Starting phenix.real_space_refine on Mon Aug 25 09:52:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x6g_38088/08_2025/8x6g_38088.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x6g_38088/08_2025/8x6g_38088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x6g_38088/08_2025/8x6g_38088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x6g_38088/08_2025/8x6g_38088.map" model { file = "/net/cci-nas-00/data/ceres_data/8x6g_38088/08_2025/8x6g_38088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x6g_38088/08_2025/8x6g_38088.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 81 5.49 5 S 98 5.16 5 C 16892 2.51 5 N 4745 2.21 5 O 5455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27271 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1726 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 214} Chain: "B" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1708 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 213} Chain: "C" Number of atoms: 9121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1153, 9121 Classifications: {'peptide': 1153} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1102} Chain: "D" Number of atoms: 9281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1176, 9281 Classifications: {'peptide': 1176} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1122} Chain breaks: 1 Chain: "E" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 709 Classifications: {'peptide': 84} Link IDs: {'TRANS': 83} Chain: "F" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 491 Classifications: {'peptide': 62} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 56} Chain: "G" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 596 Classifications: {'peptide': 69} Link IDs: {'TRANS': 68} Chain: "H" Number of atoms: 1978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1978 Classifications: {'peptide': 244} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "T" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 809 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain breaks: 1 Chain: "N" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 852 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain breaks: 1 Time building chain proxies: 7.92, per 1000 atoms: 0.29 Number of scatterers: 27271 At special positions: 0 Unit cell: (149.94, 145.18, 136.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 98 16.00 P 81 15.00 O 5455 8.00 N 4745 7.00 C 16892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6014 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 45 sheets defined 44.6% alpha, 18.1% beta 36 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 4.11 Creating SS restraints... Processing helix chain 'A' and resid 31 through 47 Processing helix chain 'A' and resid 74 through 84 removed outlier: 3.516A pdb=" N GLN A 84 " --> pdb=" O MET A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 150 through 155 Processing helix chain 'A' and resid 205 through 226 removed outlier: 4.090A pdb=" N ILE A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE A 224 " --> pdb=" O HIS A 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 47 removed outlier: 3.614A pdb=" N THR B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 84 removed outlier: 3.554A pdb=" N GLN B 84 " --> pdb=" O MET B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 155 Processing helix chain 'B' and resid 205 through 226 removed outlier: 4.067A pdb=" N ILE B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE B 224 " --> pdb=" O HIS B 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 removed outlier: 3.804A pdb=" N SER C 36 " --> pdb=" O ILE C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 53 Processing helix chain 'C' and resid 77 through 84 Processing helix chain 'C' and resid 192 through 200 Processing helix chain 'C' and resid 203 through 212 Processing helix chain 'C' and resid 214 through 224 Processing helix chain 'C' and resid 228 through 241 Processing helix chain 'C' and resid 247 through 260 Processing helix chain 'C' and resid 267 through 279 Processing helix chain 'C' and resid 280 through 286 removed outlier: 4.127A pdb=" N ARG C 284 " --> pdb=" O HIS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 318 Processing helix chain 'C' and resid 318 through 325 removed outlier: 3.731A pdb=" N SER C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 392 Processing helix chain 'C' and resid 410 through 437 Processing helix chain 'C' and resid 443 through 448 removed outlier: 3.683A pdb=" N LEU C 447 " --> pdb=" O THR C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 463 Processing helix chain 'C' and resid 474 through 483 Processing helix chain 'C' and resid 499 through 504 removed outlier: 4.064A pdb=" N ARG C 503 " --> pdb=" O GLN C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 510 removed outlier: 3.634A pdb=" N TYR C 510 " --> pdb=" O TYR C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 569 Processing helix chain 'C' and resid 605 through 607 No H-bonds generated for 'chain 'C' and resid 605 through 607' Processing helix chain 'C' and resid 613 through 617 removed outlier: 3.715A pdb=" N VAL C 617 " --> pdb=" O PRO C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 625 Processing helix chain 'C' and resid 627 through 631 Processing helix chain 'C' and resid 632 through 644 removed outlier: 3.904A pdb=" N ARG C 644 " --> pdb=" O ALA C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 670 removed outlier: 4.602A pdb=" N VAL C 664 " --> pdb=" O GLY C 660 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLY C 670 " --> pdb=" O ALA C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 783 Processing helix chain 'C' and resid 816 through 821 Processing helix chain 'C' and resid 854 through 865 Processing helix chain 'C' and resid 960 through 966 removed outlier: 4.263A pdb=" N SER C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG C 965 " --> pdb=" O GLY C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 984 Processing helix chain 'C' and resid 996 through 1007 Processing helix chain 'C' and resid 1066 through 1070 Processing helix chain 'C' and resid 1076 through 1087 Processing helix chain 'C' and resid 1088 through 1097 Processing helix chain 'C' and resid 1102 through 1116 removed outlier: 4.107A pdb=" N VAL C1107 " --> pdb=" O THR C1103 " (cutoff:3.500A) Processing helix chain 'C' and resid 1125 through 1138 Processing helix chain 'D' and resid 16 through 23 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 67 through 71 removed outlier: 3.637A pdb=" N TYR D 70 " --> pdb=" O ARG D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 103 through 109 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 151 through 162 Processing helix chain 'D' and resid 170 through 181 removed outlier: 3.716A pdb=" N GLY D 174 " --> pdb=" O MET D 170 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE D 175 " --> pdb=" O GLY D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 196 Processing helix chain 'D' and resid 200 through 220 Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 235 through 239 Processing helix chain 'D' and resid 245 through 247 No H-bonds generated for 'chain 'D' and resid 245 through 247' Processing helix chain 'D' and resid 252 through 275 removed outlier: 3.903A pdb=" N ASP D 256 " --> pdb=" O SER D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 297 Processing helix chain 'D' and resid 315 through 321 removed outlier: 3.520A pdb=" N MET D 319 " --> pdb=" O SER D 315 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU D 320 " --> pdb=" O LEU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 330 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 366 through 377 Processing helix chain 'D' and resid 382 through 393 Processing helix chain 'D' and resid 394 through 405 removed outlier: 4.026A pdb=" N TRP D 398 " --> pdb=" O ASP D 394 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL D 400 " --> pdb=" O GLU D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 421 No H-bonds generated for 'chain 'D' and resid 419 through 421' Processing helix chain 'D' and resid 439 through 441 No H-bonds generated for 'chain 'D' and resid 439 through 441' Processing helix chain 'D' and resid 442 through 447 Processing helix chain 'D' and resid 462 through 473 Processing helix chain 'D' and resid 493 through 503 Processing helix chain 'D' and resid 518 through 528 Processing helix chain 'D' and resid 542 through 545 removed outlier: 3.653A pdb=" N ASN D 545 " --> pdb=" O SER D 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 542 through 545' Processing helix chain 'D' and resid 552 through 555 Processing helix chain 'D' and resid 562 through 569 Processing helix chain 'D' and resid 582 through 588 Processing helix chain 'D' and resid 591 through 593 No H-bonds generated for 'chain 'D' and resid 591 through 593' Processing helix chain 'D' and resid 597 through 601 Processing helix chain 'D' and resid 604 through 613 Processing helix chain 'D' and resid 620 through 635 Processing helix chain 'D' and resid 636 through 659 Processing helix chain 'D' and resid 663 through 667 Processing helix chain 'D' and resid 672 through 693 Processing helix chain 'D' and resid 697 through 723 Processing helix chain 'D' and resid 728 through 736 Processing helix chain 'D' and resid 741 through 750 Processing helix chain 'D' and resid 776 through 812 removed outlier: 4.018A pdb=" N HIS D 785 " --> pdb=" O PHE D 781 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY D 786 " --> pdb=" O ILE D 782 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA D 799 " --> pdb=" O ALA D 795 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP D 800 " --> pdb=" O LEU D 796 " (cutoff:3.500A) Processing helix chain 'D' and resid 842 through 848 Processing helix chain 'D' and resid 873 through 883 Processing helix chain 'D' and resid 892 through 896 Processing helix chain 'D' and resid 904 through 908 Processing helix chain 'D' and resid 922 through 938 Proline residue: D 934 - end of helix removed outlier: 4.035A pdb=" N GLN D 937 " --> pdb=" O GLU D 933 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 965 Processing helix chain 'D' and resid 989 through 991 No H-bonds generated for 'chain 'D' and resid 989 through 991' Processing helix chain 'D' and resid 1034 through 1043 Processing helix chain 