Starting phenix.real_space_refine on Sat Aug 8 07:59:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x6f_38087/08_2026/8x6f_38087.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x6f_38087/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8x6f_38087/08_2026/8x6f_38087.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x6f_38087/08_2026/8x6f_38087.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x6f_38087/08_2026/8x6f_38087.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x6f_38087/08_2026/8x6f_38087.map" } 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-2.2rc3-6140/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: 5.42, per 1000 atoms: 0.20 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: 2.41 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: 3.99 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: 8.33 Time building geometry restraints manager: 3.21 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: 36547 2.04 - 4.08: 1077 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 30.790 Find NCS groups from input model: 0.230 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.060 ------------------------------------------------------------------------------- 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 : 0.718 10.197 37694 Z= 0.508 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 0.71834 / 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 : 0.984 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: 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: 0.5363 (mm-30) REVERT: C 266 ASP cc_start: 0.6980 (t0) cc_final: 0.6139 (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: 0.6906 (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: 0.6992 (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: 0.7700 (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: 0.7690 (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: 0.5659 (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: 0.6408 (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: 0.7457 (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: 0.7020 (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: 0.5718 (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: 0.4403 (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: 0.6146 (tpt170) REVERT: E 319 PHE cc_start: 0.6081 (m-80) cc_final: 0.5742 (m-80) REVERT: E 344 ARG cc_start: 0.4847 (tmm160) cc_final: 0.3728 (ttt90) outliers start: 19 outliers final: 5 residues processed: 666 average time/residue: 0.2277 time to fit residues: 225.7874 Evaluate side-chains 369 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 362 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 718 ASN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.160522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.137698 restraints weight = 40119.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.136880 restraints weight = 60126.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.136195 restraints weight = 58864.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.135652 restraints weight = 58112.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.136087 restraints weight = 45533.728| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27614 Z= 0.149 Angle : 0.591 11.159 37694 Z= 0.322 Chirality : 0.045 0.322 4258 Planarity : 0.004 0.046 4616 Dihedral : 17.967 169.824 4529 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.98 % Allowed : 13.97 % 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: 0.98 (0.15), residues: 3159 helix: 1.29 (0.15), residues: 1222 sheet: 0.38 (0.25), residues: 427 loop : 0.33 (0.16), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 484 TYR 0.018 0.002 TYR G 58 PHE 0.021 0.002 PHE E 183 TRP 0.010 0.001 TRP B 199 HIS 0.007 0.001 HIS C 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (27614) covalent geometry : angle 0.59145 / 0.32 (37694) hydrogen bonds : bond 0.04662 / 3.16 ( 1201) hydrogen bonds : angle 5.21525 / 3.62 ( 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 490 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 408 time to evaluate : 1.070 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: B 100 ASP cc_start: 0.6413 (t0) cc_final: 0.5898 (p0) REVERT: C 458 LYS cc_start: 0.7642 (tppt) cc_final: 0.7389 (tttt) REVERT: C 506 HIS cc_start: 0.7485 (t-90) cc_final: 0.7212 (t-90) REVERT: C 517 GLU cc_start: 0.6409 (tp30) cc_final: 0.6142 (tp30) REVERT: C 751 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7609 (mm-30) REVERT: C 763 MET cc_start: 0.8156 (ptm) cc_final: 0.7866 (ptm) REVERT: C 783 ASP cc_start: 0.7517 (m-30) cc_final: 0.7168 (t0) REVERT: C 925 MET cc_start: 0.7939 (mtp) cc_final: 0.7510 (mtm) REVERT: C 944 MET cc_start: 0.8435 (mmm) cc_final: 0.7938 (mmt) REVERT: C 967 ASN cc_start: 0.8420 (p0) cc_final: 0.7772 (p0) REVERT: C 1078 MET cc_start: 0.7032 (mtp) cc_final: 0.6718 (mtm) REVERT: C 1132 MET cc_start: 0.6837 (tpp) cc_final: 0.6241 (tpp) REVERT: D 216 PHE cc_start: 0.6873 (OUTLIER) cc_final: 0.6399 (t80) REVERT: D 226 MET cc_start: 0.7633 (tpp) cc_final: 0.7081 (tpp) REVERT: D 314 LYS cc_start: 0.7800 (mtpt) cc_final: 0.7273 (mtpp) REVERT: D 696 ILE cc_start: 0.4784 (OUTLIER) cc_final: 0.4384 (tp) REVERT: D 752 ARG cc_start: 0.8143 (mtp180) cc_final: 0.7892 (mtp-110) REVERT: D 1027 VAL