Starting phenix.real_space_refine on Mon Aug 25 09:24:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x6f_38087/08_2025/8x6f_38087.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x6f_38087/08_2025/8x6f_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_2025/8x6f_38087.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x6f_38087/08_2025/8x6f_38087.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x6f_38087/08_2025/8x6f_38087.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x6f_38087/08_2025/8x6f_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 1.85 Conformation dependent library (CDL) restraints added in 892.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 3.47 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: 6.63 Time building geometry restraints manager: 2.48 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=" 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=" N VAL D 668 " pdb=" CA VAL D 668 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.17e-02 7.31e+03 1.10e+01 bond pdb=" N HIS E 356 " pdb=" CA HIS E 356 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.14e-02 7.69e+03 1.07e+01 bond pdb=" N THR C 874 " pdb=" CA THR C 874 " ideal model delta sigma weight residual 1.458 1.487 -0.029 9.00e-03 1.23e+04 1.04e+01 ... (remaining 27609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 36686 2.04 - 4.08: 942 4.08 - 6.12: 55 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=" CA PHE G 47 " pdb=" CB PHE G 47 " pdb=" CG PHE G 47 " ideal model delta sigma weight residual 113.80 118.25 -4.45 1.00e+00 1.00e+00 1.98e+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: 3522 0.059 - 0.119: 623 0.119 - 0.178: 83 0.178 - 0.237: 23 0.237 - 0.296: 7 Chirality restraints: 4258 Sorted by residual: chirality pdb=" CA VAL D 669 " pdb=" N VAL D 669 " pdb=" C VAL D 669 " pdb=" CB VAL D 669 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA LEU G 51 " pdb=" N LEU G 51 " pdb=" C LEU G 51 " pdb=" CB LEU G 51 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA VAL E 338 " pdb=" N VAL E 338 " pdb=" C VAL E 338 " pdb=" CB VAL E 338 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 4255 not shown) Planarity restraints: 4616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 873 " -0.013 2.00e-02 2.50e+03 2.70e-02 7.28e+00 pdb=" C ASP C 873 " 0.047 2.00e-02 2.50e+03 pdb=" O ASP C 873 " -0.018 2.00e-02 2.50e+03 pdb=" N THR C 874 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA T 62 " 0.014 2.00e-02 2.50e+03 1.56e-02 6.67e+00 pdb=" N9 DA T 62 " -0.007 2.00e-02 2.50e+03 pdb=" C8 DA T 62 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA T 62 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA T 62 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA T 62 " -0.006 2.00e-02 2.50e+03 pdb=" N6 DA T 62 " 0.001 2.00e-02 2.50e+03 pdb=" N1 DA T 62 " 0.035 2.00e-02 2.50e+03 pdb=" C2 DA T 62 " -0.033 2.00e-02 2.50e+03 pdb=" N3 DA T 62 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA T 62 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 376 " -0.038 5.00e-02 4.00e+02 5.80e-02 5.37e+00 pdb=" N PRO C 377 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 377 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 377 " -0.032 5.00e-02 4.00e+02 ... (remaining 4613 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3028 2.75 - 3.29: 27474 3.29 - 3.82: 46759 3.82 - 4.36: 54631 4.36 - 4.90: 91051 Nonbonded interactions: 222943 Sorted by model distance: nonbonded pdb=" N2 DG N 67 " pdb=" O2 DT T 20 " model vdw 2.210 3.120 nonbonded pdb=" O LEU C 41 " pdb=" OH TYR C 69 " model vdw 2.210 3.040 nonbonded pdb=" O PHE D 781 " pdb=" OG1 THR D 784 " model vdw 2.218 3.040 nonbonded pdb=" OG1 THR B 156 " pdb=" OD1 ASP B 158 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR G 25 " pdb=" OE1 GLU G 59 " model vdw 2.237 3.040 ... (remaining 222938 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 227) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 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: 0.310 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 26.320 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 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 0.046 27614 Z= 0.289 Angle : 0.690 10.197 37694 Z= 0.439 Chirality : 0.049 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 aren 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 covalent geometry : bond 0.00459 (27614) covalent geometry : angle 0.68968 (37694) hydrogen bonds : bond 0.14039 ( 1201) hydrogen bonds : angle 6.32339 ( 3309) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 654 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8092 (mt) REVERT: A 61 VAL cc_start: 0.6819 (t) cc_final: 0.6600 (t) REVERT: A 113 THR cc_start: 0.7595 (m) cc_final: 0.7375 (p) REVERT: A 124 GLU cc_start: 0.7664 (pm20) cc_final: 0.7458 (pm20) REVERT: B 55 TYR cc_start: 0.8200 (p90) cc_final: 0.7931 (p90) REVERT: B 100 ASP cc_start: 0.7193 (t0) cc_final: 0.6598 (p0) REVERT: B 193 LYS cc_start: 0.7705 (tttt) cc_final: 0.7327 (tttt) REVERT: C 178 ASP cc_start: 0.6526 (m-30) cc_final: 0.6170 (m-30) REVERT: C 188 ARG cc_start: 0.5461 (tmm-80) cc_final: 0.4831 (mmm-85) REVERT: C 218 ARG cc_start: 0.4621 (mmt180) cc_final: 0.4271 (mmp80) REVERT: C 222 GLU cc_start: 0.6194 (mp0) cc_final: 0.5364 (mm-30) REVERT: C 266 ASP cc_start: 0.6980 (t0) cc_final: 0.6138 (t0) REVERT: C 401 ASP cc_start: 0.7593 (m-30) cc_final: 0.6957 (t70) REVERT: C 434 MET cc_start: 0.2620 (mmp) cc_final: 0.2269 (mtp) REVERT: C 446 GLN cc_start: 0.6168 (pt0) cc_final: 0.5867 (mm110) REVERT: C 451 ARG cc_start: 0.5811 (ttp80) cc_final: 0.5012 (tpp-160) REVERT: C 458 LYS cc_start: 0.6331 (tppt) cc_final: 0.5850 (tttt) REVERT: C 468 GLN cc_start: 0.8077 (mt0) cc_final: 0.7871 (mm-40) REVERT: C 506 HIS cc_start: 0.6634 (t-90) cc_final: 0.5154 (t-90) REVERT: C 559 GLN cc_start: 0.6910 (tt0) cc_final: 0.6418 (mp10) REVERT: C 751 GLU cc_start: 0.7611 (mt-10) cc_final: 0.6905 (mm-30) REVERT: C 763 MET cc_start: 0.8006 (ptm) cc_final: 0.7576 (ptm) REVERT: C 783 ASP cc_start: 0.7835 (m-30) cc_final: 0.6991 (t0) REVERT: C 852 GLU cc_start: 0.5659 (pm20) cc_final: 0.5012 (tt0) REVERT: C 858 ARG cc_start: 0.6417 (mmm160) cc_final: 0.6124 (mtt90) REVERT: C 869 ARG cc_start: 0.6094 (ttm110) cc_final: 0.5868 (mtp180) REVERT: C 876 LEU cc_start: 0.7374 (tp) cc_final: 0.6887 (tp) REVERT: C 908 LEU cc_start: 0.7762 (tp) cc_final: 0.7536 (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: 0.7691 (mtmm) REVERT: D 40 LYS cc_start: 0.6613 (tptt) cc_final: 0.5954 (mmtp) REVERT: D 42 GLU cc_start: 0.5943 (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: 0.6407 (tpt170) REVERT: D 314 LYS cc_start: 0.7689 (mtpt) cc_final: 0.6792 (tttp) REVERT: D 391 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7476 (tp30) REVERT: D 393 MET cc_start: 0.7189 (mmt) cc_final: 0.6794 (mtm) REVERT: D 399 ASP cc_start: 0.7049 (m-30) cc_final: 0.6649 (t0) REVERT: D 402 GLU cc_start: 0.7764 (tt0) cc_final: 0.7456 (tp30) REVERT: D 407 GLU cc_start: 0.7678 (tm-30) cc_final: 0.6930 (mm-30) REVERT: D 478 