'D' and resid 1043 through 1062 removed outlier: 3.750A pdb=" N GLN D1062 " --> pdb=" O VAL D1058 " (cutoff:3.500A) Processing helix chain 'D' and resid 1067 through 1079 removed outlier: 4.163A pdb=" N VAL D1071 " --> pdb=" O ASP D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1100 through 1113 Processing helix chain 'D' and resid 1126 through 1133 Processing helix chain 'D' and resid 1136 through 1144 removed outlier: 3.842A pdb=" N ALA D1140 " --> pdb=" O SER D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1145 through 1157 Processing helix chain 'D' and resid 1164 through 1172 removed outlier: 3.848A pdb=" N ASN D1168 " --> pdb=" O GLY D1164 " (cutoff:3.500A) Processing helix chain 'D' and resid 1177 through 1180 Processing helix chain 'D' and resid 1181 through 1186 Processing helix chain 'E' and resid 9 through 14 Processing helix chain 'E' and resid 15 through 28 Processing helix chain 'E' and resid 33 through 45 Processing helix chain 'E' and resid 47 through 65 removed outlier: 4.365A pdb=" N ASN E 53 " --> pdb=" O GLU E 49 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG E 54 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN E 57 " --> pdb=" O ASN E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing helix chain 'E' and resid 83 through 91 Processing helix chain 'F' and resid 5 through 11 Processing helix chain 'F' and resid 15 through 33 Processing helix chain 'F' and resid 34 through 37 removed outlier: 3.862A pdb=" N GLU F 37 " --> pdb=" O PRO F 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 34 through 37' Processing helix chain 'F' and resid 46 through 57 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 30 through 38 Processing helix chain 'G' and resid 53 through 63 Processing helix chain 'H' and resid 14 through 27 Processing helix chain 'H' and resid 28 through 52 removed outlier: 3.568A pdb=" N GLN H 32 " --> pdb=" O ASN H 28 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LYS H 41 " --> pdb=" O LYS H 37 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LEU H 42 " --> pdb=" O HIS H 38 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR H 50 " --> pdb=" O LEU H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 75 Processing helix chain 'H' and resid 83 through 102 Proline residue: H 89 - end of helix Processing helix chain 'H' and resid 109 through 131 Proline residue: H 117 - end of helix Processing helix chain 'H' and resid 135 through 144 Processing helix chain 'H' and resid 146 through 159 Processing helix chain 'H' and resid 180 through 184 Processing helix chain 'H' and resid 189 through 204 Processing helix chain 'H' and resid 205 through 207 No H-bonds generated for 'chain 'H' and resid 205 through 207' Processing helix chain 'H' and resid 208 through 219 Processing helix chain 'H' and resid 224 through 233 Processing helix chain 'H' and resid 235 through 256 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 14 removed outlier: 5.019A pdb=" N ILE A 9 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N GLU A 26 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N THR A 11 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL A 24 " --> pdb=" O THR A 11 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP A 192 " --> pdb=" O PRO A 27 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N SER A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL A 185 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 101 removed outlier: 3.740A pdb=" N TYR A 55 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASN A 143 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N VAL A 53 " --> pdb=" O ASN A 143 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLY A 145 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA A 51 " --> pdb=" O GLY A 145 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 105 through 108 Processing sheet with id=AA5, first strand: chain 'A' and resid 148 through 149 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 14 removed outlier: 5.066A pdb=" N ILE B 9 " --> pdb=" O GLU B 26 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLU B 26 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N THR B 11 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL B 24 " --> pdb=" O THR B 11 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N PHE B 20 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR B 200 " --> pdb=" O PHE B 20 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LYS B 22 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL B 198 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL B 24 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU B 196 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N GLU B 26 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU B 194 " --> pdb=" O GLU B 26 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N SER B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL B 185 " --> pdb=" O SER B 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 112 through 113 removed outlier: 3.716A pdb=" N TYR B 55 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ASN B 143 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N VAL B 53 " --> pdb=" O ASN B 143 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY B 145 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ALA B 51 " --> pdb=" O GLY B 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 89 Processing sheet with id=AA9, first strand: chain 'B' and resid 105 through 108 removed outlier: 6.499A pdb=" N GLY B 105 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THR B 129 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL B 107 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 148 through 149 Processing sheet with id=AB2, first strand: chain 'C' and resid 4 through 8 removed outlier: 4.483A pdb=" N HIS C 986 " --> pdb=" O LYS C 13 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 988 " --> pdb=" O ARG C 15 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 55 through 56 removed outlier: 5.507A pdb=" N LEU C 64 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE C 99 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N PHE C 66 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG C 97 " --> pdb=" O PHE C 66 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP C 68 " --> pdb=" O LYS C 95 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ALA C 90 " --> pdb=" O ASP C 115 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP C 115 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU C 92 " --> pdb=" O MET C 113 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU C 105 " --> pdb=" O ILE C 100 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 125 through 127 Processing sheet with id=AB5, first strand: chain 'C' and resid 406 through 409 removed outlier: 6.374A pdb=" N SER C 136 " --> pdb=" O SER C 486 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 144 through 150 removed outlier: 6.704A pdb=" N TYR C 158 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR C 174 " --> pdb=" O TYR C 158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 288 through 289 removed outlier: 3.825A pdb=" N GLN C 288 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 294 through 295 removed outlier: 6.793A pdb=" N ILE C 294 " --> pdb=" O VAL C 303 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 328 through 331 removed outlier: 3.888A pdb=" N GLN C 345 " --> pdb=" O GLY C 364 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 535 through 536 removed outlier: 5.561A pdb=" N GLN C 559 " --> pdb=" O LYS C 548 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 535 through 536 Processing sheet with id=AC3, first strand: chain 'C' and resid 673 through 674 removed outlier: 6.421A pdb=" N ILE C 673 " --> pdb=" O LEU C 741 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 700 through 710 removed outlier: 5.107A pdb=" N GLU C 701 " --> pdb=" O GLU C 697 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU C 697 " --> pdb=" O GLU C 701 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N GLU C 703 " --> pdb=" O VAL C 695 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL C 695 " --> pdb=" O GLU C 703 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N GLU C 705 " --> pdb=" O ARG C 693 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLU C 688 " --> pdb=" O VAL C 684 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N VAL C 684 " --> pdb=" O GLU C 688 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU C 690 " --> pdb=" O GLU C 682 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 715 through 716 Processing sheet with id=AC6, first strand: chain 'C' and resid 747 through 748 Processing sheet with id=AC7, first strand: chain 'C' and resid 1014 through 1015 removed outlier: 6.897A pdb=" N VAL C 774 " --> pdb=" O LYS C 937 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL C 939 " --> pdb=" O VAL C 774 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N MET C 776 " --> pdb=" O VAL C 939 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 775 " --> pdb=" O MET C 956 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ILE C 955 " --> pdb=" O ASN C 757 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL C 759 " --> pdb=" O ILE C 955 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU C 957 " --> pdb=" O VAL C 759 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY C 761 " --> pdb=" O LEU C 957 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N SER C1031 " --> pdb=" O PHE C 762 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 804 through 805 removed outlier: 6.005A pdb=" N SER C 788 " --> pdb=" O LYS C 916 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS C 916 " --> pdb=" O SER C 788 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N HIS C 790 " --> pdb=" O VAL C 914 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL C 914 " --> pdb=" O HIS C 790 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU C 792 " --> pdb=" O TYR C 912 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR C 912 " --> pdb=" O GLU C 792 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR C 794 " --> pdb=" O ARG C 910 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ARG C 910 " --> pdb=" O TYR C 794 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N SER C 796 " --> pdb=" O LEU C 908 