Starting phenix.real_space_refine on Sun May 25 13:10:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x6f_38087/05_2025/8x6f_38087.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x6f_38087/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8x6f_38087/05_2025/8x6f_38087.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x6f_38087/05_2025/8x6f_38087.map" model { file = "/net/cci-nas-00/data/ceres_data/8x6f_38087/05_2025/8x6f_38087.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x6f_38087/05_2025/8x6f_38087.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 13.42, per 1000 atoms: 0.50 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: 6.24 Conformation dependent library (CDL) restraints added in 3.0 seconds 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5904 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 45 sheets defined 44.2% alpha, 17.6% beta 35 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 8.72 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: 12.34 Time building geometry restraints manager: 7.36 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.060 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 61.840 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.090 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.400 ------------------------------------------------------------------------------- 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 : 9.63 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.001 TRP D 105 HIS 0.005 0.001 HIS C1049 PHE 0.022 0.001 PHE G 47 TYR 0.033 0.001 TYR G 58 ARG 0.012 0.001 ARG C 951 Details of bonding type rmsd hydrogen bonds : bond 0.14039 ( 1201) hydrogen bonds : angle 6.32339 ( 3309) covalent geometry : bond 0.00459 (27614) covalent geometry : angle 0.68968 (37694) *********************** 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 : 2.678 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: 0.4696 time to fit residues: 460.0368 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 : 2.876 ------------------------------------------------------------------------------- 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 272 optimal weight: 0.9980 chunk 244 optimal weight: 10.0000 chunk 135 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 165 optimal weight: 0.0050 chunk 130 optimal weight: 2.9990 chunk 253 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 chunk 293 optimal weight: 10.0000 overall best weight: 2.2000 ------------------------------------------------------------------------------- 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 C 880 HIS D 283 ASN D 289 GLN F 43 HIS G 20 ASN ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.159513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.136063 restraints weight = 39993.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.135495 restraints weight = 57330.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.136354 restraints weight = 52909.782| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 27614 Z= 0.157 Angle : 0.571 10.225 37694 Z= 0.309 Chirality : 0.043 0.230 4258 Planarity : 0.004 0.044 4616 Dihedral : 17.861 168.925 4529 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.12 % Allowed : 14.48 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.15), residues: 3159 helix: 1.34 (0.15), residues: 1231 sheet: 0.43 (0.26), residues: 390 loop : 0.36 (0.16), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 39 HIS 0.008 0.001 HIS C 677 PHE 0.028 0.002 PHE E 183 TYR 0.016 0.002 TYR C1098 ARG 0.006 0.001 ARG C 951 Details of bonding type rmsd hydrogen bonds : bond 0.04301 ( 1201) hydrogen bonds : angle 5.08569 ( 3309) covalent geometry : bond 0.00363 (27614) covalent geometry : angle 0.57075 (37694) *********************** 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 499 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 413 time to evaluate : 2.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ASP cc_start: 0.6442 (p0) cc_final: 0.6130 (p0) REVERT: B 100 ASP cc_start: 0.6410 (t0) cc_final: 0.5886 (p0) REVERT: C 384 MET cc_start: 0.7122 (mmt) cc_final: 0.6878 (mmm) REVERT: C 458 LYS cc_start: 0.7821 (tppt) cc_final: 0.7476 (tttt) REVERT: C 506 HIS cc_start: 0.7527 (t-90) cc_final: 0.7097 (t-90) REVERT: C 517 GLU cc_start: 0.6428 (tp30) cc_final: 0.6126 (tp30) REVERT: C 642 MET cc_start: 0.7857 (ttm) cc_final: 0.7547 (ttp) REVERT: C 751 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7595 (mm-30) REVERT: C 763 MET cc_start: 0.7847 (ptm) cc_final: 0.7584 (ptm) REVERT: C 783 ASP cc_start: 0.7418 (m-30) cc_final: 0.7138 (t0) REVERT: C 925 MET cc_start: 0.7990 (mtp) cc_final: 0.7502 (mtm) REVERT: C 944 MET cc_start: 0.8519 (mmm) cc_final: 0.7936 (mmt) REVERT: C 967 ASN cc_start: 0.8450 (p0) cc_final: 0.7791 (p0) REVERT: C 1078 MET cc_start: 0.7042 (mtp) cc_final: 0.6752 (mtm) REVERT: D 216 PHE cc_start: 0.6959 (OUTLIER) cc_final: 0.6514 (t80) REVERT: D 226 MET cc_start: 0.7791 (tpp) cc_final: 0.7288 (tpp) REVERT: D 314 LYS cc_start: 0.7816 (mtpt) cc_final: 0.7268 (mtpp) REVERT: D 478 ASN cc_start: 0.8195 (m110) cc_final: 0.7962 (m110) REVERT: F 26 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.8051 (tpt170) REVERT: G 30 THR cc_start: 0.7349 (OUTLIER) cc_final: 0.6704 (m) REVERT: E 155 MET cc_start: 0.6646 (tpp) cc_final: 0.6269 (tpt) REVERT: E 310 ARG cc_start: 0.7125 (tpt-90) cc_final: 0.6362 (tpt170) REVERT: E 344 ARG cc_start: 0.5901 (tmm160) cc_final: 0.5402 (ttt90) outliers start: 86 outliers final: 50 residues processed: 467 average time/residue: 0.4152 time to fit residues: 298.6378 Evaluate side-chains 363 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 310 time to evaluate : 2.690 ------------------------------------------------------------------------------- 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 101 VAL 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 