc_final: 0.7327 (tttt) REVERT: C 178 ASP cc_start: 0.6526 (m-30) cc_final: 0.6170 (m-30) REVERT: C 188 ARG cc_start: 0.5461 (tmm-80) cc_final: 0.4831 (mmm-85) REVERT: C 218 ARG cc_start: 0.4621 (mmt180) cc_final: 0.4271 (mmp80) REVERT: C 222 GLU cc_start: 0.6194 (mp0) cc_final: 0.5364 (mm-30) REVERT: C 266 ASP cc_start: 0.6980 (t0) cc_final: 0.6138 (t0) REVERT: C 401 ASP cc_start: 0.7593 (m-30) cc_final: 0.6957 (t70) REVERT: C 434 MET cc_start: 0.2620 (mmp) cc_final: 0.2269 (mtp) REVERT: C 446 GLN cc_start: 0.6168 (pt0) cc_final: 0.5867 (mm110) REVERT: C 451 ARG cc_start: 0.5811 (ttp80) cc_final: 0.5012 (tpp-160) REVERT: C 458 LYS cc_start: 0.6330 (tppt) cc_final: 0.5850 (tttt) REVERT: C 468 GLN cc_start: 0.8077 (mt0) cc_final: 0.7871 (mm-40) REVERT: C 506 HIS cc_start: 0.6634 (t-90) cc_final: 0.5154 (t-90) REVERT: C 559 GLN cc_start: 0.6910 (tt0) cc_final: 0.6418 (mp10) REVERT: C 751 GLU cc_start: 0.7611 (mt-10) cc_final: 0.6905 (mm-30) REVERT: C 763 MET cc_start: 0.8006 (ptm) cc_final: 0.7576 (ptm) REVERT: C 783 ASP cc_start: 0.7836 (m-30) cc_final: 0.6991 (t0) REVERT: C 852 GLU cc_start: 0.5659 (pm20) cc_final: 0.5012 (tt0) REVERT: C 858 ARG cc_start: 0.6417 (mmm160) cc_final: 0.6124 (mtt90) REVERT: C 869 ARG cc_start: 0.6094 (ttm110) cc_final: 0.5868 (mtp180) REVERT: C 876 LEU cc_start: 0.7374 (tp) cc_final: 0.6887 (tp) REVERT: C 908 LEU cc_start: 0.7762 (tp) cc_final: 0.7535 (tt) REVERT: C 925 MET cc_start: 0.8158 (mtp) cc_final: 0.7699 (mtm) REVERT: C 967 ASN cc_start: 0.7963 (p0) cc_final: 0.7579 (p0) REVERT: C 1011 ARG cc_start: 0.7452 (mmm-85) cc_final: 0.6862 (ttt90) REVERT: C 1024 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7311 (mp0) REVERT: C 1078 MET cc_start: 0.6768 (mtp) cc_final: 0.6357 (mtm) REVERT: C 1108 LYS cc_start: 0.8270 (mttt) cc_final: 0.7822 (mmtt) REVERT: C 1132 MET cc_start: 0.7743 (tpp) cc_final: 0.7321 (tpp) REVERT: D 29 LYS cc_start: 0.8235 (mttt) cc_final: 0.7691 (mtmm) REVERT: D 40 LYS cc_start: 0.6613 (tptt) cc_final: 0.5954 (mmtp) REVERT: D 42 GLU cc_start: 0.5944 (mm-30) cc_final: 0.5660 (mm-30) REVERT: D 96 GLU cc_start: 0.7076 (tm-30) cc_final: 0.6622 (tm-30) REVERT: D 146 LYS cc_start: 0.6777 (tttt) cc_final: 0.6516 (ttpt) REVERT: D 186 GLU cc_start: 0.5029 (tp30) cc_final: 0.4665 (pt0) REVERT: D 189 LYS cc_start: 0.6441 (mttt) cc_final: 0.6167 (tttm) REVERT: D 190 LEU cc_start: 0.6857 (mt) cc_final: 0.6482 (mt) REVERT: D 210 LEU cc_start: 0.6878 (tp) cc_final: 0.6517 (mt) REVERT: D 222 LYS cc_start: 0.7049 (mtpp) cc_final: 0.6840 (mptt) REVERT: D 300 ARG cc_start: 0.6757 (tpt170) cc_final: 0.6407 (tpt170) REVERT: D 314 LYS cc_start: 0.7689 (mtpt) cc_final: 0.6792 (tttp) REVERT: D 391 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7476 (tp30) REVERT: D 393 MET cc_start: 0.7189 (mmt) cc_final: 0.6794 (mtm) REVERT: D 399 ASP cc_start: 0.7049 (m-30) cc_final: 0.6649 (t0) REVERT: D 402 GLU cc_start: 0.7764 (tt0) cc_final: 0.7456 (tp30) REVERT: D 407 GLU cc_start: 0.7678 (tm-30) cc_final: 0.6930 (mm-30) REVERT: D 478 ASN cc_start: 0.7829 (m110) cc_final: 0.7551 (m110) REVERT: D 642 MET cc_start: 0.6684 (tpp) cc_final: 0.6460 (ttm) REVERT: D 703 ASN cc_start: 0.7865 (m-40) cc_final: 0.7234 (t0) REVERT: D 719 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6728 (tm-30) REVERT: D 752 ARG cc_start: 0.7955 (mtp180) cc_final: 0.6927 (mtp-110) REVERT: D 848 GLU cc_start: 0.7674 (tp30) cc_final: 0.6784 (tp30) REVERT: D 873 THR cc_start: 0.7484 (p) cc_final: 0.7033 (p) REVERT: D 965 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7587 (tp30) REVERT: D 992 GLN cc_start: 0.2058 (mm110) cc_final: 0.1621 (pp30) REVERT: D 1013 ARG cc_start: 0.6300 (ptm-80) cc_final: 0.5968 (ptm160) REVERT: D 1030 GLU cc_start: 0.5476 (tt0) cc_final: 0.5255 (mm-30) REVERT: D 1048 GLU cc_start: 0.7072 (pt0) cc_final: 0.6555 (pt0) REVERT: D 1057 LYS cc_start: 0.7621 (tttt) cc_final: 0.7342 (pttt) REVERT: D 1143 PHE cc_start: 0.7351 (t80) cc_final: 0.7049 (t80) REVERT: D 1158 LYS cc_start: 0.8144 (mttt) cc_final: 0.7359 (ttmt) REVERT: D 1182 ARG cc_start: 0.6789 (mtp-110) cc_final: 0.6457 (ttp80) REVERT: F 26 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6726 (tpt170) REVERT: F 36 THR cc_start: 0.6757 (p) cc_final: 0.6144 (t) REVERT: F 54 GLU cc_start: 0.6090 (mt-10) cc_final: 0.5717 (mt-10) REVERT: F 61 ARG cc_start: 0.7738 (ttp80) cc_final: 0.7193 (tmm-80) REVERT: G 20 ASN cc_start: 0.6304 (m-40) cc_final: 0.6039 (m-40) REVERT: G 45 ILE cc_start: 0.7167 (mp) cc_final: 0.6798 (mm) REVERT: G 50 LYS cc_start: 0.6409 (mptt) cc_final: 0.5798 (tptt) REVERT: E 100 ARG cc_start: 0.7270 (mtt180) cc_final: 0.6864 (ttp-170) REVERT: E 112 LEU cc_start: 0.6546 (mt) cc_final: 0.6322 (mt) REVERT: E 122 LYS cc_start: 0.4920 (tppt) cc_final: 0.4584 (mtpt) REVERT: E 150 TYR cc_start: 0.6340 (m-80) cc_final: 0.6007 (m-80) REVERT: E 155 MET cc_start: 0.7272 (tpp) cc_final: 0.7016 (tpt) REVERT: E 181 PHE cc_start: 0.4734 (m-80) cc_final: 0.4415 (m-80) REVERT: E 280 GLU cc_start: 0.7612 (tt0) cc_final: 0.6924 (tm-30) REVERT: E 301 GLU cc_start: 0.4675 (tt0) cc_final: 0.4277 (mm-30) REVERT: E 310 ARG cc_start: 0.7115 (tpt-90) cc_final: 0.6148 (tpt170) REVERT: E 319 PHE cc_start: 0.6081 (m-80) cc_final: 0.5742 (m-80) REVERT: E 339 THR cc_start: 0.6024 (p) cc_final: 0.5698 (t) REVERT: E 342 ARG cc_start: 0.3173 (mtt180) cc_final: 0.2942 (mtt-85) REVERT: E 344 ARG cc_start: 0.4847 (tmm160) cc_final: 0.3842 (ttt180) outliers start: 19 outliers final: 5 residues processed: 666 average time/residue: 0.2243 time to fit residues: 221.4295 Evaluate side-chains 370 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 363 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain F residue 26 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 HIS B 70 ASN C 157 ASN C 389 ASN C 599 ASN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 880 HIS D 283 ASN F 43 HIS G 22 GLN ** E 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.160636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.137319 restraints weight = 40117.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.136887 restraints weight = 55964.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.137281 restraints weight = 50538.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.137584 restraints weight = 44326.