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU C 908 " --> pdb=" O SER C 796 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA C 798 " --> pdb=" O ASN C 906 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ASN C 906 " --> pdb=" O ASN C 893 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASN C 893 " --> pdb=" O ASN C 906 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU C 908 " --> pdb=" O VAL C 891 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL C 891 " --> pdb=" O LEU C 908 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG C 910 " --> pdb=" O VAL C 889 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL C 889 " --> pdb=" O ARG C 910 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR C 912 " --> pdb=" O LEU C 887 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 807 through 808 Processing sheet with id=AD1, first strand: chain 'C' and resid 840 through 842 removed outlier: 6.418A pdb=" N LEU C 876 " --> pdb=" O LEU C 841 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1049 through 1051 removed outlier: 7.856A pdb=" N ILE D 436 " --> pdb=" O ARG D 341 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL D 343 " --> pdb=" O ILE D 436 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU D 438 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA D 345 " --> pdb=" O LEU D 438 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1074 through 1075 Processing sheet with id=AD4, first strand: chain 'C' and resid 1143 through 1145 Processing sheet with id=AD5, first strand: chain 'D' and resid 24 through 27 removed outlier: 7.567A pdb=" N HIS D 94 " --> pdb=" O PHE D 25 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU D 27 " --> pdb=" O HIS D 94 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N GLU D 96 " --> pdb=" O GLU D 27 " (cutoff:3.500A) removed outlier: 10.013A pdb=" N LEU D 97 " --> pdb=" O PRO D 232 " (cutoff:3.500A) removed outlier: 10.717A pdb=" N ALA D 99 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL D 230 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 149 through 150 removed outlier: 6.796A pdb=" N VAL D 167 " --> pdb=" O VAL D 137 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 241 through 243 Processing sheet with id=AD8, first strand: chain 'D' and resid 515 through 516 Processing sheet with id=AD9, first strand: chain 'D' and resid 816 through 819 removed outlier: 6.017A pdb=" N ILE D 816 " --> pdb=" O VAL D 902 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 828 through 831 removed outlier: 4.691A pdb=" N TYR D 851 " --> pdb=" O ARG D 891 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 833 through 835 removed outlier: 6.852A pdb=" N GLU D 835 " --> pdb=" O MET D 839 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N MET D 839 " --> pdb=" O GLU D 835 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 856 through 857 removed outlier: 6.813A pdb=" N ILE D 856 " --> pdb=" O ILE D 865 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1003 through 1008 removed outlier: 6.117A pdb=" N LYS D 998 " --> pdb=" O VAL D 982 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL D 982 " --> pdb=" O LYS D 998 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1097 through 1099 removed outlier: 5.413A pdb=" N VAL D1082 " --> pdb=" O VAL D1123 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL D1123 " --> pdb=" O VAL D1082 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ILE D1084 " --> pdb=" O LYS D1121 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LYS D1121 " --> pdb=" O ILE D1084 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU D1086 " --> pdb=" O THR D1119 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1189 through 1191 Processing sheet with id=AE7, first strand: chain 'E' and resid 31 through 32 removed outlier: 6.306A pdb=" N LEU E 75 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 44 through 50 removed outlier: 6.320A pdb=" N PHE G 7 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE G 48 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LYS G 5 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 9.506A pdb=" N GLU G 69 " --> pdb=" O SER G 23 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR G 25 " --> pdb=" O GLU G 69 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 168 through 170 1174 hydrogen bonds defined for protein. 3297 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 84 hydrogen bonds 168 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 8.07 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8393 1.33 - 1.45: 4182 1.45 - 1.57: 14978 1.57 - 1.69: 159 1.69 - 1.81: 179 Bond restraints: 27891 Sorted by residual: bond pdb=" N VAL D 669 " pdb=" CA VAL D 669 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.22e-02 6.72e+03 9.58e+00 bond pdb=" N VAL D 668 " pdb=" CA VAL D 668 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.24e-02 6.50e+03 8.79e+00 bond pdb=" CA SER C 875 " pdb=" CB SER C 875 " ideal model delta sigma weight residual 1.529 1.485 0.044 1.61e-02 3.86e+03 7.57e+00 bond pdb=" N GLU C 870 " pdb=" CA GLU C 870 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.57e+00 bond pdb=" N LEU D 670 " pdb=" CA LEU D 670 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.29e-02 6.01e+03 7.44e+00 ... (remaining 27886 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 37573 2.27 - 4.54: 413 4.54 - 6.80: 29 6.80 - 9.07: 3 9.07 - 11.34: 2 Bond angle restraints: 38020 Sorted by residual: angle pdb=" N THR C 874 " pdb=" CA THR C 874 " pdb=" C THR C 874 " ideal model delta sigma weight residual 110.61 104.71 5.90 1.25e+00 6.40e-01 2.23e+01 angle pdb=" CA PRO A 172 " pdb=" N PRO A 172 " pdb=" CD PRO A 172 " ideal model delta sigma weight residual 112.00 106.15 5.85 1.40e+00 5.10e-01 1.75e+01 angle pdb=" C THR C1097 " pdb=" N TYR C1098 " pdb=" CA TYR C1098 " ideal model delta sigma weight residual 122.65 116.10 6.55 1.60e+00 3.91e-01 1.67e+01 angle pdb=" N PHE H 79 " pdb=" CA PHE H 79 " pdb=" C PHE H 79 " ideal model delta sigma weight residual 110.30 104.24 6.06 1.50e+00 4.44e-01 1.63e+01 angle pdb=" N VAL D 489 " pdb=" CA VAL D 489 " pdb=" C VAL D 489 " ideal model delta sigma weight residual 111.91 108.38 3.53 8.90e-01 1.26e+00 1.58e+01 ... (remaining 38015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.79: 15869 29.79 - 59.57: 982 59.57 - 89.36: 44 89.36 - 119.14: 3 119.14 - 148.93: 1 Dihedral angle restraints: 16899 sinusoidal: 7558 harmonic: 9341 Sorted by residual: dihedral pdb=" CA SER A 171 " pdb=" C SER A 171 " pdb=" N PRO A 172 " pdb=" CA PRO A 172 " ideal model delta harmonic sigma weight residual -180.00 -151.19 -28.81 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ARG C 10 " pdb=" C ARG C 10 " pdb=" N HIS C 11 " pdb=" CA HIS C 11 " ideal model delta harmonic sigma weight residual 180.00 -160.50 -19.50 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" C4' DC T 37 " pdb=" C3' DC T 37 " pdb=" O3' DC T 37 " pdb=" P DA T 38 " ideal model delta sinusoidal sigma weight residual 220.00 71.07 148.93 1 3.50e+01 8.16e-04 1.45e+01 ... (remaining 16896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3745 0.062 - 0.125: 513 0.125 - 0.187: 22 0.187 - 0.250: 4 0.250 - 0.312: 1 Chirality restraints: 4285 Sorted by residual: chirality pdb=" CA PHE H 79 " pdb=" N PHE H 79 " pdb=" C PHE H 79 " pdb=" CB PHE H 79 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA PRO A 172 " pdb=" N PRO A 172 " pdb=" C PRO A 172 " pdb=" CB PRO A 172 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA VAL D 669 " pdb=" N VAL D 669 " pdb=" C VAL D 669 " pdb=" CB VAL D 669 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 4282 not shown) Planarity restraints: 4689 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 171 " 0.105 5.00e-02 4.00e+02 1.59e-01 4.03e+01 pdb=" N PRO A 172 " -0.274 5.00e-02 4.00e+02 pdb=" CA PRO A 172 " 0.089 5.00e-02 4.00e+02 pdb=" CD PRO A 172 " 0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET H 77 " -0.027 2.00e-02 2.50e+03 5.46e-02 2.98e+01 pdb=" C MET H 77 " 0.094 2.00e-02 2.50e+03 pdb=" O MET H 77 " -0.036 2.00e-02 2.50e+03 pdb=" N SER H 78 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT T 54 " -0.023 2.00e-02 2.50e+03 1.15e-02 3.28e+00 pdb=" N1 DT T 54 " 0.024 2.00e-02 2.50e+03 pdb=" C2 DT T 54 " 0.003 2.00e-02 2.50e+03 pdb=" O2 DT T 54 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DT T 54 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT T 54 " -0.005 2.00e-02 2.50e+03 pdb=" O4 DT T 54 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DT T 54 " -0.003 2.00e-02 2.50e+03 pdb=" C7 DT T 54 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DT T 54 " 0.002 2.00e-02 2.50e+03 ... (remaining 4686 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2466 2.74 - 3.28: 27327 3.28 - 3.82: 47058 3.82 - 4.36: 55865 4.36 - 4.90: 94223 Nonbonded interactions: 226939 Sorted by model distance: nonbonded pdb=" OD2 ASP C1101 " pdb=" OG SER C1127 " model vdw 2.200 3.040 nonbonded pdb=" OG1 THR H 103 " pdb=" OH TYR H 160 " model vdw 2.213 3.040 nonbonded pdb=" ND2 ASN B 155 " pdb=" OE1 GLU C 834 " model vdw 2.215 3.120 nonbonded pdb=" OD1 ASP C 784 " pdb=" OG1 THR C 787 " model vdw 2.226 3.040 nonbonded pdb=" O ASP C 51 " pdb=" NZ LYS C 263 " model vdw 2.234 3.120 ... (remaining 226934 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 227) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.140 Set scattering table: 0.140 Process input model: 33.690 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 27891 Z= 0.172 Angle : 0.605 11.341 38020 Z= 0.353 Chirality : 0.043 0.312 4285 Planarity : 0.004 0.159 4689 Dihedral : 16.817 148.926 10885 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.68 % Favored : 98.26 % Rotamer: Outliers : 0.25 % Allowed : 10.12 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.15), residues: 3214 helix: 1.46 (0.15), residues: 1259 sheet: 0.57 (0.26), residues: 413 loop : 0.71 (0.17), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 61 TYR 0.014 0.001 TYR C1098 PHE 0.022 0.001 PHE B 65 TRP 0.012 0.001 TRP C 765 HIS 0.005 0.001 HIS H 238 Details of bonding type rmsd covalent geometry : bond 0.00356 (27891) covalent geometry : angle 0.60467 (38020) hydrogen bonds : bond 0.14395 ( 1256) hydrogen bonds : angle 6.37236 ( 3465) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 614 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 