815 VAL 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 137 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 606 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 778 LEU Chi-restraints excluded: chain D residue 811 VAL 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 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 26 ARG Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain E residue 205 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 203 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 8 optimal weight: 0.0050 chunk 167 optimal weight: 10.0000 chunk 202 optimal weight: 5.9990 chunk 257 optimal weight: 0.0670 chunk 198 optimal weight: 9.9990 chunk 239 optimal weight: 5.9990 chunk 255 optimal weight: 7.9990 chunk 299 optimal weight: 2.9990 chunk 286 optimal weight: 10.0000 overall best weight: 3.0138 ------------------------------------------------------------------------------- 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 880 HIS D 201 GLN D 289 GLN D 330 ASN D1144 GLN F 43 HIS G 55 HIS ** E 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 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 = 0.3944 r_free = 0.3944 target = 0.152748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.124133 restraints weight = 39910.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.123744 restraints weight = 47654.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.124621 restraints weight = 43016.427| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27614 Z= 0.179 Angle : 0.578 9.809 37694 Z= 0.313 Chirality : 0.044 0.234 4258 Planarity : 0.004 0.059 4616 Dihedral : 17.837 168.397 4523 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.67 % Allowed : 16.19 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.15), residues: 3159 helix: 1.22 (0.14), residues: 1225 sheet: 0.41 (0.25), residues: 421 loop : 0.20 (0.16), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 23 HIS 0.010 0.001 HIS C 880 PHE 0.019 0.002 PHE G 47 TYR 0.021 0.002 TYR C 37 ARG 0.007 0.001 ARG D 772 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 1201) hydrogen bonds : angle 4.97057 ( 3309) covalent geometry : bond 0.00420 (27614) covalent geometry : angle 0.57756 (37694) *********************** 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 435 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 334 time to evaluate : 2.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 ASP cc_start: 0.6873 (t0) cc_final: 0.5937 (p0) REVERT: C 188 ARG cc_start: 0.6866 (mmm-85) cc_final: 0.6010 (ptm160) REVERT: C 218 ARG cc_start: 0.5743 (mmt180) cc_final: 0.5105 (tpp-160) REVERT: C 384 MET cc_start: 0.7096 (mmt) cc_final: 0.6468 (tpp) REVERT: C 458 LYS cc_start: 0.7802 (tppt) cc_final: 0.7324 (tttt) REVERT: C 478 GLU cc_start: 0.6971 (tt0) cc_final: 0.6739 (tt0) REVERT: C 506 HIS cc_start: 0.7841 (t-90) cc_final: 0.7586 (t70) REVERT: C 602 MET cc_start: 0.6910 (OUTLIER) cc_final: 0.6101 (tpt) REVERT: C 661 MET cc_start: 0.7602 (tpp) cc_final: 0.7147 (tpt) REVERT: C 751 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7586 (mm-30) REVERT: C 776 MET cc_start: 0.8346 (ttm) cc_final: 0.7837 (mtp) REVERT: C 783 ASP cc_start: 0.7514 (m-30) cc_final: 0.7184 (t0) REVERT: C 888 ASP cc_start: 0.7046 (OUTLIER) cc_final: 0.6768 (m-30) REVERT: C 944 MET cc_start: 0.8506 (mmm) cc_final: 0.7813 (mmt) REVERT: C 1036 TYR cc_start: 0.8492 (t80) cc_final: 0.8216 (t80) REVERT: C 1078 MET cc_start: 0.7134 (mtp) cc_final: 0.6846 (mtm) REVERT: C 1141 ASP cc_start: 0.7656 (t0) cc_final: 0.7399 (t0) REVERT: D 297 ASP cc_start: 0.6968 (t0) cc_final: 0.6741 (t0) REVERT: D 314 LYS cc_start: 0.7913 (mtpt) cc_final: 0.7469 (mtpp) REVERT: D 696 ILE cc_start: 0.4823 (pt) cc_final: 0.4613 (pt) REVERT: D 1024 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7392 (ptm-80) REVERT: D 1027 VAL cc_start: 0.5904 (OUTLIER) cc_final: 0.5618 (t) REVERT: D 1048 GLU cc_start: 0.7103 (pt0) cc_final: 0.6850 (pt0) REVERT: G 55 HIS cc_start: 0.6057 (OUTLIER) cc_final: 0.5838 (t70) REVERT: E 155 MET cc_start: 0.6852 (tpp) cc_final: 0.6551 (tpt) REVERT: E 183 PHE cc_start: 0.6519 (t80) cc_final: 0.6288 (t80) REVERT: E 310 ARG cc_start: 0.7316 (tpt-90) cc_final: 0.6305 (tpt170) REVERT: E 344 ARG cc_start: 0.5843 (tmm160) cc_final: 0.5115 (ttt90) outliers start: 101 outliers final: 60 residues processed: 407 average time/residue: 0.4032 time to fit residues: 260.4909 Evaluate side-chains 353 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 288 time to evaluate : 2.695 ------------------------------------------------------------------------------- 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 127 ILE Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 138 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 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 815 VAL 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 998 ASP 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 121 SER Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 216 PHE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 873 THR Chi-restraints excluded: chain D residue 876 ILE Chi-restraints excluded: chain D residue 918 GLU Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 1024 ARG Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1100 ILE Chi-restraints excluded: chain D residue 1111 PHE Chi-restraints excluded: chain D residue 1169 VAL Chi-restraints excluded: chain F residue 9 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 276 optimal weight: 0.5980 chunk 68 optimal weight: 20.0000 chunk 312 optimal weight: 0.0770 chunk 14 optimal weight: 10.0000 chunk 198 optimal weight: 8.9990 chunk 201 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 290 optimal weight: 10.0000 chunk 175 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 overall best weight: 3.3344 ------------------------------------------------------------------------------- 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 599 ASN C 880 HIS D1144 GLN F 8 GLN G 22 GLN G 55 HIS ** E 165 ASN ** 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 = 0.3927 r_free = 0.3927 target = 0.151410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.123029 restraints weight = 40278.