ASN cc_start: 0.7829 (m110) cc_final: 0.7551 (m110) REVERT: D 642 MET cc_start: 0.6684 (tpp) cc_final: 0.6460 (ttm) REVERT: D 703 ASN cc_start: 0.7865 (m-40) cc_final: 0.7234 (t0) REVERT: D 719 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6728 (tm-30) REVERT: D 752 ARG cc_start: 0.7955 (mtp180) cc_final: 0.6927 (mtp-110) REVERT: D 848 GLU cc_start: 0.7674 (tp30) cc_final: 0.6784 (tp30) REVERT: D 873 THR cc_start: 0.7485 (p) cc_final: 0.7033 (p) REVERT: D 965 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7587 (tp30) REVERT: D 992 GLN cc_start: 0.2058 (mm110) cc_final: 0.1621 (pp30) REVERT: D 1013 ARG cc_start: 0.6300 (ptm-80) cc_final: 0.5968 (ptm160) REVERT: D 1030 GLU cc_start: 0.5476 (tt0) cc_final: 0.5255 (mm-30) REVERT: D 1048 GLU cc_start: 0.7072 (pt0) cc_final: 0.6555 (pt0) REVERT: D 1057 LYS cc_start: 0.7621 (tttt) cc_final: 0.7342 (pttt) REVERT: D 1143 PHE cc_start: 0.7351 (t80) cc_final: 0.7049 (t80) REVERT: D 1158 LYS cc_start: 0.8144 (mttt) cc_final: 0.7359 (ttmt) REVERT: D 1182 ARG cc_start: 0.6789 (mtp-110) cc_final: 0.6457 (ttp80) REVERT: F 26 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6726 (tpt170) REVERT: F 36 THR cc_start: 0.6757 (p) cc_final: 0.6144 (t) REVERT: F 54 GLU cc_start: 0.6090 (mt-10) cc_final: 0.5717 (mt-10) REVERT: F 61 ARG cc_start: 0.7738 (ttp80) cc_final: 0.7193 (tmm-80) REVERT: G 20 ASN cc_start: 0.6305 (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: 0.6339 (m-80) cc_final: 0.6007 (m-80) REVERT: E 155 MET cc_start: 0.7272 (tpp) cc_final: 0.7016 (tpt) REVERT: E 181 PHE cc_start: 0.4734 (m-80) cc_final: 0.4415 (m-80) REVERT: E 280 GLU cc_start: 0.7612 (tt0) cc_final: 0.6924 (tm-30) REVERT: E 301 GLU cc_start: 0.4675 (tt0) cc_final: 0.4277 (mm-30) REVERT: E 310 ARG cc_start: 0.7115 (tpt-90) cc_final: 0.6148 (tpt170) REVERT: E 319 PHE cc_start: 0.6081 (m-80) cc_final: 0.5742 (m-80) REVERT: E 339 THR cc_start: 0.6024 (p) cc_final: 0.5698 (t) REVERT: E 342 ARG cc_start: 0.3173 (mtt180) cc_final: 0.2943 (mtt-85) REVERT: E 344 ARG cc_start: 0.4847 (tmm160) cc_final: 0.3842 (ttt180) outliers start: 19 outliers final: 5 residues processed: 666 average time/residue: 0.2437 time to fit residues: 238.9060 Evaluate side-chains 370 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 363 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 HIS B 70 ASN C 157 ASN C 389 ASN C 599 ASN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 880 HIS D 283 ASN F 43 HIS G 22 GLN ** E 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.160506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.137593 restraints weight = 40160.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.137122 restraints weight = 54060.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.137533 restraints weight = 49191.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.137822 restraints weight = 42893.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.138213 restraints weight = 36669.665| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27614 Z= 0.142 Angle : 0.561 10.907 37694 Z= 0.304 Chirality : 0.043 0.243 4258 Planarity : 0.004 0.044 4616 Dihedral : 17.856 169.213 4529 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.09 % Allowed : 14.12 % Favored : 82.79 % 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 aren not related in a simple way. whole: 1.08 (0.15), residues: 3159 helix: 1.37 (0.15), residues: 1227 sheet: 0.56 (0.26), residues: 380 loop : 0.35 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 910 TYR 0.020 0.001 TYR G 58 PHE 0.028 0.002 PHE E 183 TRP 0.010 0.001 TRP C 39 HIS 0.008 0.001 HIS C 677 Details of bonding type rmsd covalent geometry : bond 0.00325 (27614) covalent geometry : angle 0.56077 (37694) hydrogen bonds : bond 0.04143 ( 1201) hydrogen bonds : angle 5.04692 ( 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 503 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 418 time to evaluate : 0.960 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: 0.6390 (t0) cc_final: 0.5905 (p0) REVERT: C 451 ARG cc_start: 0.6357 (ttp80) cc_final: 0.6105 (tpp-160) REVERT: C 458 LYS cc_start: 0.7776 (tppt) cc_final: 0.7397 (tttt) REVERT: C 506 HIS cc_start: 0.7507 (t-90) cc_final: 0.7011 (t-90) REVERT: C 517 GLU cc_start: 0.6445 (tp30) cc_final: 0.6174 (tp30) REVERT: C 642 MET cc_start: 0.7853 (ttm) cc_final: 0.7557 (ttp) REVERT: C 751 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7546 (mm-30) REVERT: C 763 MET cc_start: 0.7871 (ptm) cc_final: 0.7565 (ptm) REVERT: C 783 ASP cc_start: 0.7479 (m-30) cc_final: 0.7147 (t0) REVERT: C 925 MET cc_start: 0.8002 (mtp) cc_final: 0.7519 (mtm) REVERT: C 944 MET cc_start: 0.8479 (mmm) cc_final: 0.7926 (mmt) REVERT: C 967 ASN cc_start: 0.8402 (p0) cc_final: 0.7733 (p0) REVERT: C 1078 MET cc_start: 0.7041 (mtp) cc_final: 0.6738 (mtm) REVERT: D 216 PHE cc_start: 0.6882 (OUTLIER) cc_final: 0.6271 (t80) REVERT: D 226 MET cc_start: 0.7657 (tpp) cc_final: 0.6833 (tpp) REVERT: D 314 LYS cc_start: 0.7852 (mtpt) cc_final: 0.7242 (mtpp) REVERT: D 1027 VAL cc_start: 0.5701 (OUTLIER) cc_final: 0.5400 (t) REVERT: G 30 THR cc_start: 0.7315 (OUTLIER) cc_final: 0.6648 (m) REVERT: E 310 ARG cc_start: 0.7139 (tpt-90) cc_final: 0.6439 (tpt170) REVERT: E 344 ARG cc_start: 0.5872 (tmm160) cc_final: 0.5353 (ttt90) outliers start: 85 outliers final: 49 residues processed: 473 average time/residue: 0.1847 time to fit residues: 134.6993 Evaluate side-chains 357 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 305 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 161 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 91 SER 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 32 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 552 ASP Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 599 ASN Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 806 GLU Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 870 GLU Chi-restraints excluded: chain C residue 880 HIS Chi-restraints excluded: chain C residue 900 THR Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain D residue 216 PHE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 571 ILE 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 778 LEU 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 1132 LEU Chi-restraints excluded: chain D residue 1169 VAL Chi-restraints excluded: chain F residue 9 LEU 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 317 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 149 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 196 optimal weight: 1.9990 chunk 284 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 226 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 307 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 ASN C 402 HIS C 575 GLN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 880 HIS D 201 GLN D 289 GLN D 330 ASN D1144 GLN ** E 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 GLN E 285 GLN ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.154586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.126147 restraints weight = 39850.