cc_start: 0.5386 (OUTLIER) cc_final: 0.4989 (t) REVERT: F 26 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7760 (tpt170) REVERT: G 30 THR cc_start: 0.7280 (OUTLIER) cc_final: 0.6697 (m) REVERT: E 281 ASP cc_start: 0.7000 (t0) cc_final: 0.6764 (t0) REVERT: E 310 ARG cc_start: 0.7127 (tpt-90) cc_final: 0.6341 (tpt170) REVERT: E 344 ARG cc_start: 0.5787 (tmm160) cc_final: 0.5077 (ttt180) outliers start: 82 outliers final: 49 residues processed: 458 average time/residue: 0.1998 time to fit residues: 141.8546 Evaluate side-chains 356 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 302 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 171 SER 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 718 ASN 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 696 ILE 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: 10.0000 chunk 127 optimal weight: 9.9990 chunk 196 optimal weight: 4.9990 chunk 284 optimal weight: 1.9990 chunk 248 optimal weight: 10.0000 chunk 226 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 154 optimal weight: 0.4980 chunk 307 optimal weight: 10.0000 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 880 HIS D 289 GLN ** D 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN D 585 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.154797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.131808 restraints weight = 40452.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.130839 restraints weight = 61975.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.130352 restraints weight = 59030.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.129871 restraints weight = 56893.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.130571 restraints weight = 47755.018| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 27614 Z= 0.258 Angle : 0.681 10.183 37694 Z= 0.365 Chirality : 0.048 0.344 4258 Planarity : 0.005 0.062 4616 Dihedral : 18.013 168.386 4523 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.28 % Allowed : 15.54 % Favored : 80.18 % 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: 0.82 (0.14), residues: 1241 sheet: 0.26 (0.25), residues: 418 loop : 0.04 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 951 TYR 0.028 0.002 TYR C 37 PHE 0.023 0.002 PHE B 191 TRP 0.010 0.002 TRP D 23 HIS 0.010 0.002 HIS D 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.26 (27614) covalent geometry : angle 0.68088 / 0.37 (37694) hydrogen bonds : bond 0.04981 / 3.37 ( 1201) hydrogen bonds : angle 5.24513 / 3.68 ( 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 443 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 325 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 ASP cc_start: 0.6773 (t0) cc_final: 0.5890 (p0) REVERT: C 216 TYR cc_start: 0.4515 (m-80) cc_final: 0.4297 (m-80) REVERT: C 458 LYS cc_start: 0.7816 (tppt) cc_final: 0.7423 (tttt) REVERT: C 506 HIS cc_start: 0.7844 (t-90) cc_final: 0.7566 (t70) REVERT: C 661 MET cc_start: 0.7636 (tpp) cc_final: 0.7199 (tpt) REVERT: C 751 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7715 (mm-30) REVERT: C 763 MET cc_start: 0.8037 (ptm) cc_final: 0.7736 (ptm) REVERT: C 776 MET cc_start: 0.8394 (ttm) cc_final: 0.7786 (mtp) REVERT: C 783 ASP cc_start: 0.7378 (m-30) cc_final: 0.7138 (t0) REVERT: C 888 ASP cc_start: 0.6912 (OUTLIER) cc_final: 0.6600 (m-30) REVERT: C 944 MET cc_start: 0.8406 (mmm) cc_final: 0.7830 (mmt) REVERT: C 1078 MET cc_start: 0.7119 (mtp) cc_final: 0.6820 (mtm) REVERT: D 297 ASP cc_start: 0.6819 (t0) cc_final: 0.6528 (t0) REVERT: D 402 GLU cc_start: 0.7532 (tp30) cc_final: 0.7253 (tm-30) REVERT: G 20 ASN cc_start: 0.6532 (m-40) cc_final: 0.5685 (m-40) REVERT: E 310 ARG cc_start: 0.7018 (tpt-90) cc_final: 0.6188 (tpt170) REVERT: E 344 ARG cc_start: 0.5878 (tmm160) cc_final: 0.5271 (ttt180) outliers start: 118 outliers final: 83 residues processed: 411 average time/residue: 0.1894 time to fit residues: 123.4069 Evaluate side-chains 361 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 277 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 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 39 SER Chi-restraints excluded: chain B residue 101 VAL 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 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 552 ASP Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 599 ASN 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 815 VAL 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 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 137 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 216 PHE 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 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 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 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 F residue 9 LEU 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 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: 0.9990 chunk 273 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 chunk 287 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 72 optimal weight: 20.0000 chunk 262 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 199 optimal weight: 0.9980 chunk 166 optimal weight: 9.9990 chunk 121 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 365 ASN C 575 GLN C 599 ASN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 GLN F 8 GLN G 55 HIS ** E 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 GLN ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.153252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.124432 restraints weight = 40003.