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.138072 restraints weight = 37526.537| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27614 Z= 0.151 Angle : 0.595 11.252 37694 Z= 0.324 Chirality : 0.045 0.305 4258 Planarity : 0.005 0.046 4616 Dihedral : 17.992 171.701 4529 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.79 % Allowed : 14.16 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.15), residues: 3159 helix: 1.25 (0.15), residues: 1226 sheet: 0.38 (0.25), residues: 427 loop : 0.32 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1024 TYR 0.021 0.002 TYR G 58 PHE 0.022 0.002 PHE E 183 TRP 0.015 0.002 TRP B 199 HIS 0.008 0.001 HIS C 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (27614) covalent geometry : angle 0.59523 / 0.32 (37694) hydrogen bonds : bond 0.04594 / 3.11 ( 1201) hydrogen bonds : angle 5.20916 / 3.61 ( 3309) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 412 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 ASP cc_start: 0.6370 (t0) cc_final: 0.5884 (p0) REVERT: C 458 LYS cc_start: 0.7643 (tppt) cc_final: 0.7387 (tttt) REVERT: C 506 HIS cc_start: 0.7473 (t-90) cc_final: 0.7222 (t-90) REVERT: C 517 GLU cc_start: 0.6411 (tp30) cc_final: 0.6129 (tp30) REVERT: C 751 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7618 (mm-30) REVERT: C 763 MET cc_start: 0.8096 (ptm) cc_final: 0.7794 (ptm) REVERT: C 783 ASP cc_start: 0.7548 (m-30) cc_final: 0.7139 (t0) REVERT: C 925 MET cc_start: 0.7968 (mtp) cc_final: 0.7495 (mtm) REVERT: C 944 MET cc_start: 0.8448 (mmm) cc_final: 0.7963 (mmt) REVERT: C 967 ASN cc_start: 0.8409 (p0) cc_final: 0.7755 (p0) REVERT: C 1036 TYR cc_start: 0.8398 (t80) cc_final: 0.8193 (t80) REVERT: C 1078 MET cc_start: 0.7005 (mtp) cc_final: 0.6691 (mtm) REVERT: C 1098 TYR cc_start: 0.8714 (p90) cc_final: 0.8436 (p90) REVERT: C 1132 MET cc_start: 0.6834 (tpp) cc_final: 0.6238 (tpp) REVERT: D 216 PHE cc_start: 0.6858 (OUTLIER) cc_final: 0.6392 (t80) REVERT: D 226 MET cc_start: 0.7561 (tpp) cc_final: 0.7024 (tpp) REVERT: D 314 LYS cc_start: 0.7786 (mtpt) cc_final: 0.7266 (mtpp) REVERT: D 478 ASN cc_start: 0.8155 (m110) cc_final: 0.7948 (m110) REVERT: D 752 ARG cc_start: 0.8146 (mtp180) cc_final: 0.7894 (mtp-110) REVERT: D 1027 VAL cc_start: 0.5541 (OUTLIER) cc_final: 0.5206 (t) REVERT: F 26 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7771 (tpt170) REVERT: G 30 THR cc_start: 0.7260 (OUTLIER) cc_final: 0.6685 (m) REVERT: E 310 ARG cc_start: 0.7122 (tpt-90) cc_final: 0.6353 (tpt170) REVERT: E 344 ARG cc_start: 0.5775 (tmm160) cc_final: 0.5100 (ttt90) outliers start: 77 outliers final: 47 residues processed: 460 average time/residue: 0.2049 time to fit residues: 145.4933 Evaluate side-chains 357 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 306 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 552 ASP Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 599 ASN Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 806 GLU Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 870 GLU Chi-restraints excluded: chain C residue 880 HIS Chi-restraints excluded: chain C residue 900 THR Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 216 PHE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 727 THR Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 876 ILE Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1100 ILE Chi-restraints excluded: chain D residue 1101 HIS Chi-restraints excluded: chain D residue 1111 PHE Chi-restraints excluded: chain D residue 1149 VAL Chi-restraints excluded: chain D residue 1169 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 26 ARG Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 285 GLN Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 345 GLN Chi-restraints excluded: chain E residue 354 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 149 optimal weight: 8.9990 chunk 188 optimal weight: 8.9990 chunk 144 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 196 optimal weight: 3.9990 chunk 284 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 226 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 chunk 307 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 HIS C 599 ASN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 880 HIS D 201 GLN D 289 GLN ** D 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN ** D 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 ASN D1144 GLN F 43 HIS ** E 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 GLN E 282 GLN ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.151912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.128263 restraints weight = 40326.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.127717 restraints weight = 60511.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.127123 restraints weight = 54754.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.126926 restraints weight = 44364.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.127162 restraints weight = 40082.330| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 27614 Z= 0.315 Angle : 0.764 10.038 37694 Z= 0.407 Chirality : 0.051 0.337 4258 Planarity : 0.006 0.069 4616 Dihedral : 18.103 168.298 4523 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.97 % Allowed : 15.83 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.14), residues: 3159 helix: 0.50 (0.14), residues: 1229 sheet: 0.10 (0.25), residues: 420 loop : -0.16 (0.16), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 951 TYR 0.027 0.003 TYR C 37 PHE 0.026 0.003 PHE G 47 TRP 0.011 0.002 TRP A 199 HIS 0.012 0.002 HIS D 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00748 / 0.32 (27614) covalent geometry : angle 0.76362 / 0.41 (37694) hydrogen bonds : bond 0.05438 / 3.67 ( 1201) hydrogen bonds : angle 5.43094 / 3.81 ( 3309) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 317 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 ASP cc_start: 0.6765 (t0) cc_final: 0.5898 (p0) REVERT: C 384 MET cc_start: 0.6756 (mmm) cc_final: 0.6205 (tpp) REVERT: C 458 LYS cc_start: 0.7926 (tppt) cc_final: 0.7470 (tttt) REVERT: C 506 HIS cc_start: 0.7934 (t-90) cc_final: 0.7672 (t70) REVERT: C 751 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7653 (mm-30) REVERT: C 763 MET cc_start: 0.8025 (ptm) cc_final: 0.7773 (ptm) REVERT: C 776 MET cc_start: 0.8508 (ttm) cc_final: 0.7960 (mtp) REVERT: C 783 ASP cc_start: 0.7562 (m-30) cc_final: 0.7269 (t0) REVERT: C 888 ASP cc_start: 0.7035 (OUTLIER) cc_final: 0.6735 (m-30) REVERT: C 1078 MET cc_start: 0.7207 (mtp) cc_final: 0.6824 (mtm) REVERT: D 210 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6381 (tt) REVERT: D 226 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7851 (ttp) REVERT: D 297 ASP cc_start: 0.6825 (t0) cc_final: 0.6514 (t0) REVERT: D 402 GLU cc_start: 0.7535 (tp30) cc_final: 0.7283 (tm-30) REVERT: D 752 ARG cc_start: 0.8338 (mtp180) cc_final: 0.7981 (mtp-110) REVERT: D 1024 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7479 (ptm-80) REVERT: D 1027 VAL cc_start: 0.5516 (OUTLIER) cc_final: 0.5202 (t) REVERT: G 20 ASN cc_start: 0.6562 (m-40) cc_final: 0.5726 (m-40) REVERT: E 294 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7389 (mm-30) REVERT: E 310 ARG cc_start: 0.7241 (tpt-90) cc_final: 0.6255 (tpt170) REVERT: E 314 VAL cc_start: 0.6318 (t) cc_final: 0.6019 (t) REVERT: E 342 ARG cc_start: 0.2245 (mtt180) cc_final: -0.0204 (ttt180) REVERT: E 344 ARG cc_start: 0.5874 (tmm160) cc_final: 0.5043 (ttt90) outliers start: 137 outliers final: 92 residues processed: 419 average time/residue: 0.1863 time to fit residues: 124.0551 Evaluate side-chains 365 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 268 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 552 ASP Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 599 ASN Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 806 GLU Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 869 ARG Chi-restraints excluded: chain C residue 880 HIS Chi-restraints excluded: chain C residue 888 ASP Chi-restraints excluded: chain C residue 900 THR Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 965 ARG Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain C residue 1059 VAL Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1127 SER Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 216 PHE Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 778 LEU Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 873 THR Chi-restraints excluded: chain D residue 876 ILE Chi-restraints excluded: chain D residue 918 GLU Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 1024 ARG Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1092 LEU Chi-restraints excluded: chain D residue 1100 ILE Chi-restraints excluded: chain D residue 1111 PHE Chi-restraints excluded: chain D residue 1149 VAL Chi-restraints excluded: chain D residue 1169 VAL Chi-restraints excluded: chain D residue 1187 VAL Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 285 GLN Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain E residue 354 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 307 optimal weight: 10.0000 chunk 273 optimal weight: 7.9990 chunk 106 optimal weight: 0.6980 chunk 287 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 72 optimal weight: 20.0000 chunk 262 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 199 optimal weight: 0.9990 chunk 166 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1144 GLN F 8 GLN ** E 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.150127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.121645 restraints weight = 40352.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.121464 restraints weight = 45000.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.122287 restraints weight = 40835.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.122683 restraints weight = 30035.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.122702 restraints weight = 27632.813| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 27614 Z= 0.198 Angle : 0.620 8.787 37694 Z= 0.336 Chirality : 0.046 0.321 4258 Planarity : 0.005 0.049 4616 Dihedral : 18.032 169.204 4519 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.85 % Allowed : 17.93 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.14), residues: 3159 helix: 0.62 (0.14), residues: 1237 sheet: 0.18 (0.26), residues: 392 loop : -0.19 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C1121 TYR 0.020 0.002 TYR C 37 PHE 0.020 0.002 PHE D 155 TRP 0.011 0.001 TRP D 23 HIS 0.012 0.001 HIS D 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (27614) covalent geometry : angle 0.62005 / 0.34 (37694) hydrogen bonds : bond 0.04562 / 3.09 ( 1201) hydrogen bonds : angle 5.18754 / 3.63 ( 3309) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 293 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7597 (ptp-110) cc_final: 0.7354 (ptp-110) REVERT: A 174 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7327 (mt-10) REVERT: B 100 ASP cc_start: 0.7140 (t0) cc_final: 0.6051 (p0) REVERT: C 41 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7597 (tt) REVERT: C 113 MET cc_start: 0.6505 (tmm) cc_final: 0.5965 (tpp) REVERT: C 384 MET cc_start: 0.6987 (mmm) cc_final: 0.6489 (tpp) REVERT: C 458 LYS cc_start: 0.7835 (tppt) cc_final: 0.7317 (tttt) REVERT: C 506 HIS cc_start: 0.7816 (t-90) cc_final: 0.7604 (t70) REVERT: C 517 GLU cc_start: 0.6242 (tp30) cc_final: 0.6020 (tp30) REVERT: C 602 MET cc_start: 0.6841 (mtt) cc_final: 0.6119 (tpt) REVERT: C 751 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7557 (mm-30) REVERT: C 783 ASP cc_start: 0.7455 (m-30) cc_final: 0.7199 (t0) REVERT: C 888 ASP cc_start: 0.7052 (OUTLIER) cc_final: 0.6733 (m-30) REVERT: C 944 MET cc_start: 0.8583 (mmm) cc_final: 0.8171 (mmp) REVERT: C 1078 MET cc_start: 0.7309 (mtp) cc_final: 0.6884 (mtm) REVERT: C 1132 MET cc_start: 0.7137 (mmm) cc_final: 0.6704 (tpp) REVERT: D 216 PHE cc_start: 0.7302 (m-80) cc_final: 0.6975 (m-80) REVERT: D 226 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7555 (tpp) REVERT: D 402 GLU cc_start: 0.7533 (tp30) cc_final: 0.7264 (tm-30) REVERT: D 752 ARG cc_start: 0.8340 (mtp180) cc_final: 0.7905 (mtp-110) REVERT: D 1024 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7345 (ptm-80) REVERT: G 20 ASN cc_start: 0.6692 (m-40) cc_final: 0.5960 (m-40) REVERT: E 310 ARG cc_start: 0.7246 (tpt-90) cc_final: 0.6131 (tpt170) REVERT: E 314 VAL cc_start: 0.6351 (t) cc_final: 0.6105 (t) REVERT: E 344 ARG cc_start: 0.5944 (tmm160) cc_final: 0.4834 (ttt90) outliers start: 106 outliers final: 73 residues processed: 378 average time/residue: 0.1745 time to fit residues: 105.7645 Evaluate side-chains 346 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 269 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 552 ASP Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 599 ASN Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 806 GLU Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 869 ARG Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 880 HIS Chi-restraints excluded: chain C residue 888 ASP Chi-restraints excluded: chain C residue 900 THR Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 920 HIS Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 1059 VAL Chi-restraints excluded: chain C residue 1083 LEU Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 873 THR Chi-restraints excluded: chain D residue 918 GLU Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 1024 ARG Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1100 ILE Chi-restraints excluded: chain D residue 1111 PHE Chi-restraints excluded: chain D residue 1149 VAL Chi-restraints excluded: chain D residue 1169 VAL Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 338 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 23 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 93 optimal weight: 8.9990 chunk 285 optimal weight: 7.9990 chunk 257 optimal weight: 10.0000 chunk 202 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 74 optimal weight: 0.0060 chunk 65 optimal weight: 10.0000 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 345 GLN C 575 GLN C 599 ASN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN C 880 HIS D 289 GLN D 330 ASN D 385 ASN ** D1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN ** E 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.155155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.131458 restraints weight = 40097.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.130731 restraints weight = 67631.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.131007 restraints weight = 56632.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.130727 restraints weight = 40872.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.131037 restraints weight = 38639.892| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27614 Z= 0.153 Angle : 0.567 7.720 37694 Z= 0.308 Chirality : 0.045 0.319 4258 Planarity : 0.005 0.158 4616 Dihedral : 17.966 169.253 4519 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.28 % Allowed : 18.19 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.15), residues: 3159 helix: 0.88 (0.14), residues: 1238 sheet: 0.39 (0.26), residues: 397 loop : -0.17 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 342 TYR 0.021 0.002 TYR C 386 PHE 0.028 0.002 PHE D1143 TRP 0.014 0.001 TRP D 23 HIS 0.007 0.001 HIS C 880 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (27614) covalent geometry : angle 0.56663 / 0.31 (37694) hydrogen bonds : bond 0.04263 / 2.91 ( 1201) hydrogen bonds : angle 4.97926 / 3.49 ( 3309) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 299 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 ASP cc_start: 0.7165 (t0) cc_final: 0.6028 (p0) REVERT: C 41 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7564 (tt) REVERT: C 113 MET cc_start: 0.6428 (tmm) cc_final: 0.6062 (tpp) REVERT: C 384 MET cc_start: 0.6994 (mmm) cc_final: 0.6574 (tpp) REVERT: C 458 LYS cc_start: 0.7830 (tppt) cc_final: 0.7357 (tttt) REVERT: C 506 HIS cc_start: 0.7701 (t-90) cc_final: 0.7417 (t-90) REVERT: C 517 GLU cc_start: 0.6215 (tp30) cc_final: 0.5950 (tp30) REVERT: C 751 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7573 (mm-30) REVERT: C 783 ASP cc_start: 0.7472 (m-30) cc_final: 0.7199 (t0) REVERT: C 944 MET cc_start: 0.8573 (mmm) cc_final: 0.8232 (mmp) REVERT: C 1036 TYR cc_start: 0.8584 (t80) cc_final: 0.8371 (t80) REVERT: C 1078 MET cc_start: 0.7182 (mtp) cc_final: 0.6743 (mtp) REVERT: D 216 PHE cc_start: 0.7173 (m-80) cc_final: 0.6915 (m-80) REVERT: D 226 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7531 (tpp) REVERT: D 297 ASP cc_start: 0.6753 (t0) cc_final: 0.6527 (t0) REVERT: D 752 ARG cc_start: 0.8243 (mtp180) cc_final: 0.7896 (mtp-110) REVERT: D 1024 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7402 (ptm-80) REVERT: D 1027 VAL cc_start: 0.5490 (OUTLIER) cc_final: 0.5177 (t) REVERT: G 20 ASN cc_start: 0.6507 (m-40) cc_final: 0.5823 (m-40) REVERT: E 185 THR cc_start: 0.8646 (m) cc_final: 0.8407 (p) REVERT: E 299 GLN cc_start: 0.7177 (mm-40) cc_final: 0.6948 (mm-40) REVERT: E 310 ARG cc_start: 0.7223 (tpt-90) cc_final: 0.6160 (tpt170) REVERT: E 314 VAL cc_start: 0.6157 (t) cc_final: 0.5906 (t) REVERT: E 342 ARG cc_start: 0.2787 (OUTLIER) cc_final: 0.0383 (mpt-90) REVERT: E 344 ARG cc_start: 0.5892 (tmm160) cc_final: 0.5226 (ttt90) outliers start: 118 outliers final: 84 residues processed: 392 average time/residue: 0.1821 time to fit residues: 113.5478 Evaluate side-chains 361 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 272 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 552 ASP Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 599 ASN Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 806 GLU Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 869 ARG Chi-restraints excluded: chain C residue 870 GLU Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 880 HIS Chi-restraints excluded: chain C residue 900 THR Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 920 HIS Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1083 LEU Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1127 SER Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 873 THR Chi-restraints excluded: chain D residue 888 MET Chi-restraints excluded: chain D residue 918 GLU Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 1024 ARG Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1100 ILE Chi-restraints excluded: chain D residue 1111 PHE Chi-restraints excluded: chain D residue 1149 VAL Chi-restraints excluded: chain D residue 1169 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain E residue 342 ARG Chi-restraints excluded: chain E residue 354 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 186 optimal weight: 9.9990 chunk 204 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 250 optimal weight: 1.9990 chunk 266 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 599 ASN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 880 HIS D1144 GLN F 8 GLN G 55 HIS ** E 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 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 = 0.3953 r_free = 0.3953 target = 0.153004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.129909 restraints weight = 40655.