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.125974 restraints weight = 46207.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.126896 restraints weight = 41206.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.127175 restraints weight = 31055.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.127495 restraints weight = 28692.290| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27614 Z= 0.149 Angle : 0.551 10.051 37694 Z= 0.298 Chirality : 0.043 0.227 4258 Planarity : 0.004 0.058 4616 Dihedral : 17.782 168.957 4519 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.16 % Allowed : 15.86 % Favored : 80.98 % 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 aren not related in a simple way. whole: 1.03 (0.15), residues: 3159 helix: 1.35 (0.15), residues: 1226 sheet: 0.52 (0.26), residues: 409 loop : 0.31 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 342 TYR 0.020 0.001 TYR C 37 PHE 0.018 0.001 PHE E 183 TRP 0.011 0.001 TRP D 23 HIS 0.011 0.001 HIS C 880 Details of bonding type rmsd covalent geometry : bond 0.00346 (27614) covalent geometry : angle 0.55132 (37694) hydrogen bonds : bond 0.03956 ( 1201) hydrogen bonds : angle 4.86672 ( 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 420 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 333 time to evaluate : 1.072 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: 0.6661 (t0) cc_final: 0.5893 (p0) REVERT: C 188 ARG cc_start: 0.6940 (mmm-85) cc_final: 0.6042 (ptm160) REVERT: C 216 TYR cc_start: 0.4573 (m-80) cc_final: 0.4322 (m-80) REVERT: C 222 GLU cc_start: 0.5512 (mt-10) cc_final: 0.5106 (pt0) REVERT: C 451 ARG cc_start: 0.6095 (ttp80) cc_final: 0.5646 (tpp-160) REVERT: C 458 LYS cc_start: 0.7699 (tppt) cc_final: 0.7272 (tttt) REVERT: C 478 GLU cc_start: 0.6934 (tt0) cc_final: 0.6686 (tt0) REVERT: C 506 HIS cc_start: 0.7760 (t-90) cc_final: 0.7530 (t70) REVERT: C 602 MET cc_start: 0.6893 (OUTLIER) cc_final: 0.6055 (tpt) REVERT: C 661 MET cc_start: 0.7588 (tpp) cc_final: 0.7106 (tpt) REVERT: C 751 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7461 (mm-30) REVERT: C 763 MET cc_start: 0.7882 (ptm) cc_final: 0.7632 (ptm) REVERT: C 776 MET cc_start: 0.8336 (ttm) cc_final: 0.7962 (mtp) REVERT: C 783 ASP cc_start: 0.7469 (m-30) cc_final: 0.7128 (t0) REVERT: C 925 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7684 (mtm) REVERT: C 944 MET cc_start: 0.8475 (mmm) cc_final: 0.7875 (mmt) REVERT: C 1024 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: C 1078 MET cc_start: 0.7039 (mtp) cc_final: 0.6750 (mtm) REVERT: D 210 LEU cc_start: 0.6911 (mt) cc_final: 0.6446 (tt) REVERT: D 226 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7335 (tpp) REVERT: D 297 ASP cc_start: 0.6900 (t0) cc_final: 0.6660 (t0) REVERT: D 314 LYS cc_start: 0.7838 (mtpt) cc_final: 0.7339 (mtpp) REVERT: D 696 ILE cc_start: 0.4771 (pt) cc_final: 0.4461 (pt) REVERT: G 20 ASN cc_start: 0.6552 (m-40) cc_final: 0.5865 (m-40) REVERT: E 183 PHE cc_start: 0.6527 (t80) cc_final: 0.6286 (t80) REVERT: E 310 ARG cc_start: 0.7273 (tpt-90) cc_final: 0.6326 (tpt170) REVERT: E 344 ARG cc_start: 0.5717 (tmm160) cc_final: 0.5084 (ttt90) outliers start: 87 outliers final: 53 residues processed: 396 average time/residue: 0.1662 time to fit residues: 103.6925 Evaluate side-chains 352 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 295 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 161 ILE 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 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 103 THR Chi-restraints excluded: chain C residue 303 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 599 ASN Chi-restraints excluded: chain C residue 602 MET 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 880 HIS Chi-restraints excluded: chain C residue 900 THR Chi-restraints excluded: chain C residue 920 HIS Chi-restraints excluded: chain C residue 925 MET Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1059 VAL Chi-restraints excluded: chain C residue 1107 VAL 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 121 SER Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 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 873 THR 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 1100 ILE Chi-restraints excluded: chain D residue 1111 PHE Chi-restraints excluded: chain D residue 1113 HIS Chi-restraints excluded: chain D residue 1169 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 317 LEU 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: 6.9990 chunk 273 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 287 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 72 optimal weight: 30.0000 chunk 262 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 199 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 ASN C 365 ASN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 880 HIS D 289 GLN D 385 ASN F 8 GLN G 55 HIS ** E 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 GLN ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.150282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.121870 restraints weight = 40509.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.121736 restraints weight = 45087.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.122548 restraints weight = 41042.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.122889 restraints weight = 31123.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.122916 restraints weight = 28731.276| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 27614 Z= 0.217 Angle : 0.614 8.148 37694 Z= 0.331 Chirality : 0.045 0.272 4258 Planarity : 0.005 0.049 4616 Dihedral : 17.824 167.935 4519 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.25 % Allowed : 16.37 % Favored : 79.38 % 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 aren not related in a simple way. whole: 0.57 (0.15), residues: 3159 helix: 0.92 (0.14), residues: 1236 sheet: 0.50 (0.26), residues: 394 loop : 0.01 (0.16), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 858 TYR 0.022 0.002 TYR C 37 PHE 0.025 0.002 PHE D 249 TRP 0.011 0.002 TRP D 23 HIS 0.011 0.002 HIS C 880 Details of bonding type rmsd covalent geometry : bond 0.00508 (27614) covalent geometry : angle 0.61415 (37694) hydrogen bonds : bond 0.04377 ( 1201) hydrogen bonds : angle 5.00129 ( 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 426 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 309 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 100 ASP cc_start: 0.7160 (t0) cc_final: 0.5995 (p0) REVERT: C 41 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7531 (tt) REVERT: C 188 ARG cc_start: 0.6896 (mmm-85) cc_final: 0.6240 (ptm160) REVERT: C 451 ARG cc_start: 0.6206 (ttp80) cc_final: 0.5686 (tpp-160) REVERT: C 458 LYS cc_start: 0.7816 (tppt) cc_final: 0.7322 (tttt) REVERT: C 478 GLU cc_start: 0.6952 (tt0) cc_final: 0.6716 (tt0) REVERT: C 517 GLU cc_start: 0.6334 (tp30) cc_final: 0.6127 (tp30) REVERT: C 751 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7526 (mm-30) REVERT: C 783 ASP cc_start: 0.7405 (m-30) cc_final: 0.7179 (t0) REVERT: C 888 ASP cc_start: 0.6989 (OUTLIER) cc_final: 0.6724 (m-30) REVERT: C 925 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7707 (mtm) REVERT: C 1078 MET cc_start: 0.7364 (mtp) cc_final: 0.6937 (mtm) REVERT: D 170 MET cc_start: 0.8083 (ttm) cc_final: 0.7685 (ttm) REVERT: D 210 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6329 (tt) REVERT: D 268 LEU cc_start: 0.8897 (tp) cc_final: 0.8429 (tt) REVERT: D 314 LYS cc_start: 0.7914 (mtpt) cc_final: 0.7362 (mtpp) REVERT: D 696 ILE cc_start: 0.4896 (pt) cc_final: 0.4692 (pt) REVERT: D 1024 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7322 (ptm-80) REVERT: G 20 ASN cc_start: 0.6556 (m-40) cc_final: 0.5873 (m-40) REVERT: G 55 HIS cc_start: 0.6221 (OUTLIER) cc_final: 0.6009 (t70) REVERT: E 183 PHE cc_start: 0.6622 (t80) cc_final: 0.6316 (t80) REVERT: E 212 MET cc_start: 0.6763 (tpt) cc_final: 0.6458 (tpp) REVERT: E 294 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7670 (mm-30) REVERT: E 310 ARG cc_start: 0.7416 (tpt-90) cc_final: 0.6289 (tpt170) REVERT: E 314 VAL cc_start: 0.6324 (t) cc_final: 0.6123 (t) REVERT: E 342 ARG cc_start: 0.2819 (mtt180) cc_final: 0.2380 (mtt-85) REVERT: E 344 ARG cc_start: 0.5841 (tmm160) cc_final: 0.4986 (ttt90) outliers start: 117 outliers final: 83 residues processed: 396 average time/residue: 0.1864 time to fit residues: 117.1124 Evaluate side-chains 364 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 275 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 97 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 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 138 ILE Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 303 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 450 ILE 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 880 HIS 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 925 MET 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 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 210 LEU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 570 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 796 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 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 F residue 57 ASP Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain E residue 354 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 23 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 285 optimal weight: 7.9990 chunk 257 optimal weight: 20.0000 chunk 202 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 136 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 GLN C 575 GLN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1144 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.154703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.131610 restraints weight = 40204.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.131135 restraints weight = 64822.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.131288 restraints weight = 50497.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.130786 restraints weight = 43065.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.131120 restraints weight = 40060.055| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27614 Z= 0.180 Angle : 0.578 12.682 37694 Z= 0.311 Chirality : 0.044 0.194 4258 Planarity : 0.004 0.047 4616 Dihedral : 17.845 167.487 4519 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.28 % Allowed : 16.70 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.15), residues: 3159 helix: 0.94 (0.14), residues: 1231 sheet: 0.30 (0.26), residues: 377 loop : -0.05 (0.16), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 42 TYR 0.019 0.002 TYR C 37 PHE 0.019 0.002 PHE G 47 TRP 0.010 0.001 TRP A 199 HIS 0.018 0.001 HIS G 55 Details of bonding type rmsd covalent geometry : bond 0.00424 (27614) covalent geometry : angle 0.57755 (37694) hydrogen bonds : bond 0.04100 ( 1201) hydrogen bonds : angle 4.91865 ( 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 425 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 307 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 100 ASP cc_start: 0.7232 (t0) cc_final: 0.6018 (p0) REVERT: C 41 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7547 (tt) REVERT: C 451 ARG cc_start: 0.6233 (ttp80) cc_final: 0.5704 (tpp-160) REVERT: C 458 LYS cc_start: 0.7828 (tppt) cc_final: 0.7345 (tttt) REVERT: C 517 GLU cc_start: 0.6241 (tp30) cc_final: 0.5975 (tp30) REVERT: C 751 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7554 (mm-30) REVERT: C 783 ASP cc_start: 0.7651 (m-30) cc_final: 0.7348 (t0) REVERT: C 888 ASP cc_start: 0.7351 (OUTLIER) cc_final: 0.7071 (m-30) REVERT: C 944 MET cc_start: 0.8552 (mmm) cc_final: 0.8150 (mmp) REVERT: C 1078 MET cc_start: 0.7267 (mtp) cc_final: 0.6792 (mtp) REVERT: C 1141 ASP cc_start: 0.7567 (t0) cc_final: 0.7248 (t0) REVERT: D 180 GLU cc_start: 0.6123 (mt-10) cc_final: 0.5829 (mt-10) REVERT: D 210 LEU cc_start: 0.7247 (mt) cc_final: 0.6182 (tt) REVERT: D 216 PHE cc_start: 0.7065 (m-80) cc_final: 0.6864 (m-80) REVERT: D 297 ASP cc_start: 0.7043 (t0) cc_final: 0.6794 (t0) REVERT: D 314 LYS cc_start: 0.7820 (mtpt) cc_final: 0.7290 (mtpp) REVERT: D 1024 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7231 (ptm-80) REVERT: D 1027 VAL cc_start: 0.5677 (OUTLIER) cc_final: 0.5420 (t) REVERT: G 33 GLN cc_start: 0.7107 (mt0) cc_final: 0.6890 (mt0) REVERT: G 60 LYS cc_start: 0.6446 (ttpt) cc_final: 0.6011 (mttm) REVERT: E 183 PHE cc_start: 0.6552 (t80) cc_final: 0.6211 (t80) REVERT: E 212 MET cc_start: 0.6621 (tpt) cc_final: 0.6362 (tpp) REVERT: E 294 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7691 (mm-30) REVERT: E 310 ARG cc_start: 0.7329 (tpt-90) cc_final: 0.6243 (tpt170) REVERT: E 314 VAL cc_start: 0.6135 (t) cc_final: 0.5786 (t) REVERT: E 342 ARG cc_start: 0.2697 (mtt180) cc_final: 0.2199 (mtt-85) REVERT: E 344 ARG cc_start: 0.5806 (tmm160) cc_final: 0.5124 (ttt90) outliers start: 118 outliers final: 82 residues processed: 399 average time/residue: 0.1705 time to fit residues: 107.1641 Evaluate side-chains 364 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 278 time to evaluate : 1.173 ------------------------------------------------------------------------------- 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 127 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 39 SER Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 57 GLU 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 118 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 303 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 599 ASN Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 801 THR Chi-restraints excluded: chain C residue 806 GLU Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 880 HIS Chi-restraints excluded: chain C residue 888 ASP Chi-restraints excluded: chain C residue 900 THR Chi-restraints excluded: chain C residue 920 HIS Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 1083 LEU Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain 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 136 VAL Chi-restraints excluded: chain D residue 137 VAL 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 488 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 845 GLU Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 873 THR Chi-restraints excluded: chain D residue 918 GLU Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 1022 VAL Chi-restraints excluded: chain D residue 1024 ARG Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1100 ILE Chi-restraints excluded: chain D residue 1111 PHE Chi-restraints excluded: chain D residue 1187 VAL Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 289 ASP Chi-restraints excluded: chain E residue 317 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 186 optimal weight: 10.0000 chunk 204 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 250 optimal weight: 0.0870 chunk 266 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 402 HIS C 599 ASN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 880 HIS D 330 ASN D 385 ASN D1144 GLN ** 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 = 0.3999 r_free = 0.3999 target = 0.157049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.133844 restraints weight = 40157.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.132702 restraints weight = 65661.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.133360 restraints weight = 58972.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.132975 restraints weight = 45279.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.133493 restraints weight = 42776.569| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27614 Z= 0.123 Angle : 0.518 8.272 37694 Z= 0.282 Chirality : 0.042 0.201 4258 Planarity : 0.004 0.050 4616 Dihedral : 17.745 167.148 4519 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.52 % Allowed : 17.93 % Favored : 78.55 % 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 aren not related in a simple way. whole: 0.78 (0.15), residues: 3159 helix: 1.23 (0.15), residues: 1227 sheet: 0.44 (0.27), residues: 380 loop : 0.06 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 42 TYR 0.022 0.001 TYR C 386 PHE 0.016 0.001 PHE D 155 TRP 0.009 0.001 TRP D 23 HIS 0.006 0.001 HIS C1049 Details of bonding type rmsd covalent geometry : bond 0.00280 (27614) covalent geometry : angle 0.51842 (37694) hydrogen bonds : bond 0.03633 ( 1201) hydrogen bonds : angle 4.67236 ( 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 411 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 314 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 ASP cc_start: 0.7144 (t0) cc_final: 0.5959 (p0) REVERT: C 166 ARG cc_start: 0.7369 (ttp80) cc_final: 0.7115 (ttp80) REVERT: C 188 ARG cc_start: 0.7148 (mmm-85) cc_final: 0.6632 (ttt-90) REVERT: C 218 ARG cc_start: 0.6238 (mmt180) cc_final: 0.5791 (tpp-160) REVERT: C 345 GLN cc_start: 0.4475 (mm110) cc_final: 0.4130 (mt0) REVERT: C 419 PHE cc_start: 0.5303 (OUTLIER) cc_final: 0.5088 (t80) REVERT: C 451 ARG cc_start: 0.6049 (ttp80) cc_final: 0.5486 (mmm160) REVERT: C 517 GLU cc_start: 0.6158 (tp30) cc_final: 0.5900 (tp30) REVERT: C 751 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7498 (mm-30) REVERT: C 763 MET cc_start: 0.7824 (ptm) cc_final: 0.7545 (ptm) REVERT: C 783 ASP cc_start: 0.7681 (m-30) cc_final: 0.7277 (t0) REVERT: C 888 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.7024 (m-30) REVERT: C 944 MET cc_start: 0.8504 (mmm) cc_final: 0.7765 (mmt) REVERT: C 1078 MET cc_start: 0.6839 (mtp) cc_final: 0.6431 (mtp) REVERT: D 170 MET cc_start: 0.7587 (ttm) cc_final: 0.7299 (ttm) REVERT: D 180 GLU cc_start: 0.6114 (mt-10) cc_final: 0.5866 (mt-10) REVERT: D 196 GLU cc_start: 0.3287 (tt0) cc_final: 0.3022 (tt0) REVERT: D 210 LEU cc_start: 0.7218 (mt) cc_final: 0.6891 (mt) REVERT: D 216 PHE cc_start: 0.7028 (m-80) cc_final: 0.6753 (m-80) REVERT: D 226 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7443 (tpp) REVERT: D 268 LEU cc_start: 0.8819 (tp) cc_final: 0.8408 (tt) REVERT: D 314 LYS cc_start: 0.7786 (mtpt) cc_final: 0.7296 (mtpp) REVERT: D 1024 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7084 (ptm-80) REVERT: D 1027 VAL cc_start: 0.5487 (OUTLIER) cc_final: 0.5219 (t) REVERT: G 60 LYS cc_start: 0.6430 (ttpt) cc_final: 0.5901 (mttm) REVERT: E 183 PHE cc_start: 0.6449 (t80) cc_final: 0.6190 (t80) REVERT: E 212 MET cc_start: 0.6490 (tpt) cc_final: 0.6271 (tpp) REVERT: E 310 ARG cc_start: 0.7356 (tpt-90) cc_final: 0.6337 (tpt170) REVERT: E 314 VAL cc_start: 0.5964 (t) cc_final: 0.5699 (t) REVERT: E 343 ILE cc_start: 0.7276 (mp) cc_final: 0.7017 (mp) REVERT: E 344 ARG cc_start: 0.5691 (tmm160) cc_final: 0.5258 (ttt90) outliers start: 97 outliers final: 66 residues processed: 390 average time/residue: 0.1645 time to fit residues: 103.3059 Evaluate side-chains 344 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 273 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 57 GLU 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 26 LEU 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 139 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 419 PHE 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 801 THR Chi-restraints excluded: chain C residue 806 GLU Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 880 HIS Chi-restraints excluded: chain C residue 888 ASP Chi-restraints excluded: chain C residue 900 THR Chi-restraints excluded: chain C residue 920 HIS Chi-restraints excluded: chain C residue 1083 LEU Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 796 LEU 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 1066 ILE Chi-restraints excluded: chain D residue 1100 ILE Chi-restraints excluded: chain D residue 1111 PHE Chi-restraints excluded: chain D residue 1171 ILE Chi-restraints excluded: chain D residue 1187 VAL Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 363 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 246 optimal weight: 6.9990 chunk 243 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 277 optimal weight: 8.9990 chunk 221 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 159 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN C 880 HIS ** C 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 385 ASN D1144 GLN F 8 GLN ** E 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.151607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.128528 restraints weight = 40645.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.127613 restraints weight = 64378.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.127949 restraints weight = 60295.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.127181 restraints weight = 51822.