PRO cc_start: 0.7972 (Cg_endo) cc_final: 0.7724 (Cg_exo) REVERT: A 10 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6272 (pt0) REVERT: A 29 GLU cc_start: 0.6828 (mm-30) cc_final: 0.6377 (mt-10) REVERT: A 54 LYS cc_start: 0.6201 (ttpp) cc_final: 0.5696 (mtpt) REVERT: A 103 ASP cc_start: 0.6105 (p0) cc_final: 0.5463 (p0) REVERT: A 119 GLU cc_start: 0.7273 (tt0) cc_final: 0.6932 (mt-10) REVERT: A 143 ASN cc_start: 0.5494 (p0) cc_final: 0.5264 (p0) REVERT: A 190 ASP cc_start: 0.7031 (m-30) cc_final: 0.6606 (p0) REVERT: B 26 GLU cc_start: 0.7735 (pt0) cc_final: 0.6705 (pm20) REVERT: B 90 TYR cc_start: 0.7838 (m-80) cc_final: 0.7479 (m-10) REVERT: B 115 ASP cc_start: 0.6268 (p0) cc_final: 0.5862 (p0) REVERT: B 119 GLU cc_start: 0.7441 (tt0) cc_final: 0.6903 (mt-10) REVERT: B 124 GLU cc_start: 0.7678 (pm20) cc_final: 0.7379 (pm20) REVERT: B 126 LYS cc_start: 0.8168 (tttt) cc_final: 0.7904 (tttm) REVERT: B 132 LYS cc_start: 0.7424 (ttmm) cc_final: 0.7088 (tttt) REVERT: B 204 ILE cc_start: 0.7382 (tt) cc_final: 0.6902 (tp) REVERT: B 208 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6589 (tp30) REVERT: C 13 LYS cc_start: 0.7698 (mttt) cc_final: 0.7485 (mttt) REVERT: C 35 LYS cc_start: 0.7068 (mttt) cc_final: 0.6745 (mttt) REVERT: C 38 GLU cc_start: 0.7700 (tt0) cc_final: 0.7274 (mm-30) REVERT: C 47 GLU cc_start: 0.8003 (tt0) cc_final: 0.7710 (tt0) REVERT: C 50 ARG cc_start: 0.6170 (tpp-160) cc_final: 0.5906 (tpp-160) REVERT: C 51 ASP cc_start: 0.6455 (m-30) cc_final: 0.6217 (m-30) REVERT: C 67 VAL cc_start: 0.7375 (t) cc_final: 0.7053 (m) REVERT: C 98 LEU cc_start: 0.6699 (tp) cc_final: 0.6288 (tp) REVERT: C 113 MET cc_start: 0.7573 (tpp) cc_final: 0.7311 (mmm) REVERT: C 165 ASN cc_start: 0.6572 (t0) cc_final: 0.6359 (t0) REVERT: C 266 ASP cc_start: 0.6345 (t0) cc_final: 0.5549 (m-30) REVERT: C 277 LYS cc_start: 0.5923 (tttt) cc_final: 0.5645 (ttpp) REVERT: C 458 LYS cc_start: 0.7238 (tttt) cc_final: 0.6896 (tttp) REVERT: C 500 MET cc_start: 0.2977 (tpt) cc_final: 0.2428 (mmm) REVERT: C 520 GLU cc_start: 0.5969 (mt-10) cc_final: 0.5532 (pt0) REVERT: C 535 ARG cc_start: 0.6632 (mtt180) cc_final: 0.6040 (mtm180) REVERT: C 577 ASN cc_start: 0.6664 (p0) cc_final: 0.6333 (p0) REVERT: C 585 ARG cc_start: 0.5925 (mtt180) cc_final: 0.5483 (mtt-85) REVERT: C 589 ASP cc_start: 0.6053 (m-30) cc_final: 0.5307 (t70) REVERT: C 638 MET cc_start: 0.5862 (mtt) cc_final: 0.5586 (mtt) REVERT: C 797 GLU cc_start: 0.6630 (pm20) cc_final: 0.6406 (pt0) REVERT: C 799 ARG cc_start: 0.7138 (ttm110) cc_final: 0.6720 (ttm-80) REVERT: C 814 ASN cc_start: 0.6655 (m-40) cc_final: 0.6315 (t0) REVERT: C 834 GLU cc_start: 0.8155 (tt0) cc_final: 0.7726 (pm20) REVERT: C 839 ASP cc_start: 0.6880 (m-30) cc_final: 0.6439 (m-30) REVERT: C 880 HIS cc_start: 0.6354 (p-80) cc_final: 0.5923 (t-90) REVERT: C 966 MET cc_start: 0.6629 (mtm) cc_final: 0.6404 (mtm) REVERT: C 1043 MET cc_start: 0.5365 (ptt) cc_final: 0.4188 (tmm) REVERT: C 1045 ASP cc_start: 0.6814 (m-30) cc_final: 0.5776 (t0) REVERT: C 1154 MET cc_start: 0.7290 (mtm) cc_final: 0.7038 (ttm) REVERT: D 10 MET cc_start: 0.7942 (ttm) cc_final: 0.7525 (ttt) REVERT: D 11 LYS cc_start: 0.7303 (tttt) cc_final: 0.6743 (tttm) REVERT: D 43 LYS cc_start: 0.7542 (tppt) cc_final: 0.7259 (tttm) REVERT: D 86 LYS cc_start: 0.6169 (tttt) cc_final: 0.5805 (mptt) REVERT: D 130 TYR cc_start: 0.8210 (m-80) cc_final: 0.7934 (m-80) REVERT: D 154 GLU cc_start: 0.5941 (mt-10) cc_final: 0.5693 (mt-10) REVERT: D 155 PHE cc_start: 0.6608 (t80) cc_final: 0.6366 (t80) REVERT: D 216 PHE cc_start: 0.7127 (m-80) cc_final: 0.6899 (m-80) REVERT: D 237 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7698 (mm-30) REVERT: D 351 LYS cc_start: 0.7756 (mmtt) cc_final: 0.6980 (mptt) REVERT: D 406 ARG cc_start: 0.7045 (ttm170) cc_final: 0.6601 (ttp-170) REVERT: D 432 GLU cc_start: 0.7349 (mm-30) cc_final: 0.6499 (mp0) REVERT: D 453 ASP cc_start: 0.8121 (m-30) cc_final: 0.7702 (m-30) REVERT: D 473 MET cc_start: 0.8862 (mtp) cc_final: 0.8581 (mtp) REVERT: D 486 LYS cc_start: 0.7706 (mttt) cc_final: 0.7271 (mmtt) REVERT: D 494 ASP cc_start: 0.7140 (t0) cc_final: 0.6886 (t0) REVERT: D 510 VAL cc_start: 0.8544 (m) cc_final: 0.8160 (p) REVERT: D 584 GLU cc_start: 0.7114 (tt0) cc_final: 0.6875 (tm-30) REVERT: D 592 ASN cc_start: 0.8341 (m-40) cc_final: 0.7882 (t0) REVERT: D 603 GLU cc_start: 0.7021 (tp30) cc_final: 0.6658 (tt0) REVERT: D 608 GLU cc_start: 0.7099 (tt0) cc_final: 0.6741 (tt0) REVERT: D 617 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7241 (mp0) REVERT: D 633 ASN cc_start: 0.7420 (t0) cc_final: 0.7092 (t0) REVERT: D 642 MET cc_start: 0.7708 (mtp) cc_final: 0.7285 (mmm) REVERT: D 789 LYS cc_start: 0.6233 (tttt) cc_final: 0.5930 (tttp) REVERT: D 933 GLU cc_start: 0.7204 (tm-30) cc_final: 0.6976 (tm-30) REVERT: D 1044 LEU cc_start: 0.6524 (tt) cc_final: 0.6102 (tt) REVERT: D 1053 LYS cc_start: 0.8049 (tttt) cc_final: 0.7566 (ttmm) REVERT: D 1054 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6753 (mm-30) REVERT: D 1065 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6576 (tt0) REVERT: D 1109 GLU cc_start: 0.6554 (tp30) cc_final: 0.5604 (tm-30) REVERT: D 1129 LYS cc_start: 0.7015 (tttt) cc_final: 0.6411 (tptp) REVERT: D 1163 LEU cc_start: 0.8174 (mt) cc_final: 0.7942 (mt) REVERT: D 1181 MET cc_start: 0.8296 (mmm) cc_final: 0.8068 (mmm) REVERT: D 1188 LYS cc_start: 0.7355 (mttt) cc_final: 0.6653 (mtpp) REVERT: E 14 LYS cc_start: 0.5243 (OUTLIER) cc_final: 0.4828 (pttp) REVERT: F 25 LYS cc_start: 0.6788 (mttm) cc_final: 0.6308 (mptt) REVERT: G 29 GLN cc_start: 0.7103 (mm-40) cc_final: 0.6180 (mm-40) REVERT: G 39 LYS cc_start: 0.7339 (ttpp) cc_final: 0.6562 (pttt) REVERT: G 50 LYS cc_start: 0.7910 (tptt) cc_final: 0.7494 (tptp) REVERT: H 33 ASP cc_start: 0.7521 (m-30) cc_final: 0.7214 (m-30) REVERT: H 52 LYS cc_start: 0.5478 (mttt) cc_final: 0.3881 (ttpp) REVERT: H 56 HIS cc_start: 0.7265 (p90) cc_final: 0.6691 (p90) REVERT: H 65 MET cc_start: 0.6394 (mmm) cc_final: 0.5912 (mmm) REVERT: H 81 ARG cc_start: 0.5936 (mtt180) cc_final: 0.5044 (mtp180) REVERT: H 144 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6362 (tt0) REVERT: H 166 ASP cc_start: 0.6017 (m-30) cc_final: 0.5630 (m-30) REVERT: H 201 GLU cc_start: 0.6267 (mm-30) cc_final: 0.5945 (mt-10) REVERT: H 237 MET cc_start: 0.7116 (tpt) cc_final: 0.6646 (tpt) REVERT: H 245 THR cc_start: 0.7164 (m) cc_final: 0.6902 (p) REVERT: H 251 GLN cc_start: 0.5860 (mt0) cc_final: 0.5636 (mt0) outliers start: 7 outliers final: 3 residues processed: 620 average time/residue: 0.2443 time to fit residues: 223.2046 Evaluate side-chains 367 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 363 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain C residue 870 GLU Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 43 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.0030 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 8.9990 overall best weight: 1.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN C 109 GLN C 445 GLN C 683 HIS C 970 GLN D 385 ASN D 703 ASN D 744 ASN D 897 ASN D1062 GLN D1101 HIS E 57 GLN G 42 ASN H 23 HIS ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 HIS ** H 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.170622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.132414 restraints weight = 32187.421| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.68 r_work: 0.3298 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27891 Z= 0.153 Angle : 0.558 19.748 38020 Z= 0.299 Chirality : 0.044 0.302 4285 Planarity : 0.005 0.181 4689 Dihedral : 16.716 145.499 4453 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.56 % Favored : 98.41 % Rotamer: Outliers : 1.78 % Allowed : 12.25 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.15), residues: 3214 helix: 1.47 (0.14), residues: 1287 sheet: 0.51 (0.26), residues: 404 loop : 0.59 (0.16), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 644 TYR 0.020 0.002 TYR C1098 PHE 0.022 0.002 PHE E 40 TRP 0.011 0.001 TRP A 199 HIS 0.006 0.001 HIS C 677 Details of bonding type rmsd covalent geometry : bond 0.00361 (27891) covalent geometry : angle 0.55774 (38020) hydrogen bonds : bond 0.04357 ( 1256) hydrogen bonds : angle 4.93375 ( 3465) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 391 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7321 (pt0) REVERT: A 54 LYS cc_start: 0.6928 (ttpp) cc_final: 0.6601 (mtpt) REVERT: A 103 ASP cc_start: 0.6046 (p0) cc_final: 0.5373 (p0) REVERT: A 106 GLU cc_start: 0.6635 (mp0) cc_final: 0.6329 (mt-10) REVERT: A 126 LYS cc_start: 0.6656 (tttt) cc_final: 0.6020 (pttp) REVERT: B 16 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6280 (mm-30) REVERT: B 74 ASP cc_start: 0.7973 (p0) cc_final: 0.7607 (p0) REVERT: B 132 LYS cc_start: 0.7285 (ttmm) cc_final: 0.7066 (tttt) REVERT: B 167 ASP cc_start: 0.8318 (m-30) cc_final: 0.8047 (m-30) REVERT: B 182 ASN cc_start: 0.7627 (t0) cc_final: 0.7370 (t0) REVERT: C 51 ASP cc_start: 0.6627 (m-30) cc_final: 0.6233 (m-30) REVERT: C 109 GLN cc_start: 0.4914 (tt0) cc_final: 0.4570 (tt0) REVERT: C 116 PHE cc_start: 0.7355 (t80) cc_final: 0.7148 (t80) REVERT: C 148 GLU cc_start: 0.4959 (tt0) cc_final: 0.4547 (tt0) REVERT: C 163 ILE cc_start: 0.7053 (mt) cc_final: 0.6717 (tt) REVERT: C 165 ASN cc_start: 0.6821 (t0) cc_final: 0.6569 (t0) REVERT: C 178 ASP cc_start: 0.5709 (m-30) cc_final: 0.5264 (t70) REVERT: C 263 LYS cc_start: 0.7538 (mmmt) cc_final: 0.6073 (mmmt) REVERT: C 458 LYS cc_start: 0.7732 (tttt) cc_final: 0.7494 (tttp) REVERT: C 500 MET cc_start: 0.3801 (tpt) cc_final: 0.3560 (mmm) REVERT: C 579 LYS cc_start: 0.6778 (mtpt) cc_final: 0.6503 (mmtt) REVERT: C 598 ASN cc_start: 0.7231 (m-40) cc_final: 0.6987 (m110) REVERT: C 610 MET cc_start: 0.8165 (ttt) cc_final: 0.7909 (ttt) REVERT: C 638 MET cc_start: 0.7896 (mtt) cc_final: 0.7606 (mtt) REVERT: C 677 HIS cc_start: 0.8605 (m-70) cc_final: 0.8131 (m90) REVERT: C 684 VAL cc_start: 0.8579 (t) cc_final: 0.8335 (p) REVERT: C 799 ARG cc_start: 0.7702 (ttm110) cc_final: 0.7267 (ttm-80) REVERT: C 814 ASN cc_start: 0.6834 (m-40) cc_final: 0.6307 (t0) REVERT: C 839 ASP cc_start: 0.7682 (m-30) cc_final: 0.7465 (m-30) REVERT: C 1045 ASP cc_start: 0.6811 (m-30) cc_final: 0.6252 (t0) REVERT: D 11 LYS cc_start: 0.8334 (tttt) cc_final: 0.7865 (tttt) REVERT: D 154 GLU cc_start: 0.6274 (mt-10) cc_final: 0.5919 (mt-10) REVERT: D 260 ARG