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.122824 restraints weight = 44597.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.123515 restraints weight = 41619.491| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 27614 Z= 0.186 Angle : 0.580 8.413 37694 Z= 0.312 Chirality : 0.044 0.314 4258 Planarity : 0.005 0.051 4616 Dihedral : 17.841 168.416 4519 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.96 % Allowed : 16.95 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.15), residues: 3159 helix: 1.12 (0.14), residues: 1224 sheet: 0.41 (0.26), residues: 397 loop : 0.06 (0.16), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 199 HIS 0.011 0.001 HIS G 55 PHE 0.019 0.002 PHE G 47 TYR 0.021 0.002 TYR C 37 ARG 0.009 0.001 ARG D 89 Details of bonding type rmsd hydrogen bonds : bond 0.04174 ( 1201) hydrogen bonds : angle 4.95322 ( 3309) covalent geometry : bond 0.00444 (27614) covalent geometry : angle 0.58034 (37694) *********************** 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 412 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 303 time to evaluate : 2.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 100 ASP cc_start: 0.6965 (t0) cc_final: 0.5876 (p0) REVERT: C 41 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7512 (tt) REVERT: C 384 MET cc_start: 0.7196 (mmt) cc_final: 0.6611 (tpp) REVERT: C 458 LYS cc_start: 0.7782 (tppt) cc_final: 0.7289 (tttt) REVERT: C 478 GLU cc_start: 0.6930 (tt0) cc_final: 0.6720 (tt0) REVERT: C 517 GLU cc_start: 0.6318 (tp30) cc_final: 0.6109 (tp30) REVERT: C 751 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7517 (mm-30) REVERT: C 763 MET cc_start: 0.7952 (ptm) cc_final: 0.7641 (ptm) REVERT: C 783 ASP cc_start: 0.7458 (m-30) cc_final: 0.7148 (t0) REVERT: C 806 GLU cc_start: 0.5505 (pt0) cc_final: 0.5224 (pt0) REVERT: C 888 ASP cc_start: 0.7041 (OUTLIER) cc_final: 0.6750 (m-30) REVERT: C 944 MET cc_start: 0.8570 (mmm) cc_final: 0.7863 (mmt) REVERT: C 1036 TYR cc_start: 0.8487 (t80) cc_final: 0.8266 (t80) REVERT: C 1078 MET cc_start: 0.7262 (mtp) cc_final: 0.6849 (mtt) REVERT: D 216 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.7006 (m-80) REVERT: D 314 LYS cc_start: 0.7937 (mtpt) cc_final: 0.7385 (mtpp) REVERT: D 696 ILE cc_start: 0.4899 (pt) cc_final: 0.4678 (pt) REVERT: D 1024 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7324 (ptm-80) REVERT: D 1027 VAL cc_start: 0.5916 (OUTLIER) cc_final: 0.5628 (t) REVERT: D 1048 GLU cc_start: 0.7217 (pt0) cc_final: 0.6955 (pt0) REVERT: E 155 MET cc_start: 0.6965 (tpp) cc_final: 0.6618 (tpt) REVERT: E 183 PHE cc_start: 0.6659 (t80) cc_final: 0.6412 (t80) REVERT: E 212 MET cc_start: 0.6738 (tpt) cc_final: 0.6485 (tpp) REVERT: E 310 ARG cc_start: 0.7405 (tpt-90) cc_final: 0.6285 (tpt170) REVERT: E 342 ARG cc_start: 0.2516 (mtt180) cc_final: 0.0859 (mpt-90) REVERT: E 344 ARG cc_start: 0.5775 (tmm160) cc_final: 0.5035 (ttt90) outliers start: 109 outliers final: 82 residues processed: 388 average time/residue: 0.3888 time to fit residues: 239.7592 Evaluate side-chains 362 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 275 time to evaluate : 3.248 ------------------------------------------------------------------------------- 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 161 ILE Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 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 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 689 ILE Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 815 VAL 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 998 ASP Chi-restraints excluded: chain C residue 1083 LEU Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 216 PHE Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 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 768 THR Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 845 GLU Chi-restraints excluded: chain D residue 873 THR Chi-restraints excluded: chain D residue 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 1092 LEU Chi-restraints excluded: chain D residue 1100 ILE Chi-restraints excluded: chain D residue 1111 PHE Chi-restraints excluded: chain D residue 1169 VAL Chi-restraints excluded: chain D residue 1187 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain E residue 354 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 142 optimal weight: 10.0000 chunk 192 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 chunk 322 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 306 optimal weight: 10.0000 chunk 320 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 44 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 385 ASN ** D 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1144 GLN F 8 GLN F 43 HIS ** E 165 ASN ** 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 = 0.3870 r_free = 0.3870 target = 0.146385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.118809 restraints weight = 40890.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.118638 restraints weight = 48899.