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.124240 restraints weight = 44844.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.124840 restraints weight = 42381.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.125365 restraints weight = 32427.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.125682 restraints weight = 29169.947| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27614 Z= 0.140 Angle : 0.564 8.764 37694 Z= 0.308 Chirality : 0.044 0.340 4258 Planarity : 0.004 0.058 4616 Dihedral : 17.939 168.578 4519 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.63 % Allowed : 16.59 % Favored : 79.78 % 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: 0.71 (0.15), residues: 3159 helix: 1.10 (0.14), residues: 1233 sheet: 0.33 (0.26), residues: 393 loop : 0.12 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1121 TYR 0.019 0.001 TYR C 37 PHE 0.026 0.001 PHE D1143 TRP 0.012 0.001 TRP D 23 HIS 0.010 0.001 HIS C 880 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (27614) covalent geometry : angle 0.56441 / 0.31 (37694) hydrogen bonds : bond 0.04204 / 2.86 ( 1201) hydrogen bonds : angle 4.97212 / 3.48 ( 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 408 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 308 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 ASP cc_start: 0.6947 (t0) cc_final: 0.5976 (p0) REVERT: C 41 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7535 (tt) REVERT: C 113 MET cc_start: 0.6439 (tmm) cc_final: 0.5900 (tpp) REVERT: C 458 LYS cc_start: 0.7744 (tppt) cc_final: 0.7286 (tttt) REVERT: C 506 HIS cc_start: 0.7763 (t-90) cc_final: 0.7546 (t70) REVERT: C 751 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7577 (mm-30) REVERT: C 783 ASP cc_start: 0.7463 (m-30) cc_final: 0.7150 (t0) REVERT: C 888 ASP cc_start: 0.7039 (OUTLIER) cc_final: 0.6774 (m-30) REVERT: C 944 MET cc_start: 0.8653 (mmm) cc_final: 0.8221 (mmp) REVERT: C 1078 MET cc_start: 0.7104 (mtp) cc_final: 0.6726 (mtt) REVERT: C 1132 MET cc_start: 0.6977 (tpp) cc_final: 0.6410 (tpp) REVERT: D 216 PHE cc_start: 0.7133 (OUTLIER) cc_final: 0.6904 (m-80) REVERT: D 402 GLU cc_start: 0.7517 (tp30) cc_final: 0.7243 (tm-30) REVERT: D 1027 VAL cc_start: 0.5721 (OUTLIER) cc_final: 0.5416 (t) REVERT: G 20 ASN cc_start: 0.6767 (m-40) cc_final: 0.6056 (m-40) REVERT: G 55 HIS cc_start: 0.6036 (OUTLIER) cc_final: 0.5756 (t70) REVERT: E 310 ARG cc_start: 0.7302 (tpt-90) cc_final: 0.6276 (tpt170) REVERT: E 344 ARG cc_start: 0.5833 (tmm160) cc_final: 0.4854 (ttt90) outliers start: 100 outliers final: 63 residues processed: 381 average time/residue: 0.1730 time to fit residues: 106.0939 Evaluate side-chains 349 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 281 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 197 ASP Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 138 ILE 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 376 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 530 LEU 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 812 ILE 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 888 ASP Chi-restraints excluded: chain C residue 900 THR 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 117 LEU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 216 PHE Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 496 VAL 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 647 MET 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 918 GLU 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 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 G residue 55 HIS Chi-restraints excluded: chain E residue 205 THR 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: 5.9990 chunk 39 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 285 optimal weight: 7.9990 chunk 257 optimal weight: 9.9990 chunk 202 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN C 345 GLN C 365 ASN C 599 ASN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 880 HIS D 243 GLN D 289 GLN D 330 ASN D 385 ASN D1144 GLN F 8 GLN ** G 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.149116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.120871 restraints weight = 40404.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.120657 restraints weight = 44913.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.121445 restraints weight = 42671.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.121693 restraints weight = 32342.