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.127490 restraints weight = 51120.462| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 27614 Z= 0.187 Angle : 0.576 7.528 37694 Z= 0.310 Chirality : 0.044 0.233 4258 Planarity : 0.004 0.053 4616 Dihedral : 17.745 166.961 4519 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.10 % Allowed : 17.57 % Favored : 78.33 % 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 aren not related in a simple way. whole: 0.52 (0.15), residues: 3159 helix: 1.03 (0.15), residues: 1232 sheet: 0.22 (0.26), residues: 410 loop : -0.09 (0.16), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 42 TYR 0.019 0.002 TYR C 386 PHE 0.029 0.002 PHE D 894 TRP 0.010 0.001 TRP A 199 HIS 0.006 0.001 HIS D 103 Details of bonding type rmsd covalent geometry : bond 0.00445 (27614) covalent geometry : angle 0.57554 (37694) hydrogen bonds : bond 0.04017 ( 1201) hydrogen bonds : angle 4.80703 ( 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 390 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 277 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 100 ASP cc_start: 0.7233 (t0) cc_final: 0.5968 (p0) REVERT: C 113 MET cc_start: 0.5733 (tpt) cc_final: 0.5494 (tpt) REVERT: C 188 ARG cc_start: 0.6914 (mmm-85) cc_final: 0.6516 (mpt180) REVERT: C 218 ARG cc_start: 0.6222 (mmt180) cc_final: 0.5786 (tpp-160) REVERT: C 345 GLN cc_start: 0.4687 (mm110) cc_final: 0.4426 (mt0) REVERT: C 376 THR cc_start: 0.7941 (OUTLIER) cc_final: 0.7533 (p) REVERT: C 451 ARG cc_start: 0.6321 (ttp80) cc_final: 0.5607 (tpp-160) REVERT: C 517 GLU cc_start: 0.6247 (tp30) cc_final: 0.5930 (tp30) REVERT: C 751 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7583 (mm-30) REVERT: C 763 MET cc_start: 0.7795 (ptm) cc_final: 0.7515 (ptm) REVERT: C 783 ASP cc_start: 0.7504 (m-30) cc_final: 0.7255 (t0) REVERT: C 888 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.7026 (m-30) REVERT: C 944 MET cc_start: 0.8521 (mmm) cc_final: 0.7819 (mmt) REVERT: C 1078 MET cc_start: 0.7275 (mtp) cc_final: 0.6841 (mtp) REVERT: C 1132 MET cc_start: 0.6927 (mmm) cc_final: 0.6490 (tpp) REVERT: D 180 GLU cc_start: 0.5997 (mt-10) cc_final: 0.5795 (mt-10) REVERT: D 196 GLU cc_start: 0.3222 (tt0) cc_final: 0.2960 (tt0) REVERT: D 226 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7727 (ttp) REVERT: D 268 LEU cc_start: 0.8724 (tp) cc_final: 0.8292 (tt) REVERT: D 314 LYS cc_start: 0.7833 (mtpt) cc_final: 0.7336 (mtpp) REVERT: D 1024 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6993 (ptm-80) REVERT: D 1027 VAL cc_start: 0.5629 (OUTLIER) cc_final: 0.5374 (t) REVERT: G 60 LYS cc_start: 0.6464 (ttpt) cc_final: 0.6004 (mttm) REVERT: E 183 PHE cc_start: 0.6532 (t80) cc_final: 0.6226 (t80) REVERT: E 212 MET cc_start: 0.6492 (tpt) cc_final: 0.6291 (tpp) REVERT: E 310 ARG cc_start: 0.7294 (tpt-90) cc_final: 0.6229 (tpt170) REVERT: E 314 VAL cc_start: 0.5961 (t) cc_final: 0.5734 (t) REVERT: E 343 ILE cc_start: 0.7364 (mp) cc_final: 0.7074 (mp) REVERT: E 344 ARG cc_start: 0.5735 (tmm160) cc_final: 0.5266 (ttt90) outliers start: 113 outliers final: 92 residues processed: 366 average time/residue: 0.1643 time to fit residues: 97.1210 Evaluate side-chains 358 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 261 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 204 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 57 GLU 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 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 118 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 180 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 592 VAL 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 801 THR Chi-restraints excluded: chain C residue 806 GLU Chi-restraints excluded: chain C residue 859 LEU Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 880 HIS Chi-restraints excluded: chain C residue 888 ASP Chi-restraints excluded: chain C residue 900 THR Chi-restraints excluded: chain C residue 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 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 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 488 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 510 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 670 LEU Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 845 GLU 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 1101 HIS Chi-restraints excluded: chain D residue 1111 PHE Chi-restraints excluded: chain D residue 1169 VAL Chi-restraints excluded: chain D residue 1187 VAL Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 363 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 171 optimal weight: 7.9990 chunk 254 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 251 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 87 optimal weight: 0.3980 chunk 190 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 304 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 142 optimal weight: 0.2980 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 599 ASN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 880 HIS ** C 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN D1144 GLN F 43 HIS ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.151155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.127932 restraints weight = 40789.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.126778 restraints weight = 67981.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.126929 restraints weight = 64302.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.126468 restraints weight = 53146.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.126917 restraints weight = 50462.410| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27614 Z= 0.186 Angle : 0.582 7.698 37694 Z= 0.313 Chirality : 0.044 0.189 4258 Planarity : 0.004 0.055 4616 Dihedral : 17.732 165.890 4519 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.17 % Allowed : 18.11 % Favored : 77.71 % 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 aren not related in a simple way. whole: 0.40 (0.15), residues: 3159 helix: 0.97 (0.14), residues: 1227 sheet: 0.17 (0.26), residues: 391 loop : -0.18 (0.16), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 858 TYR 0.027 0.002 TYR C 386 PHE 0.018 0.002 PHE D 249 TRP 0.010 0.001 TRP A 199 HIS 0.007 0.001 HIS C1049 Details of bonding type rmsd covalent geometry : bond 0.00443 (27614) covalent geometry : angle 0.58201 (37694) hydrogen bonds : bond 0.04050 ( 1201) hydrogen bonds : angle 4.84190 ( 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 388 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 273 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6426 (mm-30) REVERT: B 100 ASP cc_start: 0.7201 (t0) cc_final: 0.5957 (p0) REVERT: C 188 ARG cc_start: 0.6818 (mmm-85) cc_final: 0.6512 (mpt180) REVERT: C 218 ARG cc_start: 0.6151 (mmt180) cc_final: 0.5726 (tpp-160) REVERT: C 376 THR cc_start: 0.7766 (OUTLIER) cc_final: 0.7495 (p) REVERT: C 396 TYR cc_start: 0.5991 (OUTLIER) cc_final: 0.5295 (p90) REVERT: C 451 ARG cc_start: 0.6502 (ttp80) cc_final: 0.5687 (tpp-160) REVERT: C 517 GLU cc_start: 0.6265 (tp30) cc_final: 0.5923 (tp30) REVERT: C 751 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7577 (mm-30) REVERT: C 763 MET cc_start: 0.7836 (ptm) cc_final: 0.7546 (ptm) REVERT: C 888 ASP cc_start: 0.7289 (OUTLIER) cc_final: 0.7015 (m-30) REVERT: C 944 MET cc_start: 0.8427 (mmm) cc_final: 0.7794 (mmt) REVERT: C 1078 MET cc_start: 0.7164 (mtp) cc_final: 0.6761 (mtp) REVERT: D 180 GLU cc_start: 0.6189 (mt-10) cc_final: 0.5968 (mt-10) REVERT: D 196 GLU