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.119414 restraints weight = 42745.642| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 27614 Z= 0.311 Angle : 0.734 8.857 37694 Z= 0.390 Chirality : 0.049 0.205 4258 Planarity : 0.006 0.080 4616 Dihedral : 18.048 163.777 4519 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 5.34 % Allowed : 17.42 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.14), residues: 3159 helix: 0.38 (0.14), residues: 1235 sheet: 0.05 (0.25), residues: 409 loop : -0.46 (0.16), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C1001 HIS 0.037 0.003 HIS C 880 PHE 0.027 0.003 PHE G 47 TYR 0.026 0.003 TYR C1098 ARG 0.008 0.001 ARG D 89 Details of bonding type rmsd hydrogen bonds : bond 0.05191 ( 1201) hydrogen bonds : angle 5.36628 ( 3309) covalent geometry : bond 0.00746 (27614) covalent geometry : angle 0.73447 (37694) *********************** 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 452 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 305 time to evaluate : 2.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.5362 (OUTLIER) cc_final: 0.5138 (tp) REVERT: B 100 ASP cc_start: 0.7181 (t0) cc_final: 0.6056 (p0) REVERT: B 175 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7722 (mtp180) REVERT: C 188 ARG cc_start: 0.7094 (mmm-85) cc_final: 0.6311 (ptm160) REVERT: C 376 THR cc_start: 0.7776 (OUTLIER) cc_final: 0.7424 (p) REVERT: C 384 MET cc_start: 0.7391 (mmt) cc_final: 0.7009 (tpp) REVERT: C 458 LYS cc_start: 0.7984 (tppt) cc_final: 0.7339 (tttt) REVERT: C 517 GLU cc_start: 0.6247 (tp30) cc_final: 0.6021 (tp30) REVERT: C 751 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7559 (mm-30) REVERT: C 888 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.7043 (m-30) REVERT: C 944 MET cc_start: 0.8588 (mmm) cc_final: 0.8232 (mmp) REVERT: C 1038 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7989 (mt) REVERT: C 1078 MET cc_start: 0.7416 (mtp) cc_final: 0.7019 (mtm) REVERT: D 226 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7654 (ttp) REVERT: D 297 ASP cc_start: 0.7286 (t0) cc_final: 0.6801 (t0) REVERT: D 352 MET cc_start: 0.8117 (tpp) cc_final: 0.7663 (ttt) REVERT: D 739 ARG cc_start: 0.5223 (OUTLIER) cc_final: 0.4969 (ttt180) REVERT: D 1024 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7373 (ptm-80) REVERT: D 1048 GLU cc_start: 0.7424 (pt0) cc_final: 0.7107 (pt0) REVERT: G 20 ASN cc_start: 0.6869 (m110) cc_final: 0.5978 (p0) REVERT: G 33 GLN cc_start: 0.7381 (mt0) cc_final: 0.5176 (tm-30) REVERT: G 60 LYS cc_start: 0.6532 (ttpt) cc_final: 0.6026 (mttm) REVERT: E 155 MET cc_start: 0.7133 (tpp) cc_final: 0.6709 (tpt) REVERT: E 212 MET cc_start: 0.6820 (tpt) cc_final: 0.6568 (tpp) REVERT: E 249 LYS cc_start: 0.7960 (tptt) cc_final: 0.7641 (tppt) REVERT: E 310 ARG cc_start: 0.7542 (tpt-90) cc_final: 0.6358 (tpt170) REVERT: E 342 ARG cc_start: 0.2729 (mtt180) cc_final: 0.0706 (mpt-90) REVERT: E 344 ARG cc_start: 0.5974 (tmm160) cc_final: 0.5543 (ttp80) outliers start: 147 outliers final: 101 residues processed: 427 average time/residue: 0.3845 time to fit residues: 257.4158 Evaluate side-chains 372 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 263 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 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 138 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 175 ARG 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 103 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 552 ASP Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 599 ASN Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 801 THR Chi-restraints excluded: chain C residue 812 ILE 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 970 GLN Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain C residue 1032 VAL Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1083 LEU Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 90 GLU 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 138 ASP Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 431 VAL 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 739 ARG Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 845 GLU Chi-restraints excluded: chain D residue 873 THR Chi-restraints excluded: chain D residue 876 ILE Chi-restraints excluded: chain D residue 918 GLU Chi-restraints excluded: chain D residue 954 THR 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 1092 LEU Chi-restraints excluded: chain D residue 1100 ILE Chi-restraints excluded: chain D residue 1101 HIS Chi-restraints excluded: chain D residue 1111 PHE Chi-restraints excluded: chain D residue 1149 VAL Chi-restraints excluded: chain D residue 1187 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain E residue 354 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 69 optimal weight: 9.9990 chunk 280 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 147 optimal weight: 6.9990 chunk 88 optimal weight: 0.0770 chunk 5 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 269 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- 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 725 GLN C 880 HIS D1144 GLN ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.152750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.129376 restraints weight = 40568.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.129070 restraints weight = 66965.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.129515 restraints weight = 58857.037| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27614 Z= 0.130 Angle : 0.548 8.398 37694 Z= 0.297 Chirality : 0.042 0.170 4258 Planarity : 0.004 0.049 4616 Dihedral : 17.858 165.562 4519 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.05 % Allowed : 19.56 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.15), residues: 3159 helix: 1.03 (0.15), residues: 1221 sheet: 0.29 (0.26), residues: 388 loop : -0.20 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 199 HIS 0.007 0.001 HIS C1049 PHE 0.014 0.001 PHE D 155 TYR 0.020 0.001 TYR C 37 ARG 0.010 0.000 ARG D 377 Details of bonding type rmsd hydrogen bonds : bond 0.03853 ( 1201) hydrogen bonds : angle 4.82221 ( 3309) covalent geometry : bond 0.00295 (27614) covalent geometry : angle 0.54788 (37694) *********************** 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 382 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 298 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7305 (ptp-110) cc_final: 0.7092 (ptp-110) REVERT: B 100 ASP cc_start: 0.7258 (t0) cc_final: 0.5969 (p0) REVERT: C 376 THR cc_start: 0.7723 (OUTLIER) cc_final: 0.7454 (p) REVERT: C 384 MET cc_start: 0.6920 (mmt) cc_final: 0.6430 (tpp) REVERT: C 396 TYR cc_start: 0.5859 (OUTLIER) cc_final: 0.4861 (p90) REVERT: C 446 GLN cc_start: 0.5870 (mm110) cc_final: 0.5633 (mm110) REVERT: C 517 GLU cc_start: 0.5993 (tp30) cc_final: 0.5758 (tp30) REVERT: C 751 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7325 (mm-30) REVERT: C 944 MET cc_start: 0.8352 (mmm) cc_final: 0.7726 (mmt) REVERT: C 1078 MET cc_start: 0.7131 (mtp) cc_final: 0.6696 (mtp) REVERT: D 180 GLU cc_start: 0.5885 (mt-10) cc_final: 0.5636 (mt-10) REVERT: D 226 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7593 (tpp) REVERT: D 297 ASP cc_start: 0.6825 (t0) cc_final: 0.6596 (t0) REVERT: D 1024 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.7125 (ptm-80) REVERT: D 1027 VAL cc_start: 0.5464 (OUTLIER) cc_final: 0.5172 (t) REVERT: D 1048 GLU cc_start: 0.7166 (pt0) cc_final: 0.6895 (pt0) REVERT: G 33 GLN cc_start: 0.7218 (mt0) cc_final: 0.5070 (tm-30) REVERT: G 60 LYS cc_start: 0.6503 (ttpt) cc_final: 0.6062 (mttm) REVERT: E 155 MET cc_start: 0.6970 (tpp) cc_final: 0.6705 (tpt) REVERT: E 183 PHE cc_start: 0.6535 (t80) cc_final: 0.6247 (t80) REVERT: E 344 ARG cc_start: 0.5762 (tmm160) cc_final: 0.5256 (ttt90) outliers start: 84 outliers final: 56 residues processed: 366 average time/residue: 0.3733 time to fit residues: 221.4334 Evaluate side-chains 327 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 266 time to evaluate : 2.744 ------------------------------------------------------------------------------- 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 204 ILE Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 185 VAL 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 248 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 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 801 THR Chi-restraints excluded: chain C residue 859 LEU 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 1131 LEU Chi-restraints excluded: chain D residue 10 MET 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 565 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 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 1071 VAL Chi-restraints excluded: chain D residue 1100 ILE Chi-restraints excluded: chain D residue 1111 PHE Chi-restraints excluded: chain D residue 1132 LEU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 44 optimal weight: 10.0000 chunk 276 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 238 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 chunk 313 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 221 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 880 HIS C 906 ASN D1144 GLN F 43 HIS ** E 165 ASN ** 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 = 0.3919 r_free = 0.3919 target = 0.149975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.126639 restraints weight = 40872.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.125345 restraints weight = 69805.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.125899 restraints weight = 64440.015| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 27614 Z= 0.205 Angle : 0.612 7.326 37694 Z= 0.328 Chirality : 0.044 0.179 4258 Planarity : 0.005 0.063 4616 Dihedral : 17.806 165.639 4519 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.21 % Allowed : 19.09 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.15), residues: 3159 helix: 0.83 (0.14), residues: 1224 sheet: 0.07 (0.25), residues: 421 loop : -0.35 (0.16), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 199 HIS 0.007 0.001 HIS C1049 PHE 0.018 0.002 PHE G 47 TYR 0.019 0.002 TYR C 37 ARG 0.006 0.001 ARG D 377 Details of bonding type rmsd hydrogen bonds : bond 0.04336 ( 1201) hydrogen bonds : angle 4.97504 ( 3309) covalent geometry : bond 0.00489 (27614) covalent geometry : angle 0.61171 (37694) *********************** 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 398 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 282 time to evaluate : 2.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6498 (mm-30) REVERT: B 100 ASP cc_start: 0.7284 (t0) cc_final: 0.6122 (p0) REVERT: C 376 THR cc_start: 0.7775 (OUTLIER) cc_final: 0.7502 (p) REVERT: C 384 MET cc_start: 0.6972 (mmt) cc_final: 0.6516 (tpp) REVERT: C 396 TYR cc_start: 0.5508 (OUTLIER) cc_final: 0.4961 (p90) REVERT: C 458 LYS cc_start: 0.7960 (tppt) cc_final: 0.7470 (tttt) REVERT: C 517 GLU cc_start: 0.6087 (tp30) cc_final: 0.5789 (tp30) REVERT: C 751 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7548 (mm-30) REVERT: C 925 MET cc_start: 0.8181 (mmm) cc_final: 0.7737 (mmm) REVERT: C 944 MET cc_start: 0.8371 (mmm) cc_final: 0.7630 (mmt) REVERT: C 1073 GLN cc_start: 0.8078 (mp10) cc_final: 0.7738 (mp10) REVERT: C 1078 MET cc_start: 0.7226 (mtp) cc_final: 0.6812 (mtp) REVERT: D 105 TRP cc_start: 0.8752 (OUTLIER) cc_final: 0.7851 (m-10) REVERT: D 170 MET cc_start: 0.7705 (ttm) cc_final: 0.7408 (ttm) REVERT: D 180 GLU cc_start: 0.6010 (mt-10) cc_final: 0.5786 (mt-10) REVERT: D 214 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.5984 (tp30) REVERT: D 226 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7596 (ttp) REVERT: D 268 LEU cc_start: 0.8761 (tp) cc_final: 0.8380 (tt) REVERT: D 287 MET cc_start: 0.5789 (mtp) cc_final: 0.5470 (mtp) REVERT: D 1024 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.7112 (ptm-80) REVERT: D 1027 VAL cc_start: 0.5492 (OUTLIER) cc_final: 0.5211 (t) REVERT: D 1048 GLU cc_start: 0.7289 (pt0) cc_final: 0.7039 (pt0) REVERT: G 60 LYS cc_start: 0.6466 (ttpt) cc_final: 0.6090 (mttm) REVERT: E 112 LEU cc_start: 0.6440 (OUTLIER) cc_final: 0.6051 (mm) REVERT: E 155 MET cc_start: 0.7046 (tpp) cc_final: 0.6825 (tpt) REVERT: E 344 ARG