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.121813 restraints weight = 29976.847| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 27614 Z= 0.240 Angle : 0.656 8.713 37694 Z= 0.351 Chirality : 0.047 0.342 4258 Planarity : 0.005 0.050 4616 Dihedral : 17.932 167.836 4519 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.46 % Allowed : 16.88 % Favored : 78.66 % 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: 0.25 (0.15), residues: 3159 helix: 0.72 (0.14), residues: 1231 sheet: 0.11 (0.25), residues: 417 loop : -0.16 (0.16), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 752 TYR 0.021 0.002 TYR C1098 PHE 0.021 0.002 PHE G 47 TRP 0.010 0.002 TRP D 23 HIS 0.019 0.002 HIS G 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.24 (27614) covalent geometry : angle 0.65559 / 0.35 (37694) hydrogen bonds : bond 0.04713 / 3.19 ( 1201) hydrogen bonds : angle 5.13548 / 3.60 ( 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 421 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 298 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 100 ASP cc_start: 0.7128 (t0) cc_final: 0.6054 (p0) REVERT: C 41 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7505 (tt) REVERT: C 48 MET cc_start: 0.6681 (tpp) cc_final: 0.6473 (tpt) REVERT: C 458 LYS cc_start: 0.7838 (tppt) cc_final: 0.7306 (tttt) REVERT: C 506 HIS cc_start: 0.7787 (t-90) cc_final: 0.7543 (t70) REVERT: C 661 MET cc_start: 0.7577 (tpp) cc_final: 0.7120 (tpt) REVERT: C 751 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7500 (mm-30) REVERT: C 763 MET cc_start: 0.7906 (ptm) cc_final: 0.7630 (ptm) REVERT: C 783 ASP cc_start: 0.7454 (m-30) cc_final: 0.7192 (t0) REVERT: C 888 ASP cc_start: 0.7058 (OUTLIER) cc_final: 0.6750 (m-30) REVERT: C 944 MET cc_start: 0.8537 (mmm) cc_final: 0.7840 (mmt) REVERT: C 1078 MET cc_start: 0.7352 (mtp) cc_final: 0.6949 (mtm) REVERT: D 226 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7853 (ttp) REVERT: D 297 ASP cc_start: 0.6800 (t0) cc_final: 0.6504 (t0) REVERT: D 402 GLU cc_start: 0.7567 (tp30) cc_final: 0.7298 (tm-30) REVERT: D 752 ARG cc_start: 0.8363 (mtp180) cc_final: 0.7924 (mtp-110) REVERT: D 1024 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7352 (ptm-80) REVERT: G 20 ASN cc_start: 0.6656 (m-40) cc_final: 0.5929 (m-40) REVERT: G 60 LYS cc_start: 0.6596 (ttpt) cc_final: 0.5941 (mttm) REVERT: E 294 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7551 (mm-30) REVERT: E 310 ARG cc_start: 0.7368 (tpt-90) cc_final: 0.6237 (tpt170) REVERT: E 314 VAL cc_start: 0.6303 (t) cc_final: 0.6077 (t) REVERT: E 342 ARG cc_start: 0.2720 (mtt180) cc_final: 0.2238 (mtt-85) outliers start: 123 outliers final: 95 residues processed: 396 average time/residue: 0.1856 time to fit residues: 117.5418 Evaluate side-chains 373 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 274 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 174 GLU Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 204 ILE 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 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 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 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 430 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 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 888 ASP Chi-restraints excluded: chain C residue 900 THR Chi-restraints excluded: chain C residue 920 HIS 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 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 121 SER 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 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 811 VAL Chi-restraints excluded: chain D residue 845 GLU 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 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 1169 VAL Chi-restraints excluded: chain D residue 1187 VAL 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 155 MET Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 338 VAL 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: 7.9990 chunk 204 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 250 optimal weight: 5.9990 chunk 266 optimal weight: 10.0000 chunk 25 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 599 ASN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 GLN D 385 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.156830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.134077 restraints weight = 40090.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.132880 restraints weight = 62883.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.132469 restraints weight = 57807.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.132363 restraints weight = 49149.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.132966 restraints weight = 42943.933| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27614 Z= 0.122 Angle : 0.549 7.072 37694 Z= 0.299 Chirality : 0.044 0.337 4258 Planarity : 0.004 0.049 4616 Dihedral : 17.865 167.524 4519 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.45 % Allowed : 18.40 % Favored : 78.15 % 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: 0.68 (0.15), residues: 3159 helix: 1.15 (0.15), residues: 1228 sheet: 0.36 (0.26), residues: 397 loop : 0.01 (0.16), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 42 TYR 0.023 0.001 TYR E 102 PHE 0.019 0.001 PHE D 155 TRP 0.015 0.001 TRP D 23 HIS 0.009 0.001 HIS G 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (27614) covalent geometry : angle 0.54878 / 0.30 (37694) hydrogen bonds : bond 0.03993 / 2.71 ( 1201) hydrogen bonds : angle 4.85891 / 3.40 ( 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 403 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 308 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 100 ASP cc_start: 0.6982 (t0) cc_final: 0.5897 (p0) REVERT: B 207 GLN cc_start: 0.7881 (pm20) cc_final: 0.7662 (pm20) REVERT: C 113 MET cc_start: 0.6211 (tmm) cc_final: 0.5940 (tpp) REVERT: C 458 LYS cc_start: 0.7782 (tppt) cc_final: 0.7407 (tttt) REVERT: C 751 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7519 (mm-30) REVERT: C 783 ASP cc_start: 0.7385 (m-30) cc_final: 0.7123 (t0) REVERT: C 944 MET cc_start: 0.8579 (mmm) cc_final: 0.7841 (mmt) REVERT: C 1078 MET cc_start: 0.7047 (mtp) cc_final: 0.6617 (mtp) REVERT: D 214 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.5865 (tp30) REVERT: D 216 PHE cc_start: 0.7200 (OUTLIER) cc_final: 0.6947 (m-80) REVERT: D 226 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7632 (tpp) REVERT: D 407 GLU cc_start: 0.7323 (tm-30) cc_final: 0.6953 (tm-30) REVERT: D 752 ARG cc_start: 0.8167 (mtp180) cc_final: 0.7857 (mtp-110) REVERT: D 1024 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7279 (ptm-80) REVERT: D 1027 VAL cc_start: 0.5377 (OUTLIER) cc_final: 0.5060 (t) REVERT: G 20 ASN cc_start: 0.6340 (m-40) cc_final: 0.5665 (m-40) REVERT: E 185 THR cc_start: 0.8614 (m) cc_final: 0.8399 (p) REVERT: E 310 ARG cc_start: 0.7215 (tpt-90) cc_final: 0.6332 (tpt170) outliers start: 95 outliers final: 66 residues processed: 375 average time/residue: 0.1826 time to fit residues: 110.1041 Evaluate side-chains 349 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 278 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 161 ILE Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 163 VAL 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 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 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 900 THR Chi-restraints excluded: chain C residue 920 HIS Chi-restraints excluded: chain C residue 966 MET 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 1131 LEU Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 214 GLU Chi-restraints excluded: chain D residue 216 PHE Chi-restraints excluded: chain D residue 226 MET 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 495 MET Chi-restraints excluded: chain D residue 496 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 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 1024 ARG Chi-restraints excluded: chain D residue 1027 VAL 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 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 155 MET Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain E residue 354 LEU 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: 9.9990 chunk 277 optimal weight: 0.0770 chunk 221 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 chunk 54 optimal weight: 0.1980 chunk 6 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 162 optimal weight: 0.6980 overall best weight: 1.5340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN D 385 ASN ** 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 = 0.3998 r_free = 0.3998 target = 0.157066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.133656 restraints weight = 39778.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.132428 restraints weight = 66850.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.132827 restraints weight = 58634.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.132578 restraints weight = 44852.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.133216 restraints weight = 41822.411| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27614 Z= 0.127 Angle : 0.543 7.649 37694 Z= 0.294 Chirality : 0.044 0.338 4258 Planarity : 0.004 0.056 4616 Dihedral : 17.804 167.453 4519 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.38 % Allowed : 18.33 % Favored : 78.29 % 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: 0.76 (0.15), residues: 3159 helix: 1.23 (0.15), residues: 1228 sheet: 0.42 (0.26), residues: 392 loop : 0.04 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 342 TYR 0.028 0.001 TYR C 386 PHE 0.019 0.001 PHE D 155 TRP 0.010 0.001 TRP D 23 HIS 0.006 0.001 HIS C 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (27614) covalent geometry : angle 0.54301 / 0.29 (37694) hydrogen bonds : bond 0.03863 / 2.62 ( 1201) hydrogen bonds : angle 4.77600 / 3.34 ( 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 383 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 290 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 ASP cc_start: 0.7035 (t0) cc_final: 0.5907 (p0) REVERT: C 41 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7524 (tt) REVERT: C 113 MET cc_start: 0.6183 (tmm) cc_final: 0.5692 (tpp) REVERT: C 458 LYS cc_start: 0.7787 (tppt) cc_final: 0.7372 (tttt) REVERT: C 506 HIS cc_start: 0.7428 (t70) cc_final: 0.7223 (t-90) REVERT: C 751 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7502 (mm-30) REVERT: C 763 MET cc_start: 0.8029 (ptm) cc_final: 0.7800 (ptm) REVERT: C 783 ASP cc_start: 0.7558 (m-30) cc_final: 0.7261 (t0) REVERT: C 925 MET cc_start: 0.8255 (mmm) cc_final: 0.7559 (mmm) REVERT: C 944 MET cc_start: 0.8506 (mmm) cc_final: 0.7880 (mmt) REVERT: C 1073 GLN cc_start: 0.7936 (mp10) cc_final: 0.7683 (mp10) REVERT: C 1078 MET cc_start: 0.7005 (mtp) cc_final: 0.6613 (mtt) REVERT: D 170 MET cc_start: 0.7756 (ttm) cc_final: 0.7426 (ttm) REVERT: D 214 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.5853 (tp30) REVERT: D 216 PHE cc_start: 0.7090 (OUTLIER) cc_final: 0.6795 (m-80) REVERT: D 226 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7482 (tpp) REVERT: D 268 LEU cc_start: 0.8759 (tp) cc_final: 0.8333 (tt) REVERT: D 691 PHE cc_start: 0.3260 (t80) cc_final: 0.2400 (t80) REVERT: D 1024 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7267 (ptm-80) REVERT: D 1027 VAL cc_start: 0.5313 (OUTLIER) cc_final: 0.5017 (t) REVERT: G 20 ASN cc_start: 0.6338 (m-40) cc_final: 0.5722 (m-40) REVERT: E 185 THR cc_start: 0.8624 (m) cc_final: 0.8409 (p) REVERT: E 310 ARG cc_start: 0.7269 (tpt-90) cc_final: 0.6363 (tpt170) REVERT: E 314 VAL cc_start: 0.6020 (t) cc_final: 0.5809 (t) outliers start: 93 outliers final: 71 residues processed: 355 average time/residue: 0.1718 time to fit residues: 99.8124 Evaluate side-chains 353 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 276 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 161 ILE Chi-restraints excluded: chain A residue 174 GLU 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 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 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 612 VAL Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 806 GLU Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 900 THR Chi-restraints excluded: chain C residue 920 HIS Chi-restraints excluded: chain C residue 966 MET 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 1131 LEU Chi-restraints excluded: chain D residue 10 MET 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 188 LEU Chi-restraints excluded: chain D residue 214 GLU Chi-restraints excluded: chain D residue 216 PHE 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 570 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 730 ILE Chi-restraints excluded: chain D residue 765 LEU 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 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 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 G residue 11 ASN Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 317 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: 20.0000 chunk 4 optimal weight: 7.9990 chunk 251 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 190 optimal weight: 6.9990 chunk 164 optimal weight: 9.9990 chunk 304 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.152602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.129359 restraints weight = 40425.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.128850 restraints weight = 67223.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.129091 restraints weight = 54851.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.128486 restraints weight = 42896.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.128933 restraints weight = 40370.148| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 27614 Z= 0.239 Angle : 0.664 8.554 37694 Z= 0.353 Chirality : 0.048 0.351 4258 Planarity : 0.005 0.058 4616 Dihedral : 17.846 166.642 4519 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.81 % Allowed : 18.51 % Favored : 77.68 % 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: 0.20 (0.15), residues: 3159 helix: 0.75 (0.14), residues: 1237 sheet: 0.08 (0.25), residues: 422 loop : -0.27 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 342 TYR 0.021 0.002 TYR C1098 PHE 0.022 0.002 PHE G 47 TRP 0.010 0.002 TRP A 199 HIS 0.009 0.002 HIS D 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.24 (27614) covalent geometry : angle 0.66402 / 0.35 (37694) hydrogen bonds : bond 0.04582 / 3.09 ( 1201) hydrogen bonds : angle 5.04630 / 3.54 ( 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 384 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 279 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.5233 (OUTLIER) cc_final: 0.4985 (tp) REVERT: B 100 ASP cc_start: 0.7214 (t0) cc_final: 0.6035 (p0) REVERT: B 207 GLN cc_start: 0.8057 (pm20) cc_final: 0.7845 (pm20) REVERT: C 41 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7513 (tt) REVERT: C 376 THR cc_start: 0.7743 (OUTLIER) cc_final: 0.7397 (p) REVERT: C 458 LYS cc_start: 0.7896 (tppt) cc_final: 0.7398 (tttt) REVERT: C 751 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7522 (mm-30) REVERT: C 783 ASP cc_start: 0.7655 (m-30) cc_final: 0.7355 (t0) REVERT: C 925 MET cc_start: 0.8336 (mmm) cc_final: 0.7920 (mmm) REVERT: C 944 MET cc_start: 0.8406 (mmm) cc_final: 0.7863 (mmt) REVERT: C 1078 MET cc_start: 0.7336 (mtp) cc_final: 0.6897 (mtp) REVERT: D 214 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.5921 (tp30) REVERT: D 226 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7767 (ttp) REVERT: D 268 LEU cc_start: 0.8855 (tp) cc_final: 0.8433 (tt) REVERT: D 1024 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7271 (ptm-80) REVERT: D 1027 VAL cc_start: 0.5757 (OUTLIER) cc_final: 0.5472 (t) REVERT: G 60 LYS cc_start: 0.6392 (ttpt) cc_final: 0.6018 (mttm) REVERT: E 102 TYR cc_start: 0.6974 (t80) cc_final: 0.6769 (t80) REVERT: E 310 ARG cc_start: 0.7352 (tpt-90) cc_final: 0.6406 (tpt170) outliers start: 105 outliers final: 87 residues processed: 359 average time/residue: 0.1795 time to fit residues: 103.7228 Evaluate side-chains 359 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 265 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 154 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 174 GLU 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 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 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 118 LEU 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 430 VAL Chi-restraints excluded: chain C residue 552 ASP Chi-restraints excluded: chain C residue 564 THR 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 812 ILE 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 920 HIS Chi-restraints excluded: chain C residue 970 GLN 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 C residue 1131 LEU Chi-restraints excluded: chain C residue 1145 MET 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 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 284 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 431 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 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 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 D residue 1169 VAL 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 205 THR Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 317 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: 6.9990 chunk 270 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 168 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 236 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 446 GLN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN D 330 ASN ** 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 = 0.3963 r_free = 0.3963 target = 0.153963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.130921 restraints weight = 40366.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.129986 restraints weight = 64377.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.129850 restraints weight = 59640.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.129436 restraints weight = 52606.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.130072 restraints weight = 47116.646| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27614 Z= 0.179 Angle : 0.597 7.366 37694 Z= 0.321 Chirality : 0.045 0.353 4258 Planarity : 0.004 0.058 4616 Dihedral : 17.814 166.348 4519 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.48 % Allowed : 18.95 % Favored : 77.57 % 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: 0.30 (0.15), residues: 3159 helix: 0.88 (0.14), residues: 1235 sheet: 0.12 (0.25), residues: 419 loop : -0.24 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 377 TYR 0.020 0.002 TYR C 386 PHE 0.018 0.002 PHE G 47 TRP 0.011 0.001 TRP D 23 HIS 0.007 0.001 HIS C1049 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (27614) covalent geometry : angle 0.59692 / 0.32 (37694) hydrogen bonds : bond 0.04173 / 2.82 ( 1201) hydrogen bonds : angle 4.93116 / 3.46 ( 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 376 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 280 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 ASP cc_start: 0.7327 (t0) cc_final: 0.6014 (p0) REVERT: C 41 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7638 (tt) REVERT: C 376 THR cc_start: 0.7681 (OUTLIER) cc_final: 0.7362 (p) REVERT: C 458 LYS cc_start: 0.7893 (tppt) cc_final: 0.7435 (tttt) REVERT: C 751 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7612 (mm-30) REVERT: C 925 MET cc_start: 0.8342 (mmm) cc_final: 0.8138 (ttm) REVERT: C 944 MET cc_start: 0.8285 (mmm) cc_final: 0.7795 (mmt) REVERT: C 1078 MET cc_start: 0.7119 (mtp) cc_final: 0.6696 (mtp) REVERT: D 180 GLU cc_start: 0.5946 (mt-10) cc_final: 0.5626 (mt-10) REVERT: D 214 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.5858 (tp30) REVERT: D 226 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7729 (ttp) REVERT: D 268 LEU cc_start: 0.8794 (tp) cc_final: 0.8374 (tt) REVERT: D 1024 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7210 (ptm-80) REVERT: D 1027 VAL cc_start: 0.5502 (OUTLIER) cc_final: 0.5237 (t) REVERT: G 60 LYS cc_start: 0.6389 (ttpt) cc_final: 0.6068 (mttm) REVERT: E 310 ARG cc_start: 0.7293 (tpt-90) cc_final: 0.6334 (tpt170) outliers start: 96 outliers final: 77 residues processed: 355 average time/residue: 0.1818 time to fit residues: 104.6364 Evaluate side-chains 349 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 266 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 161 ILE Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 14 ILE 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 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 118 LEU Chi-restraints excluded: chain C residue 139 VAL 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 612 VAL Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 806 GLU Chi-restraints excluded: chain C residue 871 VAL 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 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 1131 LEU Chi-restraints excluded: chain D residue 10 MET 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 137 VAL 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 431 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 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 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 D residue 1187 VAL 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 E residue 149 ARG Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain E residue 304 LEU 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 253 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 219 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 308 optimal weight: 5.9990 chunk 79 optimal weight: 40.0000 chunk 4 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 chunk 319 optimal weight: 50.0000 chunk 92 optimal weight: 8.9990 chunk 216 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.156403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.133094 restraints weight = 39783.