cc_start: 0.3191 (tt0) cc_final: 0.2934 (tt0) REVERT: D 210 LEU cc_start: 0.6768 (mt) cc_final: 0.6527 (tp) REVERT: D 216 PHE cc_start: 0.7064 (m-80) cc_final: 0.6712 (m-80) REVERT: D 226 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7658 (ttp) REVERT: D 268 LEU cc_start: 0.8656 (tp) cc_final: 0.8184 (tt) REVERT: D 314 LYS cc_start: 0.7832 (mtpt) cc_final: 0.7323 (mtpp) REVERT: D 1024 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6954 (ptm-80) REVERT: D 1027 VAL cc_start: 0.5612 (OUTLIER) cc_final: 0.5358 (t) REVERT: G 60 LYS cc_start: 0.6466 (ttpt) cc_final: 0.5993 (mttm) REVERT: E 310 ARG cc_start: 0.7413 (tpt-90) cc_final: 0.6474 (tpt170) REVERT: E 343 ILE cc_start: 0.7478 (mp) cc_final: 0.7256 (mp) REVERT: E 344 ARG cc_start: 0.5742 (tmm160) cc_final: 0.5185 (ttt90) outliers start: 115 outliers final: 94 residues processed: 364 average time/residue: 0.1675 time to fit residues: 97.0988 Evaluate side-chains 360 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 259 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 197 ASP Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 208 GLU 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 57 GLU Chi-restraints excluded: chain B residue 72 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 94 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 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 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 801 THR Chi-restraints excluded: chain C residue 806 GLU Chi-restraints excluded: chain C residue 859 LEU Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 880 HIS Chi-restraints excluded: chain C residue 888 ASP Chi-restraints excluded: chain C residue 900 THR Chi-restraints excluded: chain C residue 920 HIS Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 1083 LEU Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 46 LEU 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 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 488 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 570 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 796 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 1136 SER Chi-restraints excluded: chain D residue 1169 VAL Chi-restraints excluded: chain D residue 1187 VAL Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 363 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 273 optimal weight: 9.9990 chunk 270 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 chunk 187 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 236 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 880 HIS ** C 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1144 GLN F 8 GLN F 43 HIS E 285 GLN ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.151239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.128295 restraints weight = 40900.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.127314 restraints weight = 65496.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.127447 restraints weight = 61300.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.126953 restraints weight = 52990.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.127355 restraints weight = 52446.175| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27614 Z= 0.174 Angle : 0.579 7.960 37694 Z= 0.312 Chirality : 0.044 0.215 4258 Planarity : 0.004 0.056 4616 Dihedral : 17.689 164.997 4519 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.99 % Allowed : 18.58 % Favored : 77.42 % 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 aren not related in a simple way. whole: 0.38 (0.15), residues: 3159 helix: 0.98 (0.15), residues: 1227 sheet: 0.08 (0.26), residues: 401 loop : -0.20 (0.16), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 377 TYR 0.032 0.002 TYR E 102 PHE 0.016 0.002 PHE G 47 TRP 0.010 0.001 TRP A 199 HIS 0.008 0.001 HIS C1049 Details of bonding type rmsd covalent geometry : bond 0.00414 (27614) covalent geometry : angle 0.57923 (37694) hydrogen bonds : bond 0.03998 ( 1201) hydrogen bonds : angle 4.84104 ( 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 384 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 274 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 208 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6392 (mm-30) REVERT: B 100 ASP cc_start: 0.7192 (t0) cc_final: 0.6034 (p0) REVERT: C 188 ARG cc_start: 0.6818 (mmm-85) cc_final: 0.6550 (mpt180) REVERT: C 218 ARG cc_start: 0.5974 (mmt180) cc_final: 0.5522 (tpp-160) REVERT: C 376 THR cc_start: 0.7782 (OUTLIER) cc_final: 0.7499 (p) REVERT: C 396 TYR cc_start: 0.5441 (OUTLIER) cc_final: 0.4853 (p90) REVERT: C 451 ARG cc_start: 0.6265 (ttp80) cc_final: 0.5435 (tpp-160) REVERT: C 517 GLU cc_start: 0.6167 (tp30) cc_final: 0.5849 (tp30) REVERT: C 751 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7628 (mm-30) REVERT: C 763 MET cc_start: 0.7818 (ptm) cc_final: 0.7551 (ptm) REVERT: C 888 ASP cc_start: 0.7288 (OUTLIER) cc_final: 0.7003 (m-30) REVERT: C 944 MET cc_start: 0.8386 (mmm) cc_final: 0.7803 (mmt) REVERT: C 1078 MET cc_start: 0.7145 (mtp) cc_final: 0.6748 (mtp) REVERT: D 180 GLU cc_start: 0.6179 (mt-10) cc_final: 0.5969 (mt-10) REVERT: D 196 GLU cc_start: 0.3073 (tt0) cc_final: 0.2815 (tt0) REVERT: D 216 PHE cc_start: 0.7058 (m-80) cc_final: 0.6710 (m-80) REVERT: D 226 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7707 (ttp) REVERT: D 268 LEU cc_start: 0.8633 (tp) cc_final: 0.8157 (tt) REVERT: D 1024 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6939 (ptm-80) REVERT: D 1027 VAL cc_start: 0.5639 (OUTLIER) cc_final: 0.5381 (t) REVERT: G 33 GLN cc_start: 0.7498 (mt0) cc_final: 0.5142 (tm-30) REVERT: G 60 LYS cc_start: 0.6448 (ttpt) cc_final: 0.6049 (mttm) REVERT: E 112 LEU cc_start: 0.6247 (OUTLIER) cc_final: 0.5892 (mm) REVERT: E 183 PHE cc_start: 0.6567 (t80) cc_final: 0.6224 (t80) REVERT: E 310 ARG cc_start: 0.7427 (tpt-90) cc_final: 0.6476 (tpt170) REVERT: E 344 ARG cc_start: 0.5749 (tmm160) cc_final: 0.5163 (ttt90) outliers start: 110 outliers final: 88 residues processed: 360 average time/residue: 0.1732 time to fit residues: 99.9447 Evaluate side-chains 355 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 259 time to evaluate : 1.174 ------------------------------------------------------------------------------- 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 204 ILE Chi-restraints excluded: chain A residue 208 GLU 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 57 GLU Chi-restraints excluded: chain B residue 72 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 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 32 ILE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 552 ASP Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 599 ASN Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 801 THR Chi-restraints excluded: chain C residue 806 GLU Chi-restraints excluded: chain C residue 859 LEU 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 1107 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 136 VAL 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 488 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 570 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 796 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 1136 SER Chi-restraints excluded: chain D residue 1169 VAL Chi-restraints excluded: chain D residue 1187 VAL Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 354 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 253 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 219 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 308 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 319 optimal weight: 20.0000 chunk 92 optimal weight: 1.9990 chunk 216 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN C 575 GLN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1144 GLN G 20 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.154308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.131313 restraints weight = 40296.