cc_start: 0.5856 (tmm160) cc_final: 0.5406 (ttp80) outliers start: 116 outliers final: 84 residues processed: 376 average time/residue: 0.3934 time to fit residues: 234.0709 Evaluate side-chains 354 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 261 time to evaluate : 2.865 ------------------------------------------------------------------------------- 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 154 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 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 94 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 248 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 735 VAL Chi-restraints excluded: chain C residue 763 MET Chi-restraints excluded: chain C residue 801 THR 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 971 VAL Chi-restraints excluded: chain C residue 1083 LEU Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 46 LEU 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 212 VAL Chi-restraints excluded: chain D residue 214 GLU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 488 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 637 ILE Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 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 954 THR 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 1132 LEU 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 304 LEU Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 354 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 253 optimal weight: 3.9990 chunk 285 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 57 optimal weight: 0.2980 chunk 5 optimal weight: 10.0000 chunk 142 optimal weight: 0.0570 chunk 300 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 overall best weight: 1.6704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 575 GLN D1144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.153145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.129724 restraints weight = 40397.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.128482 restraints weight = 70561.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.129421 restraints weight = 63755.038| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27614 Z= 0.131 Angle : 0.543 7.320 37694 Z= 0.293 Chirality : 0.042 0.172 4258 Planarity : 0.004 0.054 4616 Dihedral : 17.659 164.320 4519 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.30 % Allowed : 19.96 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.15), residues: 3159 helix: 1.18 (0.15), residues: 1214 sheet: 0.16 (0.27), residues: 370 loop : -0.22 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 199 HIS 0.006 0.001 HIS C1049 PHE 0.013 0.001 PHE G 47 TYR 0.028 0.001 TYR C 386 ARG 0.010 0.000 ARG E 316 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 1201) hydrogen bonds : angle 4.73066 ( 3309) covalent geometry : bond 0.00302 (27614) covalent geometry : angle 0.54254 (37694) *********************** 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 391 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 300 time to evaluate : 2.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6370 (mm-30) REVERT: B 100 ASP cc_start: 0.7248 (t0) cc_final: 0.6004 (p0) REVERT: C 376 THR cc_start: 0.7935 (OUTLIER) cc_final: 0.7640 (p) REVERT: C 384 MET cc_start: 0.6995 (mmt) cc_final: 0.6482 (tpp) REVERT: C 396 TYR cc_start: 0.5682 (OUTLIER) cc_final: 0.4796 (p90) REVERT: C 517 GLU cc_start: 0.6022 (tp30) cc_final: 0.5745 (tp30) REVERT: C 682 GLU cc_start: 0.5488 (mm-30) cc_final: 0.5169 (mm-30) REVERT: C 751 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7559 (mm-30) REVERT: C 925 MET cc_start: 0.7946 (mmm) cc_final: 0.7174 (mmm) REVERT: C 944 MET cc_start: 0.8433 (mmm) cc_final: 0.7663 (mmt) REVERT: C 1078 MET cc_start: 0.6929 (mtp) cc_final: 0.6497 (mtp) REVERT: D 105 TRP cc_start: 0.8625 (OUTLIER) cc_final: 0.7795 (m-10) REVERT: D 214 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.6034 (tp30) REVERT: D 226 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7427 (tpp) REVERT: D 268 LEU cc_start: 0.8730 (tp) cc_final: 0.8355 (tt) REVERT: D 287 MET cc_start: 0.5702 (mtp) cc_final: 0.5441 (mtp) REVERT: D 691 PHE cc_start: 0.3271 (t80) cc_final: 0.2940 (t80) REVERT: D 1024 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.7140 (ptm-80) REVERT: D 1027 VAL cc_start: 0.5632 (OUTLIER) cc_final: 0.5366 (t) REVERT: D 1048 GLU cc_start: 0.7231 (pt0) cc_final: 0.6983 (pt0) REVERT: G 60 LYS cc_start: 0.6360 (ttpt) cc_final: 0.6024 (mttm) REVERT: E 112 LEU cc_start: 0.5999 (OUTLIER) cc_final: 0.5645 (mm) REVERT: E 183 PHE cc_start: 0.6584 (t80) cc_final: 0.6247 (t80) REVERT: E 344 ARG cc_start: 0.5619 (tmm160) cc_final: 0.5264 (ttt90) outliers start: 91 outliers final: 67 residues processed: 370 average time/residue: 0.3676 time to fit residues: 215.1761 Evaluate side-chains 345 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 269 time to evaluate : 3.043 ------------------------------------------------------------------------------- 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 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 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 B residue 210 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 552 ASP Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 569 ASP 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 763 MET Chi-restraints excluded: chain C residue 801 THR Chi-restraints excluded: chain C residue 859 LEU 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 4 VAL Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 214 GLU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 355 CYS 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 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 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 954 THR Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 1024 ARG Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1100 ILE Chi-restraints excluded: chain D residue 1111 PHE Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 317 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 270 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 236 optimal weight: 7.9990 chunk 264 optimal weight: 8.9990 chunk 196 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 189 optimal weight: 0.9980 chunk 237 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 297 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 880 HIS D1101 HIS D1144 GLN F 43 HIS ** E 165 ASN ** 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 = 0.3926 r_free = 0.3926 target = 0.150574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.128135 restraints weight = 40976.