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.129916 restraints weight = 68091.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.129962 restraints weight = 53726.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.129365 restraints weight = 42674.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.129776 restraints weight = 38881.137| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 27614 Z= 0.217 Angle : 0.626 10.204 37694 Z= 0.336 Chirality : 0.047 0.320 4258 Planarity : 0.005 0.079 4616 Dihedral : 17.966 168.553 4519 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.94 % Allowed : 18.04 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.15), residues: 3159 helix: 0.71 (0.14), residues: 1235 sheet: 0.17 (0.26), residues: 409 loop : -0.27 (0.16), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 342 TYR 0.019 0.002 TYR C1098 PHE 0.021 0.002 PHE D1143 TRP 0.010 0.002 TRP D 23 HIS 0.012 0.002 HIS C 880 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 (27614) covalent geometry : angle 0.62574 / 0.34 (37694) hydrogen bonds : bond 0.04529 / 3.06 ( 1201) hydrogen bonds : angle 5.06864 / 3.55 ( 3309) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 289 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.5390 (OUTLIER) cc_final: 0.5190 (tp) REVERT: B 100 ASP cc_start: 0.7200 (t0) cc_final: 0.6054 (p0) REVERT: C 41 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7549 (tt) REVERT: C 345 GLN cc_start: 0.4490 (mm110) cc_final: 0.4240 (mt0) REVERT: C 376 THR cc_start: 0.7732 (OUTLIER) cc_final: 0.7394 (p) REVERT: C 384 MET cc_start: 0.6979 (mmm) cc_final: 0.6681 (tpp) REVERT: C 458 LYS cc_start: 0.7877 (tppt) cc_final: 0.7349 (tttt) REVERT: C 506 HIS cc_start: 0.7733 (t-90) cc_final: 0.7437 (t-90) REVERT: C 517 GLU cc_start: 0.6307 (tp30) cc_final: 0.6015 (tp30) REVERT: C 661 MET cc_start: 0.7615 (tpp) cc_final: 0.7196 (tpt) REVERT: C 751 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7526 (mm-30) REVERT: C 783 ASP cc_start: 0.7614 (m-30) cc_final: 0.7324 (t0) REVERT: C 888 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.6923 (m-30) REVERT: C 944 MET cc_start: 0.8570 (mmm) cc_final: 0.7716 (mmt) REVERT: C 1078 MET cc_start: 0.7259 (mtp) cc_final: 0.6818 (mtp) REVERT: D 195 LEU cc_start: 0.5500 (OUTLIER) cc_final: 0.5284 (mm) REVERT: D 226 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7494 (tpp) REVERT: D 1024 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7374 (ptm-80) REVERT: D 1027 VAL cc_start: 0.5516 (OUTLIER) cc_final: 0.5219 (t) REVERT: F 41 GLU cc_start: 0.7029 (tm-30) cc_final: 0.6793 (tm-30) REVERT: G 60 LYS cc_start: 0.6413 (ttpt) cc_final: 0.5993 (mttm) REVERT: E 185 THR cc_start: 0.8625 (m) cc_final: 0.8424 (p) REVERT: E 310 ARG cc_start: 0.7238 (tpt-90) cc_final: 0.6172 (tpt170) REVERT: E 342 ARG cc_start: 0.2701 (mtt180) cc_final: 0.2434 (mtt-85) REVERT: E 344 ARG cc_start: 0.5984 (tmm160) cc_final: 0.5196 (ttt90) outliers start: 136 outliers final: 103 residues processed: 395 average time/residue: 0.1835 time to fit residues: 115.2906 Evaluate side-chains 377 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 266 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 552 ASP Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 806 GLU Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 869 ARG Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 880 HIS Chi-restraints excluded: chain C residue 888 ASP Chi-restraints excluded: chain C residue 900 THR Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 920 HIS Chi-restraints excluded: chain C residue 970 GLN Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1083 LEU Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1127 SER Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 570 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 873 THR Chi-restraints excluded: chain D residue 918 GLU Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 1022 VAL Chi-restraints excluded: chain D residue 1024 ARG Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1100 ILE Chi-restraints excluded: chain D residue 1111 PHE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 338 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 246 optimal weight: 5.9990 chunk 243 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 277 optimal weight: 0.6980 chunk 221 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 159 optimal weight: 5.9990 chunk 54 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 446 GLN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 880 HIS D1144 GLN ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.155862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.133554 restraints weight = 39948.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.132628 restraints weight = 58563.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.130453 restraints weight = 48627.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.130673 restraints weight = 43044.