cc_start: 0.8399 (ttm170) cc_final: 0.8146 (ttm-80) REVERT: D 303 ARG cc_start: 0.7377 (mmt180) cc_final: 0.6966 (tpt90) REVERT: D 351 LYS cc_start: 0.8380 (mmtt) cc_final: 0.8136 (mptt) REVERT: D 432 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7022 (mp0) REVERT: D 510 VAL cc_start: 0.9061 (OUTLIER) cc_final: 0.8574 (p) REVERT: D 609 TYR cc_start: 0.8129 (t80) cc_final: 0.7890 (t80) REVERT: D 668 VAL cc_start: 0.7580 (p) cc_final: 0.7343 (p) REVERT: D 690 GLN cc_start: 0.5328 (OUTLIER) cc_final: 0.4943 (tm-30) REVERT: D 789 LYS cc_start: 0.7306 (tttt) cc_final: 0.7073 (ttmm) REVERT: D 835 GLU cc_start: 0.6314 (tp30) cc_final: 0.6058 (pt0) REVERT: D 1053 LYS cc_start: 0.8458 (tttt) cc_final: 0.7972 (ttmm) REVERT: D 1188 LYS cc_start: 0.8114 (mttt) cc_final: 0.7727 (mtpp) REVERT: E 57 GLN cc_start: 0.3776 (OUTLIER) cc_final: 0.3159 (mm110) REVERT: E 78 LEU cc_start: 0.5938 (OUTLIER) cc_final: 0.5736 (mm) REVERT: F 25 LYS cc_start: 0.8348 (mttm) cc_final: 0.7886 (mptt) REVERT: F 31 ASP cc_start: 0.7714 (t70) cc_final: 0.7501 (t70) REVERT: F 32 GLU cc_start: 0.7147 (tt0) cc_final: 0.6706 (tt0) REVERT: G 29 GLN cc_start: 0.7102 (mm-40) cc_final: 0.6809 (tt0) REVERT: G 50 LYS cc_start: 0.8114 (tptt) cc_final: 0.7687 (tptp) REVERT: H 52 LYS cc_start: 0.6539 (mttt) cc_final: 0.4782 (ttpp) REVERT: H 56 HIS cc_start: 0.7277 (p90) cc_final: 0.6979 (p90) REVERT: H 144 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6597 (tt0) REVERT: H 198 MET cc_start: 0.8002 (mtp) cc_final: 0.7549 (mtp) REVERT: H 237 MET cc_start: 0.7672 (tpt) cc_final: 0.7385 (tpt) outliers start: 50 outliers final: 25 residues processed: 430 average time/residue: 0.2215 time to fit residues: 145.7332 Evaluate side-chains 344 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 315 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 852 GLU Chi-restraints excluded: chain C residue 859 LEU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 920 HIS Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1103 THR Chi-restraints excluded: chain C residue 1132 MET Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 690 GLN Chi-restraints excluded: chain D residue 730 ILE Chi-restraints excluded: chain E residue 57 GLN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 243 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 322 optimal weight: 10.0000 chunk 273 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 237 optimal weight: 20.0000 chunk 276 optimal weight: 8.9990 chunk 196 optimal weight: 0.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 472 GLN D 218 ASN D 675 GLN D 744 ASN D 897 ASN ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.167494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.130150 restraints weight = 32364.837| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.68 r_work: 0.3219 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 27891 Z= 0.189 Angle : 0.579 21.591 38020 Z= 0.308 Chirality : 0.045 0.283 4285 Planarity : 0.005 0.186 4689 Dihedral : 16.608 142.649 4443 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.77 % Favored : 98.20 % Rotamer: Outliers : 2.73 % Allowed : 13.67 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.15), residues: 3214 helix: 1.22 (0.14), residues: 1286 sheet: 0.49 (0.27), residues: 376 loop : 0.34 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 910 TYR 0.025 0.002 TYR C1098 PHE 0.021 0.002 PHE G 47 TRP 0.012 0.001 TRP C 765 HIS 0.006 0.001 HIS D 785 Details of bonding type rmsd covalent geometry : bond 0.00451 (27891) covalent geometry : angle 0.57930 (38020) hydrogen bonds : bond 0.04391 ( 1256) hydrogen bonds : angle 4.87000 ( 3465) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 331 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7259 (pt0) REVERT: A 54 LYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6676 (mtpt) REVERT: A 103 ASP cc_start: 0.6245 (p0) cc_final: 0.5487 (p0) REVERT: A 106 GLU cc_start: 0.6586 (mp0) cc_final: 0.6346 (mt-10) REVERT: A 126 LYS cc_start: 0.6555 (tttt) cc_final: 0.6089 (pttp) REVERT: B 80 MET cc_start: 0.8362 (mmt) cc_final: 0.8113 (mmt) REVERT: B 132 LYS cc_start: 0.7552 (ttmm) cc_final: 0.7313 (tttt) REVERT: C 47 GLU cc_start: 0.8056 (tt0) cc_final: 0.7766 (tt0) REVERT: C 51 ASP cc_start: 0.6486 (m-30) cc_final: 0.6064 (m-30) REVERT: C 84 ARG cc_start: 0.7161 (mtp180) cc_final: 0.6866 (mtp85) REVERT: C 116 PHE cc_start: 0.7321 (t80) cc_final: 0.7086 (t80) REVERT: C 165 ASN cc_start: 0.6322 (t0) cc_final: 0.6103 (t0) REVERT: C 178 ASP cc_start: 0.5792 (m-30) cc_final: 0.5352 (t0) REVERT: C 263 LYS cc_start: 0.7734 (mmmt) cc_final: 0.6248 (mmmt) REVERT: C 419 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7800 (m-80) REVERT: C 458 LYS cc_start: 0.8006 (tttt) cc_final: 0.7766 (tttp) REVERT: C 500 MET cc_start: 0.4048 (tpt) cc_final: 0.3279 (mmm) REVERT: C 504 ASP cc_start: 0.8049 (m-30) cc_final: 0.7692 (m-30) REVERT: C 638 MET cc_start: 0.7785 (mtt) cc_final: 0.7552 (mtt) REVERT: C 793 GLU cc_start: 0.7385 (pt0) cc_final: 0.6986 (pt0) REVERT: C 799 ARG cc_start: 0.7693 (ttm110) cc_final: 0.7391 (ttm-80) REVERT: C 802 LYS cc_start: 0.6983 (ptmm) cc_final: 0.6781 (pttp) REVERT: C 814 ASN cc_start: 0.6777 (m-40) cc_final: 0.6357 (t0) REVERT: C 839 ASP cc_start: 0.7709 (m-30) cc_final: 0.7477 (m-30) REVERT: C 978 MET cc_start: 0.9161 (tpt) cc_final: 0.8855 (tpt) REVERT: C 1045 ASP cc_start: 0.6869 (m-30) cc_final: 0.6335 (t0) REVERT: D 11 LYS cc_start: 0.8327 (tttt) cc_final: 0.7948 (tttm) REVERT: D 154 GLU cc_start: 0.6257 (mt-10) cc_final: 0.5838 (mt-10) REVERT: D 260 ARG cc_start: 0.8374 (ttm170) cc_final: 0.7930 (mtp85) REVERT: D 319 MET cc_start: 0.8230 (mtp) cc_final: 0.7977 (mtp) REVERT: D 351 LYS cc_start: 0.8501 (mmtt) cc_final: 0.8182 (mptt) REVERT: D 432 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7209 (mp0) REVERT: D 451 ASP cc_start: 0.8223 (p0) cc_final: 0.7779 (p0) REVERT: D 471 MET cc_start: 0.8616 (mmm) cc_final: 0.8381 (mmp) REVERT: D 789 LYS cc_start: 0.7418 (tttt) cc_final: 0.7104 (ttmm) REVERT: D 835 GLU cc_start: 0.6465 (tp30) cc_final: 0.6176 (pt0) REVERT: D 1053 LYS cc_start: 0.8465 (tttt) cc_final: 0.7924 (ttmm) REVERT: D 1109 GLU cc_start: 0.6119 (tp30) cc_final: 0.5655 (tm-30) REVERT: D 1188 LYS cc_start: 0.8226 (mttt) cc_final: 0.7728 (mtpp) REVERT: E 78 LEU cc_start: 0.6045 (OUTLIER) cc_final: 0.5776 (mp) REVERT: F 25 LYS cc_start: 0.8311 (mttm) cc_final: 0.8057 (mttt) REVERT: F 32 GLU cc_start: 0.7256 (tt0) cc_final: 0.6861 (tt0) REVERT: G 29 GLN cc_start: 0.7198 (mm-40) cc_final: 0.6917 (mp10) REVERT: G 50 LYS cc_start: 0.8090 (tptt) cc_final: 0.7742 (tptp) REVERT: H 52 LYS cc_start: 0.6804 (mttt) cc_final: 0.4837 (ttpt) REVERT: H 56 HIS cc_start: 0.7191 (p90) cc_final: 0.6785 (p90) REVERT: H 144 GLU cc_start: 0.7561 (mt-10) cc_final: 0.6976 (tt0) REVERT: H 195 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7639 (mt-10) REVERT: H 198 MET cc_start: 0.8215 (mtp) cc_final: 0.7767 (mtp) REVERT: H 202 LYS cc_start: 0.7347 (OUTLIER) cc_final: 0.7101 (tptt) REVERT: H 237 MET cc_start: 0.7540 (tpt) cc_final: 0.7266 (tpt) REVERT: H 251 GLN cc_start: 0.5870 (mt0) cc_final: 0.5611 (mt0) outliers start: 77 outliers final: 42 residues processed: 391 average time/residue: 0.2218 time to fit residues: 134.3897 Evaluate side-chains 336 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 290 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 419 PHE Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 852 GLU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1132 MET Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 552 GLU Chi-restraints excluded: chain D residue 730 ILE Chi-restraints excluded: chain D residue 864 ILE Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1064 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain H residue 202 LYS Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 228 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 201 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 275 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 167 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 99 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN C 575 GLN C 598 ASN C1042 HIS D 218 ASN D 703 ASN D 744 ASN D 785 HIS ** D 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.169729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.132461 restraints weight = 32319.448| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.68 r_work: 0.3253 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27891 Z= 0.125 Angle : 0.512 20.421 38020 Z= 0.272 Chirality : 0.042 0.285 4285 Planarity : 0.005 0.183 4689 Dihedral : 16.440 139.559 4443 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.37 % Favored : 98.60 % Rotamer: Outliers : 2.02 % Allowed : 14.88 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.15), residues: 3214 helix: 1.48 (0.14), residues: 1283 sheet: 0.47 (0.26), residues: 395 loop : 0.44 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 644 TYR 0.018 0.001 TYR C1098 PHE 0.017 0.001 PHE G 47 TRP 0.011 0.001 TRP C 765 HIS 0.004 0.001 HIS D 785 Details of bonding type rmsd covalent geometry : bond 0.00289 (27891) covalent geometry : angle 0.51244 (38020) hydrogen bonds : bond 0.03733 ( 1256) hydrogen bonds : angle 4.62235 ( 3465) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 322 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7238 (pt0) REVERT: A 103 ASP cc_start: 0.6148 (p0) cc_final: 0.5308 (p0) REVERT: A 106 GLU cc_start: 0.6547 (mp0) cc_final: 0.6184 (mt-10) REVERT: A 174 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7494 (mm-30) REVERT: B 132 LYS cc_start: 0.7667 (ttmm) cc_final: 0.7345 (tttt) REVERT: C 47 GLU cc_start: 0.7814 (tt0) cc_final: 0.7576 (tt0) REVERT: C 51 ASP cc_start: 0.6374 (m-30) cc_final: 0.6000 (m-30) REVERT: C 84 ARG cc_start: 0.7283 (mtp180) cc_final: 0.6867 (mtm-85) REVERT: C 116 PHE cc_start: 0.7364 (t80) cc_final: 0.7098 (t80) REVERT: C 178 ASP cc_start: 0.5778 (m-30) cc_final: 0.5354 (t0) REVERT: C 263 LYS cc_start: 0.7660 (mmmt) cc_final: 0.6377 (mmmt) REVERT: C 458 LYS cc_start: 0.8051 (tttt) cc_final: 0.7761 (tttp) REVERT: C 500 MET cc_start: 0.4067 (tpt) cc_final: 0.3278 (mmm) REVERT: C 504 ASP cc_start: 0.8212 (m-30) cc_final: 0.7830 (m-30) REVERT: C 579 LYS cc_start: 0.6852 (mtpt) cc_final: 0.6532 (mmtt) REVERT: C 607 MET cc_start: 0.7988 (mmp) cc_final: 0.7566 (mmp) REVERT: C 638 MET cc_start: 0.7565 (mtt) cc_final: 0.7291 (mtt) REVERT: C 752 MET cc_start: 0.8252 (tpp) cc_final: 0.7907 (tpp) REVERT: C 793 GLU cc_start: 0.7381 (pt0) cc_final: 0.6995 (pt0) REVERT: C 799 ARG cc_start: 0.7665 (ttm110) cc_final: 0.7353 (ttm-80) REVERT: C 814 ASN cc_start: 0.6908 (m-40) cc_final: 0.6431 (t0) REVERT: C 839 ASP cc_start: 0.7695 (m-30) cc_final: 0.7398 (m-30) REVERT: C 1045 ASP cc_start: 0.6922 (m-30) cc_final: 0.6425 (t0) REVERT: D 11 LYS cc_start: 0.8222 (tttt) cc_final: 0.7891 (tttm) REVERT: D 154 GLU cc_start: 0.6385 (mt-10) cc_final: 0.5821 (mt-10) REVERT: D 260 ARG cc_start: 0.8283 (ttm170) cc_final: 0.7880 (mtp85) REVERT: D 351 LYS cc_start: 0.8441 (mmtt) cc_final: 0.8120 (mptt) REVERT: D 432 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7184 (mp0) REVERT: D 451 ASP cc_start: 0.8216 (p0) cc_final: 0.7851 (p0) REVERT: D 471 MET cc_start: 0.8610 (mmm) cc_final: 0.8350 (mmp) REVERT: D 739 ARG cc_start: 0.6968 (mmt90) cc_final: 0.6737 (mmm-85) REVERT: D 789 LYS cc_start: 0.7227 (tttt) cc_final: 0.6925 (ttmm) REVERT: D 835 GLU cc_start: 0.6403 (tp30) cc_final: 0.6186 (pt0) REVERT: D 1053 LYS cc_start: 0.8425 (tttt) cc_final: 0.7816 (ttmm) REVERT: D 1109 GLU cc_start: 0.5911 (tp30) cc_final: 0.5480 (tm-30) REVERT: D 1181 MET cc_start: 0.8988 (mmm) cc_final: 0.8714 (mmm) REVERT: D 1188 LYS cc_start: 0.8165 (mttt) cc_final: 0.7732 (mtpp) REVERT: E 78 LEU cc_start: 0.5955 (OUTLIER) cc_final: 0.5318 (mm) REVERT: F 25 LYS cc_start: 0.8268 (mttm) cc_final: 0.7826 (mptt) REVERT: F 32 GLU cc_start: 0.7095 (tt0) cc_final: 0.6734 (tt0) REVERT: G 29 GLN cc_start: 0.7307 (mm-40) cc_final: 0.6968 (mp10) REVERT: G 50 LYS cc_start: 0.7946 (tptt) cc_final: 0.7638 (tptp) REVERT: H 52 LYS cc_start: 0.6756 (mttt) cc_final: 0.4757 (ttpt) REVERT: H 56 HIS cc_start: 0.7121 (p90) cc_final: 0.6738 (p90) REVERT: H 144 GLU cc_start: 0.7526 (mt-10) cc_final: 0.6996 (tt0) REVERT: H 198 MET cc_start: 0.8213 (mtp) cc_final: 0.7668 (mtp) REVERT: H 237 MET cc_start: 0.7841 (tpt) cc_final: 0.7506 (tpt) REVERT: H 251 GLN cc_start: 0.5824 (mt0) cc_final: 0.5584 (mt0) outliers start: 57 outliers final: 36 residues processed: 369 average time/residue: 0.1899 time to fit residues: 108.3761 Evaluate side-chains 332 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 295 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 529 SER Chi-restraints excluded: chain C residue 797 GLU Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 852 GLU Chi-restraints excluded: chain C residue 859 LEU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1132 MET Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 824 THR Chi-restraints excluded: chain D residue 864 ILE Chi-restraints excluded: chain D residue 1044 LEU Chi-restraints excluded: chain D residue 1099 ASP Chi-restraints excluded: chain E residue 25 ASN Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 239 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 14 optimal weight: 6.9990 chunk 316 optimal weight: 9.9990 chunk 291 optimal weight: 9.9990 chunk 136 optimal weight: 10.0000 chunk 138 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 202 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 724 ASN D 218 ASN D 744 ASN ** D 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.165835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.127892 restraints weight = 32435.170| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.70 r_work: 0.3211 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 27891 Z= 0.220 Angle : 0.595 23.931 38020 Z= 0.313 Chirality : 0.045 0.271 4285 Planarity : 0.005 0.190 4689 Dihedral : 16.492 139.140 4443 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.21 % Favored : 97.76 % Rotamer: Outliers : 2.59 % Allowed : 15.41 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.15), residues: 3214 helix: 1.19 (0.14), residues: 1277 sheet: 0.36 (0.26), residues: 387 loop : 0.21 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 752 TYR 0.026 0.002 TYR C1098 PHE 0.024 0.002 PHE D 654 TRP 0.012 0.001 TRP A 199 HIS 0.006 0.001 HIS D 785 Details of bonding type rmsd covalent geometry : bond 0.00533 (27891) covalent geometry : angle 0.59475 (38020) hydrogen bonds : bond 0.04357 ( 1256) hydrogen bonds : angle 4.80620 ( 3465) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 316 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7245 (pt0) REVERT: A 103 ASP cc_start: 0.6409 (p0) cc_final: 0.5489 (p0) REVERT: A 126 LYS cc_start: 0.6631 (tttm) cc_final: 0.6187 (pttp) REVERT: A 174 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7542 (mm-30) REVERT: B 132 LYS cc_start: 0.7875 (ttmm) cc_final: 0.7487 (tttt) REVERT: B 140 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8256 (mt) REVERT: B 146 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7958 (mtp85) REVERT: C 51 ASP cc_start: 0.6373 (m-30) cc_final: 0.5979 (m-30) REVERT: C 178 ASP cc_start: 0.5677 (m-30) cc_final: 0.5464 (t0) REVERT: C 263 LYS cc_start: 0.7360 (mmmt) cc_final: 0.6370 (mmmt) REVERT: C 458 LYS cc_start: 0.7942 (tttt) cc_final: 0.7668 (tttp) REVERT: C 500 MET cc_start: 0.4599 (tpt) cc_final: 0.3778 (mmm) REVERT: C 504 ASP cc_start: 0.8157 (m-30) cc_final: 0.7659 (m-30) REVERT: C 579 LYS cc_start: 0.6823 (mtpt) cc_final: 0.6549 (mmtm) REVERT: C 602 MET cc_start: 0.7733 (mtt) cc_final: 0.7139 (mtt) REVERT: C 638 MET cc_start: 0.7655 (mtt) cc_final: 0.7423 (mtt) REVERT: C 793 GLU cc_start: 0.7505 (pt0) cc_final: 0.7114 (pt0) REVERT: C 814 ASN cc_start: 0.6691 (m-40) cc_final: 0.6290 (t0) REVERT: C 839 ASP cc_start: 0.7748 (m-30) cc_final: 0.7486 (m-30) REVERT: C 1045 ASP cc_start: 0.6979 (m-30) cc_final: 0.6473 (t0) REVERT: D 10 MET cc_start: 0.8166 (ttm) cc_final: 0.7965 (ttt) REVERT: D 11 LYS cc_start: 0.8321 (tttt) cc_final: 0.8004 (tttm) REVERT: D 260 ARG cc_start: 0.8349 (ttm170) cc_final: 0.7959 (mtp85) REVERT: D 351 LYS cc_start: 0.8555 (mmtt) cc_final: 0.8227 (mptt) REVERT: D 432 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7162 (mp0) REVERT: D 471 MET cc_start: 0.8677 (mmm) cc_final: 0.8422 (mmp) REVERT: D 622 LYS cc_start: 0.7802 (mmmt) cc_final: 0.7550 (mmmt) REVERT: D 647 MET cc_start: 0.7820 (ttm) cc_final: 0.7598 (ttm) REVERT: D 754 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6635 (pp) REVERT: D 789 LYS cc_start: 0.7509 (tttt) cc_final: 0.7199 (ttmm) REVERT: D 1053 LYS cc_start: 0.8434 (tttt) cc_final: 0.7857 (ttmm) REVERT: D 1109 GLU cc_start: 0.6128 (tp30) cc_final: 0.5686 (tm-30) REVERT: D 1181 MET cc_start: 0.9066 (mmm) cc_final: 0.8808 (mmm) REVERT: D 1188 LYS cc_start: 0.8072 (mttt) cc_final: 0.7700 (mtpp) REVERT: E 78 LEU cc_start: 0.6024 (OUTLIER) cc_final: 0.5646 (mm) REVERT: F 32 GLU cc_start: 0.7156 (tt0) cc_final: 0.6752 (tt0) REVERT: G 27 GLU cc_start: 0.8001 (tp30) cc_final: 0.7684 (tp30) REVERT: G 29 GLN cc_start: 0.7552 (mm-40) cc_final: 0.7220 (mp10) REVERT: G 50 LYS cc_start: 0.7966 (tptt) cc_final: 0.7640 (tptp) REVERT: H 52 LYS cc_start: 0.6960 (mttt) cc_final: 0.4751 (ttpt) REVERT: H 56 HIS cc_start: 0.7271 (p90) cc_final: 0.6896 (p90) REVERT: H 144 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7000 (tt0) REVERT: H 198 MET cc_start: 0.8284 (mtp) cc_final: 0.7734 (mtp) REVERT: H 237 MET cc_start: 0.7715 (tpt) cc_final: 0.7454 (tpt) REVERT: H 251 GLN cc_start: 0.5815 (mt0) cc_final: 0.5595 (mt0) outliers start: 73 outliers final: 52 residues processed: 376 average time/residue: 0.2111 time to fit residues: 122.8061 Evaluate side-chains 351 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 295 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 280 HIS Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 401 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 529 SER Chi-restraints excluded: chain C residue 650 MET Chi-restraints excluded: chain C residue 797 GLU Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 852 GLU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 964 SER Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1132 MET Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 730 ILE Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 824 THR Chi-restraints excluded: chain D residue 864 ILE Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1044 LEU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 239 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 246 optimal weight: 3.9990 chunk 93 optimal weight: 0.0670 chunk 35 optimal weight: 9.9990 chunk 278 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 214 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 300 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 465 GLN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 GLN D 218 ASN D 744 ASN D 785 HIS ** D 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1101 HIS ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.170608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.132342 restraints weight = 32243.206| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.69 r_work: 0.3308 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 27891 Z= 0.103 Angle : 0.491 21.644 38020 Z= 0.261 Chirality : 0.041 0.283 4285 Planarity : 0.005 0.184 4689 Dihedral : 16.316 135.593 4443 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.59 % Favored : 98.38 % Rotamer: Outliers : 2.13 % Allowed : 16.41 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.15), residues: 3214 helix: 1.60 (0.14), residues: 1271 sheet: 0.39 (0.26), residues: 409 loop : 0.42 (0.16), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 644 TYR 0.023 0.001 TYR A 178 PHE 0.018 0.001 PHE D 155 TRP 0.014 0.001 TRP C 765 HIS 0.008 0.001 HIS D1101 Details of bonding type rmsd covalent geometry : bond 0.00229 (27891) covalent geometry : angle 0.49126 (38020) hydrogen bonds : bond 0.03396 ( 1256) hydrogen bonds : angle 4.49100 ( 3465) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 333 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7180 (pt0) REVERT: A 87 LEU cc_start: 0.8631 (mp) cc_final: 0.8232 (mt) REVERT: A 103 ASP cc_start: 0.6285 (p0) cc_final: 0.5518 (p0) REVERT: A 174 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7429 (mm-30) REVERT: B 132 LYS cc_start: 0.7791 (ttmm) cc_final: 0.7384 (tttt) REVERT: B 140 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8058 (mt) REVERT: C 51 ASP cc_start: 0.6280 (m-30) cc_final: 