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.131975 restraints weight = 62759.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.131851 restraints weight = 57049.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.131511 restraints weight = 53208.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.132247 restraints weight = 45150.603| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27614 Z= 0.125 Angle : 0.559 7.974 37694 Z= 0.303 Chirality : 0.044 0.351 4258 Planarity : 0.004 0.057 4616 Dihedral : 17.751 166.498 4519 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.47 % Allowed : 19.96 % Favored : 77.57 % 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: 0.61 (0.15), residues: 3159 helix: 1.19 (0.15), residues: 1217 sheet: 0.31 (0.27), residues: 388 loop : -0.12 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 377 TYR 0.025 0.001 TYR C 386 PHE 0.014 0.001 PHE G 47 TRP 0.012 0.001 TRP D 23 HIS 0.006 0.001 HIS C1049 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (27614) covalent geometry : angle 0.55943 / 0.30 (37694) hydrogen bonds : bond 0.03784 / 2.56 ( 1201) hydrogen bonds : angle 4.77597 / 3.35 ( 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 357 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 289 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 ASP cc_start: 0.7320 (t0) cc_final: 0.6007 (p0) REVERT: C 376 THR cc_start: 0.8003 (OUTLIER) cc_final: 0.7676 (p) REVERT: C 458 LYS cc_start: 0.7663 (tppt) cc_final: 0.7292 (tttt) REVERT: C 751 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7573 (mm-30) REVERT: C 944 MET cc_start: 0.8417 (mmm) cc_final: 0.7901 (mmt) REVERT: C 1078 MET cc_start: 0.7115 (mtp) cc_final: 0.6689 (mtt) REVERT: D 180 GLU cc_start: 0.5989 (mt-10) cc_final: 0.5739 (mt-10) REVERT: D 214 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.5942 (tp30) REVERT: D 226 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7613 (tpp) REVERT: D 268 LEU cc_start: 0.8796 (tp) cc_final: 0.8339 (tt) REVERT: D 691 PHE cc_start: 0.3403 (t80) cc_final: 0.2566 (t80) REVERT: D 1024 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7146 (ptm-80) REVERT: D 1027 VAL cc_start: 0.5528 (OUTLIER) cc_final: 0.5265 (t) REVERT: G 60 LYS cc_start: 0.6440 (ttpt) cc_final: 0.5898 (mttm) REVERT: E 296 LEU cc_start: 0.8394 (tp) cc_final: 0.8066 (tp) REVERT: E 310 ARG cc_start: 0.7318 (tpt-90) cc_final: 0.6259 (tpt170) REVERT: E 314 VAL cc_start: 0.5995 (t) cc_final: 0.5784 (t) REVERT: E 344 ARG cc_start: 0.5527 (ttp80) cc_final: 0.5205 (ttt180) outliers start: 68 outliers final: 60 residues processed: 341 average time/residue: 0.1783 time to fit residues: 98.2770 Evaluate side-chains 336 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 271 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 174 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 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 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 610 MET 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 877 ARG Chi-restraints excluded: chain C residue 900 THR 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 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 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 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 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 E residue 149 ARG Chi-restraints excluded: chain E residue 317 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 301 optimal weight: 0.0770 chunk 223 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 182 optimal weight: 0.0470 chunk 262 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 299 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 overall best weight: 2.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.155410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.132935 restraints weight = 39864.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.132242 restraints weight = 61482.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.131797 restraints weight = 53886.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.131623 restraints weight = 47851.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.132032 restraints weight = 41753.355| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 27614 Z= 0.147 Angle : 0.581 18.043 37694 Z= 0.310 Chirality : 0.044 0.345 4258 Planarity : 0.004 0.062 4616 Dihedral : 17.728 166.249 4519 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.61 % Allowed : 20.18 % Favored : 77.21 % 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: 0.53 (0.15), residues: 3159 helix: 1.09 (0.15), residues: 1224 sheet: 0.34 (0.27), residues: 388 loop : -0.15 (0.16), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 377 TYR 0.024 0.002 TYR E 102 PHE 0.015 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 0.00337 / 0.15 (27614) covalent geometry : angle 0.58058 / 0.31 (37694) hydrogen bonds : bond 0.03888 / 2.64 ( 1201) hydrogen bonds : angle 4.82172 / 3.38 ( 3309) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4138.56 seconds wall clock time: 72 minutes 45.98 seconds (4365.98 seconds total)