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.130368 restraints weight = 65986.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.130570 restraints weight = 59828.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.129991 restraints weight = 51195.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.130614 restraints weight = 45825.971| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27614 Z= 0.124 Angle : 0.537 7.720 37694 Z= 0.290 Chirality : 0.042 0.176 4258 Planarity : 0.004 0.049 4616 Dihedral : 17.541 163.537 4519 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.94 % Allowed : 19.93 % Favored : 77.13 % 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 aren not related in a simple way. whole: 0.64 (0.15), residues: 3159 helix: 1.25 (0.15), residues: 1219 sheet: 0.17 (0.27), residues: 373 loop : -0.09 (0.16), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 377 TYR 0.032 0.001 TYR E 102 PHE 0.013 0.001 PHE D 894 TRP 0.008 0.001 TRP A 199 HIS 0.022 0.001 HIS D 318 Details of bonding type rmsd covalent geometry : bond 0.00283 (27614) covalent geometry : angle 0.53679 (37694) hydrogen bonds : bond 0.03547 ( 1201) hydrogen bonds : angle 4.65636 ( 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 369 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 288 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6045 (mm-30) REVERT: B 100 ASP cc_start: 0.7304 (t0) cc_final: 0.6006 (p0) REVERT: C 188 ARG cc_start: 0.6797 (mmm-85) cc_final: 0.6406 (mpt180) REVERT: C 218 ARG cc_start: 0.5945 (mmt180) cc_final: 0.5518 (tpp-160) REVERT: C 376 THR cc_start: 0.7949 (OUTLIER) cc_final: 0.7640 (p) REVERT: C 396 TYR cc_start: 0.5806 (OUTLIER) cc_final: 0.4637 (p90) REVERT: C 451 ARG cc_start: 0.6374 (ttp80) cc_final: 0.5574 (tpp-160) REVERT: C 517 GLU cc_start: 0.6110 (tp30) cc_final: 0.5817 (tp30) REVERT: C 751 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7579 (mm-30) REVERT: C 763 MET cc_start: 0.7848 (ptm) cc_final: 0.7596 (ptm) REVERT: C 776 MET cc_start: 0.7994 (ttm) cc_final: 0.7719 (ttm) REVERT: C 944 MET cc_start: 0.8451 (mmm) cc_final: 0.7928 (mmt) REVERT: C 1078 MET cc_start: 0.6864 (mtp) cc_final: 0.6442 (mtp) REVERT: D 105 TRP cc_start: 0.8602 (OUTLIER) cc_final: 0.7792 (m-10) REVERT: D 196 GLU cc_start: 0.3026 (tt0) cc_final: 0.2746 (tt0) REVERT: D 216 PHE cc_start: 0.7006 (m-80) cc_final: 0.6594 (m-80) REVERT: D 226 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7496 (tpp) REVERT: D 268 LEU cc_start: 0.8566 (tp) cc_final: 0.8061 (tt) REVERT: D 691 PHE cc_start: 0.3226 (t80) cc_final: 0.2921 (t80) REVERT: D 1024 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6954 (ptm-80) REVERT: G 33 GLN cc_start: 0.7324 (mt0) cc_final: 0.5152 (tm-30) REVERT: G 60 LYS cc_start: 0.6359 (ttpt) cc_final: 0.5964 (mttm) REVERT: E 112 LEU cc_start: 0.5934 (OUTLIER) cc_final: 0.5582 (mm) REVERT: E 128 ASP cc_start: 0.3023 (m-30) cc_final: 0.2746 (t0) REVERT: E 183 PHE cc_start: 0.6664 (t80) cc_final: 0.6334 (t80) REVERT: E 310 ARG cc_start: 0.7422 (tpt-90) cc_final: 0.6468 (tpt170) REVERT: E 342 ARG cc_start: 0.2560 (mtt180) cc_final: 0.1928 (mpt-90) REVERT: E 344 ARG cc_start: 0.5559 (tmm160) cc_final: 0.5301 (ttt90) outliers start: 81 outliers final: 64 residues processed: 350 average time/residue: 0.1687 time to fit residues: 93.8227 Evaluate side-chains 341 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 270 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 64 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 185 VAL 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 180 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 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 806 GLU Chi-restraints excluded: chain C residue 859 LEU 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 1083 LEU Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 796 LEU 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 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 1136 SER Chi-restraints excluded: chain D residue 1187 VAL Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 354 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 301 optimal weight: 0.8980 chunk 223 optimal weight: 9.9990 chunk 176 optimal weight: 6.9990 chunk 152 optimal weight: 3.9990 chunk 182 optimal weight: 0.2980 chunk 262 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 143 optimal weight: 0.0010 chunk 19 optimal weight: 10.0000 chunk 299 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 overall best weight: 1.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN C 575 GLN C 599 ASN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 880 HIS ** C 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1101 HIS G 20 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.153999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.131048 restraints weight = 40402.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.130018 restraints weight = 69598.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.130196 restraints weight = 62932.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.129618 restraints weight = 52565.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.130036 restraints weight = 44049.359| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27614 Z= 0.131 Angle : 0.543 8.611 37694 Z= 0.293 Chirality : 0.042 0.217 4258 Planarity : 0.004 0.047 4616 Dihedral : 17.460 164.197 4517 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.87 % Allowed : 19.93 % 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 aren not related in a simple way. whole: 0.66 (0.15), residues: 3159 helix: 1.29 (0.15), residues: 1218 sheet: 0.26 (0.27), residues: 382 loop : -0.11 (0.16), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 377 TYR 0.023 0.001 TYR C 386 PHE 0.013 0.001 PHE C 112 TRP 0.010 0.001 TRP A 199 HIS 0.008 0.001 HIS D 318 Details of bonding type rmsd covalent geometry : bond 0.00305 (27614) covalent geometry : angle 0.54346 (37694) hydrogen bonds : bond 0.03571 ( 1201) hydrogen bonds : angle 4.62282 ( 3309) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3814.46 seconds wall clock time: 67 minutes 6.86 seconds (4026.86 seconds total)