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.127372 restraints weight = 63720.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.126823 restraints weight = 58797.984| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 27614 Z= 0.191 Angle : 0.602 7.792 37694 Z= 0.322 Chirality : 0.044 0.176 4258 Planarity : 0.005 0.057 4616 Dihedral : 17.628 164.599 4519 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.67 % Allowed : 19.64 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.15), residues: 3159 helix: 0.97 (0.15), residues: 1219 sheet: 0.10 (0.27), residues: 377 loop : -0.34 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 199 HIS 0.006 0.001 HIS C1049 PHE 0.016 0.002 PHE D 654 TYR 0.021 0.002 TYR E 102 ARG 0.010 0.001 ARG E 316 Details of bonding type rmsd hydrogen bonds : bond 0.04163 ( 1201) hydrogen bonds : angle 4.91649 ( 3309) covalent geometry : bond 0.00455 (27614) covalent geometry : angle 0.60238 (37694) *********************** 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 370 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 269 time to evaluate : 2.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6470 (mm-30) REVERT: B 100 ASP cc_start: 0.7286 (t0) cc_final: 0.6079 (p0) REVERT: C 48 MET cc_start: 0.6653 (tpp) cc_final: 0.6414 (tpt) REVERT: C 218 ARG cc_start: 0.6341 (mmt180) cc_final: 0.5866 (tpp-160) REVERT: C 376 THR cc_start: 0.7953 (OUTLIER) cc_final: 0.7664 (p) REVERT: C 384 MET cc_start: 0.7014 (mmt) cc_final: 0.6492 (tpp) REVERT: C 396 TYR cc_start: 0.5759 (OUTLIER) cc_final: 0.4359 (p90) REVERT: C 517 GLU cc_start: 0.6184 (tp30) cc_final: 0.5911 (tp30) REVERT: C 682 GLU cc_start: 0.5576 (mm-30) cc_final: 0.5250 (mm-30) REVERT: C 751 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7565 (mm-30) REVERT: C 944 MET cc_start: 0.8361 (mmm) cc_final: 0.7732 (mmt) REVERT: C 1078 MET cc_start: 0.7135 (mtp) cc_final: 0.6732 (mtp) REVERT: D 105 TRP cc_start: 0.8721 (OUTLIER) cc_final: 0.7822 (m-10) REVERT: D 170 MET cc_start: 0.7718 (ttm) cc_final: 0.7470 (ttm) REVERT: D 214 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.6049 (tp30) REVERT: D 216 PHE cc_start: 0.7075 (m-80) cc_final: 0.6702 (m-80) REVERT: D 226 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7635 (ttp) REVERT: D 268 LEU cc_start: 0.8707 (tp) cc_final: 0.8323 (tt) REVERT: D 1024 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.7101 (ptm-80) REVERT: D 1027 VAL cc_start: 0.5748 (OUTLIER) cc_final: 0.5494 (t) REVERT: D 1048 GLU cc_start: 0.7345 (pt0) cc_final: 0.7067 (pt0) REVERT: G 60 LYS cc_start: 0.6474 (ttpt) cc_final: 0.6092 (mttm) REVERT: E 112 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.5864 (mm) REVERT: E 155 MET cc_start: 0.7150 (tpp) cc_final: 0.6873 (ttm) REVERT: E 183 PHE cc_start: 0.6534 (t80) cc_final: 0.6223 (t80) REVERT: E 344 ARG cc_start: 0.5753 (tmm160) cc_final: 0.5229 (ttt90) outliers start: 101 outliers final: 82 residues processed: 349 average time/residue: 0.3767 time to fit residues: 211.7466 Evaluate side-chains 350 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 259 time to evaluate : 2.766 ------------------------------------------------------------------------------- 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 129 THR Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 14 ILE 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 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 118 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 552 ASP Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 569 ASP 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 763 MET Chi-restraints excluded: chain C residue 801 THR 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 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 68 VAL 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 212 VAL Chi-restraints excluded: chain D residue 214 GLU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 488 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 637 ILE Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 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 954 THR Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 1024 ARG Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1100 ILE Chi-restraints excluded: chain D residue 1111 PHE Chi-restraints excluded: chain D residue 1132 LEU 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 149 ARG Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 317 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 274 optimal weight: 2.9990 chunk 301 optimal weight: 7.9990 chunk 229 optimal weight: 0.8980 chunk 213 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 318 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 880 HIS F 8 GLN F 43 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.151978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.129655 restraints weight = 40492.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.129084 restraints weight = 64941.