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.131186 restraints weight = 37229.162| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27614 Z= 0.129 Angle : 0.555 9.393 37694 Z= 0.301 Chirality : 0.044 0.319 4258 Planarity : 0.004 0.065 4616 Dihedral : 17.885 168.633 4519 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.67 % Allowed : 19.82 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.15), residues: 3159 helix: 1.02 (0.15), residues: 1231 sheet: 0.26 (0.26), residues: 400 loop : -0.15 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 377 TYR 0.026 0.001 TYR C 386 PHE 0.021 0.001 PHE C 112 TRP 0.012 0.001 TRP D 23 HIS 0.020 0.001 HIS C 880 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (27614) covalent geometry : angle 0.55484 / 0.30 (37694) hydrogen bonds : bond 0.03965 / 2.68 ( 1201) hydrogen bonds : angle 4.85380 / 3.39 ( 3309) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 288 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: B 100 ASP cc_start: 0.7269 (t0) cc_final: 0.6015 (p0) REVERT: C 41 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7576 (tt) REVERT: C 345 GLN cc_start: 0.4579 (mm110) cc_final: 0.4350 (mt0) REVERT: C 376 THR cc_start: 0.7836 (OUTLIER) cc_final: 0.7386 (p) REVERT: C 384 MET cc_start: 0.7022 (mmm) cc_final: 0.6787 (tpp) REVERT: C 458 LYS cc_start: 0.7790 (tppt) cc_final: 0.7305 (tttt) REVERT: C 506 HIS cc_start: 0.7631 (t-90) cc_final: 0.7357 (t-90) REVERT: C 517 GLU cc_start: 0.6127 (tp30) cc_final: 0.5880 (tp30) REVERT: C 751 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7541 (mm-30) REVERT: C 783 ASP cc_start: 0.7468 (m-30) cc_final: 0.7158 (t0) REVERT: C 944 MET cc_start: 0.8395 (mmm) cc_final: 0.7828 (mmt) REVERT: C 1036 TYR cc_start: 0.8561 (t80) cc_final: 0.8350 (t80) REVERT: C 1078 MET cc_start: 0.7135 (mtp) cc_final: 0.6682 (mtt) REVERT: D 214 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.6023 (tp30) REVERT: D 216 PHE cc_start: 0.7071 (m-80) cc_final: 0.6807 (m-80) REVERT: D 226 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7530 (tpp) REVERT: D 1024 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.7218 (ptm-80) REVERT: D 1027 VAL cc_start: 0.5577 (OUTLIER) cc_final: 0.5306 (t) REVERT: G 60 LYS cc_start: 0.6330 (ttpt) cc_final: 0.5920 (mttm) REVERT: E 296 LEU cc_start: 0.8355 (tp) cc_final: 0.8104 (tp) REVERT: E 344 ARG cc_start: 0.5838 (tmm160) cc_final: 0.5054 (ttt90) outliers start: 101 outliers final: 71 residues processed: 363 average time/residue: 0.1619 time to fit residues: 95.0729 Evaluate side-chains 338 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 261 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 552 ASP Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 599 ASN Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 806 GLU Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 869 ARG Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 900 THR Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 920 HIS Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 1083 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 214 GLU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 783 SER Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 873 THR Chi-restraints excluded: chain D residue 876 ILE Chi-restraints excluded: chain D residue 888 MET Chi-restraints excluded: chain D residue 918 GLU Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 1024 ARG Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1100 ILE Chi-restraints excluded: chain D residue 1111 PHE Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 363 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 171 optimal weight: 3.9990 chunk 254 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 251 optimal weight: 7.9990 chunk 248 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 190 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 304 optimal weight: 8.9990 chunk 172 optimal weight: 7.9990 chunk 142 optimal weight: 0.0870 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1144 GLN F 8 GLN ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.156110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.133339 restraints weight = 40098.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.132537 restraints weight = 60014.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.132108 restraints weight = 55600.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.131835 restraints weight = 49070.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.132049 restraints weight = 40450.398| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27614 Z= 0.128 Angle : 0.549 8.580 37694 Z= 0.296 Chirality : 0.044 0.390 4258 Planarity : 0.004 0.060 4616 Dihedral : 17.830 169.806 4519 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.77 % Allowed : 19.82 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.15), residues: 3159 helix: 1.10 (0.15), residues: 1236 sheet: 0.41 (0.27), residues: 390 loop : -0.10 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 377 TYR 0.020 0.001 TYR C 386 PHE 0.015 0.001 PHE D 155 TRP 0.011 0.001 TRP D 23 HIS 0.007 0.001 HIS C1049 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (27614) covalent geometry : angle 0.54870 / 0.30 (37694) hydrogen bonds : bond 0.03857 / 2.61 ( 1201) hydrogen bonds : angle 4.78106 / 3.34 ( 3309) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 286 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 ASP cc_start: 0.7183 (t0) cc_final: 0.5965 (p0) REVERT: C 41 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7607 (tt) REVERT: C 345 GLN cc_start: 0.4671 (mm110) cc_final: 0.4391 (mt0) REVERT: C 384 MET cc_start: 0.6856 (mmm) cc_final: 0.6634 (tpp) REVERT: C 458 LYS cc_start: 0.7695 (tppt) cc_final: 0.7389 (tttt) REVERT: C 506 HIS cc_start: 0.7577 (t-90) cc_final: 0.7304 (t-90) REVERT: C 517 GLU cc_start: 0.6106 (tp30) cc_final: 0.5809 (tp30) REVERT: C 661 MET cc_start: 0.7720 (tpp) cc_final: 0.7320 (tpt) REVERT: C 751 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7542 (mm-30) REVERT: C 783 ASP cc_start: 0.7495 (m-30) cc_final: 0.7154 (t0) REVERT: C 944 MET cc_start: 0.8571 (mmm) cc_final: 0.8003 (mmt) REVERT: C 1073 GLN cc_start: 0.7895 (mp10) cc_final: 0.7628 (mp10) REVERT: C 1078 MET cc_start: 0.7020 (mtp) cc_final: 0.6558 (mtp) REVERT: D 180 GLU cc_start: 0.6030 (mt-10) cc_final: 0.5812 (mt-10) REVERT: D 214 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.5994 (tp30) REVERT: D 216 PHE cc_start: 0.7019 (m-80) cc_final: 0.6757 (m-80) REVERT: D 226 MET cc_start: 0.8041 (tpp) cc_final: 0.7336 (tpp) REVERT: D 691 PHE cc_start: 0.3351 (t80) cc_final: 0.2525 (t80) REVERT: D 1024 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.7185 (ptm-80) REVERT: D 1027 VAL cc_start: 0.5441 (OUTLIER) cc_final: 0.5159 (t) REVERT: G 60 LYS cc_start: 0.6312 (ttpt) cc_final: 0.6005 (mttm) REVERT: E 342 ARG cc_start: 0.2144 (mtt-85) cc_final: -0.0527 (mpt-90) REVERT: E 344 ARG cc_start: 0.5812 (tmm160) cc_final: 0.5274 (ttt90) outliers start: 104 outliers final: 77 residues processed: 370 average time/residue: 0.1652 time to fit residues: 99.9537 Evaluate side-chains 350 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 269 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 552 ASP Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 599 ASN Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 806 GLU Chi-restraints excluded: chain C residue 869 ARG Chi-restraints excluded: chain C residue 900 THR Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 920 HIS Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 1083 LEU Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 214 GLU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 783 SER Chi-restraints excluded: chain D residue 873 THR Chi-restraints excluded: chain D residue 876 ILE Chi-restraints excluded: chain D residue 918 GLU Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 1024 ARG Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1100 ILE Chi-restraints excluded: chain D residue 1111 PHE Chi-restraints excluded: chain D residue 1187 VAL Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 363 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 273 optimal weight: 10.0000 chunk 270 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 37 optimal weight: 0.0270 chunk 104 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 187 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 236 optimal weight: 2.9990 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1144 GLN F 8 GLN F 43 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.154639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.130825 restraints weight = 40340.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.129021 restraints weight = 53781.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.129988 restraints weight = 53564.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.130164 restraints weight = 40104.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.130107 restraints weight = 39788.739| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27614 Z= 0.163 Angle : 0.577 9.475 37694 Z= 0.310 Chirality : 0.045 0.330 4258 Planarity : 0.004 0.057 4616 Dihedral : 17.820 168.928 4519 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.67 % Allowed : 20.15 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.15), residues: 3159 helix: 0.99 (0.15), residues: 1234 sheet: 0.28 (0.26), residues: 410 loop : -0.18 (0.16), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 377 TYR 0.021 0.002 TYR C 386 PHE 0.016 0.001 PHE G 47 TRP 0.010 0.001 TRP A 199 HIS 0.007 0.001 HIS C1049 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (27614) covalent geometry : angle 0.57665 / 0.31 (37694) hydrogen bonds : bond 0.03990 / 2.71 ( 1201) hydrogen bonds : angle 4.84180 / 3.39 ( 3309) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 276 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 ASP cc_start: 0.7290 (t0) cc_final: 0.6034 (p0) REVERT: C 41 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7586 (tt) REVERT: C 282 LYS cc_start: 0.6811 (tttt) cc_final: 0.6603 (tmmt) REVERT: C 345 GLN cc_start: 0.4731 (mm110) cc_final: 0.4516 (mt0) REVERT: C 384 MET cc_start: 0.6942 (mmm) cc_final: 0.6727 (tpp) REVERT: C 458 LYS cc_start: 0.7737 (tppt) cc_final: 0.7389 (tttt) REVERT: C 506 HIS cc_start: 0.7616 (t-90) cc_final: 0.7345 (t-90) REVERT: C 517 GLU cc_start: 0.6122 (tp30) cc_final: 0.5785 (tp30) REVERT: C 661 MET cc_start: 0.7659 (tpp) cc_final: 0.7306 (tpt) REVERT: C 751 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7596 (mm-30) REVERT: C 783 ASP cc_start: 0.7413 (m-30) cc_final: 0.7160 (t0) REVERT: C 888 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.7022 (m-30) REVERT: C 944 MET cc_start: 0.8609 (mmm) cc_final: 0.7870 (mmt) REVERT: C 1073 GLN cc_start: 0.8049 (mp10) cc_final: 0.7759 (mp10) REVERT: C 1078 MET cc_start: 0.7087 (mtp) cc_final: 0.6678 (mtt) REVERT: D 180 GLU cc_start: 0.5935 (mt-10) cc_final: 0.5645 (mt-10) REVERT: D 214 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.6041 (tp30) REVERT: D 216 PHE cc_start: 0.7035 (m-80) cc_final: 0.6791 (m-80) REVERT: D 226 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7377 (tpp) REVERT: D 1024 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7264 (ptm-80) REVERT: D 1027 VAL cc_start: 0.5678 (OUTLIER) cc_final: 0.5427 (t) REVERT: G 60 LYS cc_start: 0.6347 (ttpt) cc_final: 0.5989 (mttm) REVERT: E 342 ARG cc_start: 0.2450 (mtt-85) cc_final: 0.1483 (mpt-90) REVERT: E 344 ARG cc_start: 0.5755 (tmm160) cc_final: 0.5121 (ttt90) outliers start: 101 outliers final: 84 residues processed: 354 average time/residue: 0.1747 time to fit residues: 99.9172 Evaluate side-chains 356 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 266 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 552 ASP Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 599 ASN Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 763 MET Chi-restraints excluded: chain C residue 806 GLU Chi-restraints excluded: chain C residue 859 LEU Chi-restraints excluded: chain C residue 869 ARG Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 888 ASP Chi-restraints excluded: chain C residue 900 THR Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 920 HIS Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 1083 LEU Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 214 GLU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 783 SER Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 873 THR Chi-restraints excluded: chain D residue 876 ILE Chi-restraints excluded: chain D residue 918 GLU Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 1024 ARG Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1100 ILE Chi-restraints excluded: chain D residue 1111 PHE Chi-restraints excluded: chain D residue 1169 VAL Chi-restraints excluded: chain D residue 1187 VAL Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 363 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 253 optimal weight: 7.9990 chunk 144 optimal weight: 7.9990 chunk 219 optimal weight: 0.7980 chunk 136 optimal weight: 7.9990 chunk 308 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 220 optimal weight: 1.9990 chunk 319 optimal weight: 50.0000 chunk 92 optimal weight: 9.9990 chunk 216 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1144 GLN F 43 HIS E 282 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.157537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.134518 restraints weight = 39865.