0.5919 (m-30) REVERT: C 178 ASP cc_start: 0.5641 (m-30) cc_final: 0.5245 (t0) REVERT: C 263 LYS cc_start: 0.7535 (mmmt) cc_final: 0.6302 (mmmt) REVERT: C 500 MET cc_start: 0.4458 (tpt) cc_final: 0.3609 (mmm) REVERT: C 504 ASP cc_start: 0.8121 (m-30) cc_final: 0.7641 (m-30) REVERT: C 590 GLU cc_start: 0.6583 (pm20) cc_final: 0.6108 (tt0) REVERT: C 602 MET cc_start: 0.7676 (mtt) cc_final: 0.7330 (mtt) REVERT: C 638 MET cc_start: 0.7509 (mtt) cc_final: 0.7242 (mtt) REVERT: C 748 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8161 (tt0) REVERT: C 752 MET cc_start: 0.8272 (tpp) cc_final: 0.7914 (tpp) REVERT: C 793 GLU cc_start: 0.7365 (pt0) cc_final: 0.7009 (pt0) REVERT: C 799 ARG cc_start: 0.7631 (ttm110) cc_final: 0.7096 (ttm110) REVERT: C 814 ASN cc_start: 0.6469 (m-40) cc_final: 0.6153 (t0) REVERT: C 839 ASP cc_start: 0.7645 (m-30) cc_final: 0.7354 (m-30) REVERT: C 1045 ASP cc_start: 0.6961 (m-30) cc_final: 0.6443 (t0) REVERT: D 10 MET cc_start: 0.8096 (ttm) cc_final: 0.7893 (ttt) REVERT: D 138 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7180 (m-30) REVERT: D 260 ARG cc_start: 0.8221 (ttm170) cc_final: 0.7823 (mtp85) REVERT: D 303 ARG cc_start: 0.8041 (tpt170) cc_final: 0.7573 (tpt90) REVERT: D 351 LYS cc_start: 0.8427 (mmtt) cc_final: 0.8082 (mptt) REVERT: D 388 SER cc_start: 0.8140 (m) cc_final: 0.7891 (t) REVERT: D 432 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7135 (mp0) REVERT: D 451 ASP cc_start: 0.8246 (p0) cc_final: 0.7827 (p0) REVERT: D 471 MET cc_start: 0.8668 (mmm) cc_final: 0.8375 (mmp) REVERT: D 642 MET cc_start: 0.7902 (mtp) cc_final: 0.7676 (mmm) REVERT: D 693 ARG cc_start: 0.4435 (OUTLIER) cc_final: 0.3448 (ptm160) REVERT: D 789 LYS cc_start: 0.7234 (tttt) cc_final: 0.6942 (ttmm) REVERT: D 1053 LYS cc_start: 0.8390 (tttt) cc_final: 0.7923 (ttmm) REVERT: D 1109 GLU cc_start: 0.5971 (tp30) cc_final: 0.5568 (tm-30) REVERT: D 1188 LYS cc_start: 0.7852 (mttt) cc_final: 0.7480 (mtpp) REVERT: F 8 GLN cc_start: 0.7621 (mt0) cc_final: 0.7318 (mt0) REVERT: F 25 LYS cc_start: 0.8098 (mttm) cc_final: 0.7631 (mptt) REVERT: F 31 ASP cc_start: 0.7713 (t70) cc_final: 0.7369 (t70) REVERT: F 32 GLU cc_start: 0.7029 (tt0) cc_final: 0.6580 (tt0) REVERT: G 29 GLN cc_start: 0.7335 (mm-40) cc_final: 0.7031 (mp10) REVERT: H 52 LYS cc_start: 0.6847 (mttt) cc_final: 0.4694 (ttpt) REVERT: H 56 HIS cc_start: 0.7210 (p90) cc_final: 0.6847 (p90) REVERT: H 144 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7045 (tt0) REVERT: H 198 MET cc_start: 0.8199 (mtp) cc_final: 0.7632 (mtp) REVERT: H 237 MET cc_start: 0.7727 (tpt) cc_final: 0.7494 (tpt) REVERT: H 252 GLU cc_start: 0.6365 (pt0) cc_final: 0.6103 (pt0) outliers start: 60 outliers final: 47 residues processed: 383 average time/residue: 0.2087 time to fit residues: 124.0580 Evaluate side-chains 354 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 303 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 280 HIS Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 401 ASP Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 529 SER Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 650 MET Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 797 GLU Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 852 GLU Chi-restraints excluded: chain C residue 859 LEU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1132 MET Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 693 ARG Chi-restraints excluded: chain D residue 730 ILE Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 864 ILE Chi-restraints excluded: chain D residue 1044 LEU Chi-restraints excluded: chain E residue 25 ASN Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 239 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 32 optimal weight: 8.9990 chunk 171 optimal weight: 4.9990 chunk 200 optimal weight: 5.9990 chunk 322 optimal weight: 10.0000 chunk 239 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 chunk 232 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 253 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 188 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 465 GLN C 598 ASN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 ASN D1101 HIS ** H 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.166408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.128843 restraints weight = 32264.066| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.69 r_work: 0.3273 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 27891 Z= 0.191 Angle : 0.573 26.953 38020 Z= 0.300 Chirality : 0.044 0.264 4285 Planarity : 0.005 0.197 4689 Dihedral : 16.354 136.653 4443 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.30 % Favored : 97.67 % Rotamer: Outliers : 2.81 % Allowed : 15.98 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.15), residues: 3214 helix: 1.36 (0.14), residues: 1272 sheet: 0.39 (0.26), residues: 384 loop : 0.26 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 644 TYR 0.024 0.002 TYR C1098 PHE 0.021 0.002 PHE D 654 TRP 0.012 0.001 TRP C 765 HIS 0.008 0.001 HIS D1101 Details of bonding type rmsd covalent geometry : bond 0.00464 (27891) covalent geometry : angle 0.57285 (38020) hydrogen bonds : bond 0.04125 ( 1256) hydrogen bonds : angle 4.70318 ( 3465) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 309 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7328 (pt0) REVERT: A 126 LYS cc_start: 0.6664 (tttm) cc_final: 0.6422 (pttp) REVERT: A 174 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7509 (mm-30) REVERT: B 132 LYS cc_start: 0.7777 (ttmm) cc_final: 0.7454 (tttt) REVERT: B 140 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8240 (mt) REVERT: C 51 ASP cc_start: 0.6281 (m-30) cc_final: 0.5905 (m-30) REVERT: C 178 ASP cc_start: 0.5706 (m-30) cc_final: 0.5424 (t0) REVERT: C 263 LYS cc_start: 0.7535 (mmmt) cc_final: 0.7191 (mmmm) REVERT: C 396 TYR cc_start: 0.5909 (OUTLIER) cc_final: 0.5558 (m-80) REVERT: C 500 MET cc_start: 0.4695 (tpt) cc_final: 0.4009 (mmm) REVERT: C 504 ASP cc_start: 0.8104 (m-30) cc_final: 0.7623 (m-30) REVERT: C 602 MET cc_start: 0.7683 (mtt) cc_final: 0.7222 (mtt) REVERT: C 638 MET cc_start: 0.7623 (mtt) cc_final: 0.7374 (mtt) REVERT: C 748 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8155 (tt0) REVERT: C 793 GLU cc_start: 0.7399 (pt0) cc_final: 0.7027 (pt0) REVERT: C 839 ASP cc_start: 0.7710 (m-30) cc_final: 0.7457 (m-30) REVERT: C 1045 ASP cc_start: 0.6956 (m-30) cc_final: 0.6490 (t0) REVERT: D 56 LYS cc_start: 0.8217 (tptp) cc_final: 0.7345 (ptpp) REVERT: D 154 GLU cc_start: 0.6385 (mt-10) cc_final: 0.6142 (mt-10) REVERT: D 162 TYR cc_start: 0.6010 (m-80) cc_final: 0.5739 (m-80) REVERT: D 260 ARG cc_start: 0.8272 (ttm170) cc_final: 0.7902 (mtp85) REVERT: D 303 ARG cc_start: 0.8078 (tpt170) cc_final: 0.7300 (tpp80) REVERT: D 351 LYS cc_start: 0.8552 (mmtt) cc_final: 0.8192 (mptt) REVERT: D 432 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7147 (mp0) REVERT: D 471 MET cc_start: 0.8668 (mmm) cc_final: 0.8359 (mmp) REVERT: D 693 ARG cc_start: 0.4873 (OUTLIER) cc_final: 0.3927 (ptm160) REVERT: D 754 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6670 (pp) REVERT: D 789 LYS cc_start: 0.7405 (tttt) cc_final: 0.7095 (ttmm) REVERT: D 835 GLU cc_start: 0.6573 (tp30) cc_final: 0.6285 (pt0) REVERT: D 957 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7095 (mt) REVERT: D 1053 LYS cc_start: 0.8510 (tttt) cc_final: 0.7891 (ttmm) REVERT: D 1109 GLU cc_start: 0.6272 (tp30) cc_final: 0.5837 (tm-30) REVERT: D 1188 LYS cc_start: 0.8001 (mttt) cc_final: 0.7617 (mtpp) REVERT: F 32 GLU cc_start: 0.7135 (tt0) cc_final: 0.6734 (tt0) REVERT: G 10 HIS cc_start: 0.8705 (OUTLIER) cc_final: 0.8075 (m-70) REVERT: G 27 GLU cc_start: 0.7951 (tp30) cc_final: 0.7684 (tp30) REVERT: G 29 GLN cc_start: 0.7548 (mm-40) cc_final: 0.7260 (mp10) REVERT: H 52 LYS cc_start: 0.7030 (mttt) cc_final: 0.4776 (ttpt) REVERT: H 56 HIS cc_start: 0.7199 (p90) cc_final: 0.6850 (p90) REVERT: H 144 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7052 (tt0) REVERT: H 156 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.6451 (mpt) REVERT: H 182 ASP cc_start: 0.7766 (m-30) cc_final: 0.7460 (m-30) REVERT: H 198 MET cc_start: 0.8242 (mtp) cc_final: 0.7693 (mtp) REVERT: H 237 MET cc_start: 0.7786 (tpt) cc_final: 0.7553 (tpt) outliers start: 79 outliers final: 56 residues processed: 375 average time/residue: 0.2163 time to fit residues: 126.0364 Evaluate side-chains 356 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 292 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 23 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 280 HIS Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 401 ASP Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 529 SER Chi-restraints excluded: chain C residue 650 MET Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 797 GLU Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 852 GLU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1132 MET Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 693 ARG Chi-restraints excluded: chain D residue 730 ILE Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 957 LEU Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1044 LEU Chi-restraints excluded: chain D residue 1064 VAL Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain G residue 10 HIS Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 239 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 2 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 295 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 269 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 289 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 465 GLN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 ASN D 282 GLN D 785 HIS ** D 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1101 HIS ** H 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.168502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.131657 restraints weight = 32597.480| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.63 r_work: 0.3240 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27891 Z= 0.145 Angle : 0.534 26.055 38020 Z= 0.279 Chirality : 0.043 0.261 4285 Planarity : 0.005 0.195 4689 Dihedral : 16.287 134.986 4443 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.12 % Favored : 97.85 % Rotamer: Outliers : 2.73 % Allowed : 16.73 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.15), residues: 