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.128485 restraints weight = 60031.528| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27614 Z= 0.147 Angle : 0.563 8.696 37694 Z= 0.302 Chirality : 0.043 0.170 4258 Planarity : 0.004 0.054 4616 Dihedral : 17.544 163.366 4519 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.23 % Allowed : 20.40 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.15), residues: 3159 helix: 1.16 (0.15), residues: 1205 sheet: 0.07 (0.27), residues: 373 loop : -0.25 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 199 HIS 0.006 0.001 HIS C1049 PHE 0.015 0.001 PHE D 249 TYR 0.030 0.002 TYR E 102 ARG 0.007 0.000 ARG E 316 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 1201) hydrogen bonds : angle 4.77504 ( 3309) covalent geometry : bond 0.00345 (27614) covalent geometry : angle 0.56344 (37694) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 275 time to evaluate : 2.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6458 (mm-30) REVERT: B 100 ASP cc_start: 0.7348 (t0) cc_final: 0.6123 (p0) REVERT: C 172 TYR cc_start: 0.5613 (m-10) cc_final: 0.5408 (m-10) REVERT: C 218 ARG cc_start: 0.6321 (mmt180) cc_final: 0.5802 (tpp-160) REVERT: C 376 THR cc_start: 0.7971 (OUTLIER) cc_final: 0.7677 (p) REVERT: C 384 MET cc_start: 0.7034 (mmt) cc_final: 0.6519 (tpp) REVERT: C 396 TYR cc_start: 0.5834 (OUTLIER) cc_final: 0.4131 (p90) REVERT: C 517 GLU cc_start: 0.6113 (tp30) cc_final: 0.5856 (tp30) REVERT: C 682 GLU cc_start: 0.5501 (mm-30) cc_final: 0.5157 (mm-30) REVERT: C 751 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7553 (mm-30) REVERT: C 944 MET cc_start: 0.8359 (mmm) cc_final: 0.7705 (mmt) REVERT: C 1078 MET cc_start: 0.6948 (mtp) cc_final: 0.6476 (mtp) REVERT: D 105 TRP cc_start: 0.8629 (OUTLIER) cc_final: 0.7799 (m-10) REVERT: D 117 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7682 (tt) REVERT: D 214 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.6050 (tp30) REVERT: D 216 PHE cc_start: 0.7025 (m-80) cc_final: 0.6705 (m-10) REVERT: D 226 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7541 (ttp) REVERT: D 268 LEU cc_start: 0.8781 (tp) cc_final: 0.8390 (tt) REVERT: D 464 GLU cc_start: 0.7314 (tp30) cc_final: 0.7103 (tp30) REVERT: D 691 PHE cc_start: 0.3156 (t80) cc_final: 0.2843 (t80) REVERT: D 1024 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6955 (ptm-80) REVERT: D 1027 VAL cc_start: 0.5806 (OUTLIER) cc_final: 0.5568 (t) REVERT: D 1048 GLU cc_start: 0.7326 (pt0) cc_final: 0.7049 (pt0) REVERT: G 60 LYS cc_start: 0.6428 (ttpt) cc_final: 0.5996 (mttm) REVERT: E 112 LEU cc_start: 0.6215 (OUTLIER) cc_final: 0.5803 (mm) REVERT: E 183 PHE cc_start: 0.6613 (t80) cc_final: 0.6259 (t80) REVERT: E 342 ARG cc_start: 0.2048 (mtt180) cc_final: 0.0167 (mpt-90) REVERT: E 344 ARG cc_start: 0.5699 (tmm160) cc_final: 0.5377 (ttt90) outliers start: 89 outliers final: 77 residues processed: 342 average time/residue: 0.3818 time to fit residues: 209.0180 Evaluate side-chains 349 residues out of total 2755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 262 time to evaluate : 2.975 ------------------------------------------------------------------------------- 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 129 THR Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 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 118 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 552 ASP Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 569 ASP 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 763 MET Chi-restraints excluded: chain C residue 801 THR 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 68 VAL 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 212 VAL Chi-restraints excluded: chain D residue 214 GLU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 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 670 LEU Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 768 THR 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 954 THR Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 1024 ARG Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1100 ILE Chi-restraints excluded: chain D residue 1111 PHE Chi-restraints excluded: chain D residue 1132 LEU 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 158 LEU Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 317 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 39 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 316 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 229 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 308 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 506 HIS ** C 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 861 HIS C 880 HIS D 458 HIS F 43 HIS ** E 165 ASN ** 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 = 0.3877 r_free = 0.3877 target = 0.146352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.124008 restraints weight = 41737.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.123402 restraints weight = 65613.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.122947 restraints weight = 63715.564| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.102 27614 Z= 0.327 Angle : 0.757 9.568 37694 Z= 0.403 Chirality : 0.049 0.196 4258 Planarity : 0.006 0.063 4616 Dihedral : 17.780 164.211 4519 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.85 % Allowed : 20.00 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3159 helix: 0.37 (0.14), residues: 1224 sheet: -0.29 (0.26), residues: 382 loop : -0.67 (0.15), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 199 HIS 0.011 0.002 HIS B 63 PHE 0.024 0.003 PHE C 539 TYR 0.025 0.003 TYR C1098 ARG 0.008 0.001 ARG E 316 Details of bonding type rmsd hydrogen bonds : bond 0.05172 ( 1201) hydrogen bonds : angle 5.34968 ( 3309) covalent geometry : bond 0.00788 (27614) covalent geometry : angle 0.75735 (37694) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7697.03 seconds wall clock time: 136 minutes 34.73 seconds (8194.73 seconds total)