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 90)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.132700 restraints weight = 62166.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.130644 restraints weight = 42607.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.130793 restraints weight = 43051.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.130871 restraints weight = 37357.881| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 27614 Z= 0.114 Angle : 0.545 12.461 37694 Z= 0.293 Chirality : 0.043 0.327 4258 Planarity : 0.004 0.050 4616 Dihedral : 17.764 167.920 4519 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.47 % Allowed : 21.38 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.15), residues: 3159 helix: 1.19 (0.15), residues: 1222 sheet: 0.36 (0.27), residues: 374 loop : -0.05 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 377 TYR 0.023 0.001 TYR C 386 PHE 0.012 0.001 PHE G 47 TRP 0.011 0.001 TRP D 23 HIS 0.006 0.001 HIS C1049 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (27614) covalent geometry : angle 0.54536 / 0.29 (37694) hydrogen bonds : bond 0.03653 / 2.48 ( 1201) hydrogen bonds : angle 4.70933 / 3.28 ( 3309) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 296 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 ASP cc_start: 0.7309 (t0) cc_final: 0.6040 (p0) REVERT: B 102 ARG cc_start: 0.6763 (mtm-85) cc_final: 0.6263 (ttm-80) REVERT: B 207 GLN cc_start: 0.8221 (pm20) cc_final: 0.7937 (pm20) REVERT: C 282 LYS cc_start: 0.6721 (tttt) cc_final: 0.6430 (tmmt) REVERT: C 396 TYR cc_start: 0.5883 (OUTLIER) cc_final: 0.4998 (p90) REVERT: C 458 LYS cc_start: 0.7614 (tppt) cc_final: 0.7165 (tttt) REVERT: C 506 HIS cc_start: 0.7557 (t-90) cc_final: 0.7285 (t-90) REVERT: C 517 GLU cc_start: 0.6181 (tp30) cc_final: 0.5886 (tp30) REVERT: C 661 MET cc_start: 0.7603 (tpp) cc_final: 0.7236 (tpt) REVERT: C 751 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7487 (mm-30) REVERT: C 783 ASP cc_start: 0.7672 (m-30) cc_final: 0.7204 (t0) REVERT: C 944 MET cc_start: 0.8549 (mmm) cc_final: 0.7922 (mmt) REVERT: C 1078 MET cc_start: 0.7104 (mtp) cc_final: 0.6631 (mtp) REVERT: D 73 MET cc_start: 0.1633 (mmt) cc_final: 0.1144 (mmt) REVERT: D 180 GLU cc_start: 0.6151 (mt-10) cc_final: 0.5916 (mt-10) REVERT: D 214 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.5938 (tp30) REVERT: D 216 PHE cc_start: 0.6967 (m-80) cc_final: 0.6696 (m-80) REVERT: D 226 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7570 (tpp) REVERT: D 268 LEU cc_start: 0.8795 (tp) cc_final: 0.8376 (tt) REVERT: D 691 PHE cc_start: 0.3251 (t80) cc_final: 0.2420 (t80) REVERT: D 1024 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.7137 (ptm-80) REVERT: G 60 LYS cc_start: 0.6340 (ttpt) cc_final: 0.5705 (mttm) REVERT: E 342 ARG cc_start: 0.1961 (mtt-85) cc_final: 0.1151 (mpt-90) REVERT: E 344 ARG cc_start: 0.5663 (tmm160) cc_final: 0.4887 (ttt90) outliers start: 68 outliers final: 56 residues processed: 349 average time/residue: 0.1668 time to fit residues: 93.0034 Evaluate side-chains 333 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 273 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 552 ASP Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 763 MET Chi-restraints excluded: chain C residue 806 GLU Chi-restraints excluded: chain C residue 859 LEU Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 900 THR Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 920 HIS Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 1083 LEU Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 214 GLU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 783 SER Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 876 ILE Chi-restraints excluded: chain D residue 918 GLU Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 1024 ARG Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1100 ILE Chi-restraints excluded: chain D residue 1111 PHE Chi-restraints excluded: chain D residue 1187 VAL Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 363 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 301 optimal weight: 7.9990 chunk 223 optimal weight: 8.9990 chunk 176 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 182 optimal weight: 0.9990 chunk 262 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 143 optimal weight: 0.2980 chunk 19 optimal weight: 10.0000 chunk 299 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN F 43 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.156627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.134301 restraints weight = 39945.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.133705 restraints weight = 60426.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.131122 restraints weight = 45465.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.131506 restraints weight = 48783.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.131632 restraints weight = 39527.217| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 27614 Z= 0.129 Angle : 0.557 16.548 37694 Z= 0.298 Chirality : 0.044 0.325 4258 Planarity : 0.004 0.051 4616 Dihedral : 17.723 167.484 4517 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.72 % Allowed : 21.20 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.15), residues: 3159 helix: 1.18 (0.15), residues: 1227 sheet: 0.35 (0.27), residues: 381 loop : -0.07 (0.16), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 42 TYR 0.026 0.001 TYR E 102 PHE 0.013 0.001 PHE G 47 TRP 0.010 0.001 TRP D 23 HIS 0.006 0.001 HIS C1049 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (27614) covalent geometry : angle 0.55689 / 0.30 (37694) hydrogen bonds : bond 0.03707 / 2.51 ( 1201) hydrogen bonds : angle 4.71796 / 3.29 ( 3309) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4127.52 seconds wall clock time: 88 minutes 29.43 seconds (5309.43 seconds total)