3214 helix: 1.47 (0.14), residues: 1272 sheet: 0.38 (0.26), residues: 379 loop : 0.30 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 644 TYR 0.020 0.001 TYR A 178 PHE 0.019 0.001 PHE D 155 TRP 0.013 0.001 TRP C 765 HIS 0.007 0.001 HIS D1101 Details of bonding type rmsd covalent geometry : bond 0.00346 (27891) covalent geometry : angle 0.53411 (38020) hydrogen bonds : bond 0.03738 ( 1256) hydrogen bonds : angle 4.59087 ( 3465) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 299 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7294 (pt0) REVERT: A 174 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7492 (mm-30) REVERT: B 132 LYS cc_start: 0.7776 (ttmm) cc_final: 0.7454 (tttt) REVERT: B 140 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8152 (mt) REVERT: C 178 ASP cc_start: 0.5695 (m-30) cc_final: 0.5430 (t0) REVERT: C 263 LYS cc_start: 0.7597 (mmmt) cc_final: 0.7184 (mmmm) REVERT: C 396 TYR cc_start: 0.5858 (OUTLIER) cc_final: 0.5539 (m-80) REVERT: C 419 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7538 (m-80) REVERT: C 500 MET cc_start: 0.4604 (tpt) cc_final: 0.3869 (mmm) REVERT: C 504 ASP cc_start: 0.8053 (m-30) cc_final: 0.7597 (m-30) REVERT: C 590 GLU cc_start: 0.6830 (pm20) cc_final: 0.6359 (tt0) REVERT: C 602 MET cc_start: 0.7711 (mtt) cc_final: 0.7314 (mtt) REVERT: C 638 MET cc_start: 0.7573 (mtt) cc_final: 0.7331 (mtt) REVERT: C 748 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: C 793 GLU cc_start: 0.7439 (pt0) cc_final: 0.7084 (pt0) REVERT: C 839 ASP cc_start: 0.7692 (m-30) cc_final: 0.7386 (m-30) REVERT: C 1045 ASP cc_start: 0.6904 (m-30) cc_final: 0.6509 (t0) REVERT: D 10 MET cc_start: 0.8097 (ttm) cc_final: 0.7873 (ttt) REVERT: D 56 LYS cc_start: 0.8227 (tptp) cc_final: 0.7465 (ptpp) REVERT: D 162 TYR cc_start: 0.5985 (m-80) cc_final: 0.5718 (m-80) REVERT: D 169 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7688 (mtpp) REVERT: D 260 ARG cc_start: 0.8189 (ttm170) cc_final: 0.7850 (mtp85) REVERT: D 303 ARG cc_start: 0.8062 (tpt170) cc_final: 0.7274 (tpp80) REVERT: D 351 LYS cc_start: 0.8494 (mmtt) cc_final: 0.8171 (mptt) REVERT: D 432 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7061 (mp0) REVERT: D 471 MET cc_start: 0.8632 (mmm) cc_final: 0.8285 (mmp) REVERT: D 693 ARG cc_start: 0.4681 (OUTLIER) cc_final: 0.3850 (ptm160) REVERT: D 754 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6625 (pp) REVERT: D 789 LYS cc_start: 0.7356 (tttt) cc_final: 0.7060 (ttmm) REVERT: D 835 GLU cc_start: 0.6665 (tp30) cc_final: 0.6366 (pt0) REVERT: D 957 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7052 (mt) REVERT: D 1053 LYS cc_start: 0.8524 (tttt) cc_final: 0.7940 (ttmm) REVERT: D 1109 GLU cc_start: 0.6091 (tp30) cc_final: 0.5717 (tm-30) REVERT: F 32 GLU cc_start: 0.7115 (tt0) cc_final: 0.6698 (tt0) REVERT: G 27 GLU cc_start: 0.7935 (tp30) cc_final: 0.7686 (tp30) REVERT: G 29 GLN cc_start: 0.7559 (mm-40) cc_final: 0.7286 (mp10) REVERT: H 52 LYS cc_start: 0.7044 (mttt) cc_final: 0.4779 (ttpt) REVERT: H 56 HIS cc_start: 0.7086 (p90) cc_final: 0.6463 (p90) REVERT: H 144 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7041 (tt0) REVERT: H 182 ASP cc_start: 0.7875 (m-30) cc_final: 0.7565 (m-30) REVERT: H 198 MET cc_start: 0.8099 (mtp) cc_final: 0.7591 (mtp) REVERT: H 252 GLU cc_start: 0.6267 (pt0) cc_final: 0.5846 (pt0) outliers start: 77 outliers final: 59 residues processed: 364 average time/residue: 0.2035 time to fit residues: 114.4126 Evaluate side-chains 354 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 287 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 23 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 280 HIS Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 401 ASP Chi-restraints excluded: chain C residue 419 PHE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 529 SER Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 650 MET Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 797 GLU Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 852 GLU Chi-restraints excluded: chain C residue 859 LEU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1132 MET Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 693 ARG Chi-restraints excluded: chain D residue 730 ILE Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 824 THR Chi-restraints excluded: chain D residue 900 HIS Chi-restraints excluded: chain D residue 957 LEU Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1044 LEU Chi-restraints excluded: chain D residue 1064 VAL Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 239 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 40 optimal weight: 10.0000 chunk 265 optimal weight: 8.9990 chunk 294 optimal weight: 7.9990 chunk 128 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 312 optimal weight: 0.4980 chunk 53 optimal weight: 9.9990 chunk 296 optimal weight: 9.9990 chunk 306 optimal weight: 4.9990 chunk 286 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 GLN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN D 218 ASN D 703 ASN ** D 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1101 HIS ** H 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.165969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.128820 restraints weight = 32780.553| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.66 r_work: 0.3214 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 27891 Z= 0.214 Angle : 0.604 27.201 38020 Z= 0.315 Chirality : 0.045 0.250 4285 Planarity : 0.005 0.197 4689 Dihedral : 16.350 136.458 4443 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.71 % Favored : 97.26 % Rotamer: Outliers : 2.66 % Allowed : 17.12 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.15), residues: 3214 helix: 1.20 (0.14), residues: 1273 sheet: 0.22 (0.26), residues: 379 loop : 0.11 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 644 TYR 0.040 0.002 TYR D1050 PHE 0.022 0.002 PHE D 654 TRP 0.012 0.001 TRP C 765 HIS 0.007 0.001 HIS D1101 Details of bonding type rmsd covalent geometry : bond 0.00520 (27891) covalent geometry : angle 0.60434 (38020) hydrogen bonds : bond 0.04290 ( 1256) hydrogen bonds : angle 4.78715 ( 3465) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 293 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7326 (pt0) REVERT: A 174 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7516 (mm-30) REVERT: B 132 LYS cc_start: 0.7805 (ttmm) cc_final: 0.7476 (tttt) REVERT: B 146 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7756 (mtp85) REVERT: C 263 LYS cc_start: 0.7598 (mmmt) cc_final: 0.7259 (mmmm) REVERT: C 500 MET cc_start: 0.4900 (tpt) cc_final: 0.4048 (mmm) REVERT: C 504 ASP cc_start: 0.8162 (m-30) cc_final: 0.7626 (m-30) REVERT: C 590 GLU cc_start: 0.6700 (pm20) cc_final: 0.6173 (tt0) REVERT: C 638 MET cc_start: 0.7621 (mtt) cc_final: 0.7382 (mtt) REVERT: C 748 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8096 (tt0) REVERT: C 752 MET cc_start: 0.8314 (tpp) cc_final: 0.7936 (tpp) REVERT: C 793 GLU cc_start: 0.7687 (pt0) cc_final: 0.7341 (pt0) REVERT: C 839 ASP cc_start: 0.7708 (m-30) cc_final: 0.7388 (m-30) REVERT: C 840 ILE cc_start: 0.8451 (mm) cc_final: 0.8109 (tp) REVERT: C 852 GLU cc_start: 0.3943 (OUTLIER) cc_final: 0.3285 (pm20) REVERT: C 1045 ASP cc_start: 0.6888 (m-30) cc_final: 0.6501 (t0) REVERT: D 56 LYS cc_start: 0.8436 (tptp) cc_final: 0.7607 (ptpp) REVERT: D 162 TYR cc_start: 0.5985 (m-80) cc_final: 0.5735 (m-80) REVERT: D 169 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7738 (mtpp) REVERT: D 260 ARG cc_start: 0.8244 (ttm170) cc_final: 0.7882 (mtp85) REVERT: D 303 ARG cc_start: 0.8112 (tpt170) cc_final: 0.7316 (tpp80) REVERT: D 351 LYS cc_start: 0.8583 (mmtt) cc_final: 0.8234 (mptt) REVERT: D 432 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7102 (mp0) REVERT: D 471 MET cc_start: 0.8684 (mmm) cc_final: 0.8353 (mmp) REVERT: D 693 ARG cc_start: 0.5232 (OUTLIER) cc_final: 0.4374 (ptm160) REVERT: D 754 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6525 (pp) REVERT: D 789 LYS cc_start: 0.7473 (tttt) cc_final: 0.7150 (ttmm) REVERT: D 835 GLU cc_start: 0.6504 (tp30) cc_final: 0.6290 (pt0) REVERT: D 1053 LYS cc_start: 0.8497 (tttt) cc_final: 0.7898 (ttmm) REVERT: F 32 GLU cc_start: 0.7225 (tt0) cc_final: 0.6828 (tt0) REVERT: G 10 HIS cc_start: 0.8687 (OUTLIER) cc_final: 0.8158 (m-70) REVERT: G 27 GLU cc_start: 0.8004 (tp30) cc_final: 0.7782 (tp30) REVERT: G 29 GLN cc_start: 0.7748 (mm-40) cc_final: 0.7440 (mm110) REVERT: H 52 LYS cc_start: 0.7177 (mttt) cc_final: 0.4914 (ttpt) REVERT: H 56 HIS cc_start: 0.7117 (p90) cc_final: 0.6486 (p90) REVERT: H 94 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7548 (mm-30) REVERT: H 123 SER cc_start: 0.8851 (t) cc_final: 0.8558 (p) REVERT: H 144 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7133 (tt0) REVERT: H 156 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.6413 (mpt) REVERT: H 182 ASP cc_start: 0.7954 (m-30) cc_final: 0.7650 (m-30) REVERT: H 198 MET cc_start: 0.8078 (mtp) cc_final: 0.7630 (mtp) REVERT: H 237 MET cc_start: 0.7577 (tpt) cc_final: 0.7284 (tpt) outliers start: 75 outliers final: 60 residues processed: 356 average time/residue: 0.1866 time to fit residues: 103.6633 Evaluate side-chains 353 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 285 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 23 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 280 HIS Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 401 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 529 SER Chi-restraints excluded: chain C residue 650 MET Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 797 GLU Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 852 GLU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1132 MET Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 693 ARG Chi-restraints excluded: chain D residue 730 ILE Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 824 THR Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1044 LEU Chi-restraints excluded: chain D residue 1064 VAL Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 10 HIS Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 158 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 311 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 318 optimal weight: 10.0000 chunk 312 optimal weight: 0.9990 chunk 247 optimal weight: 9.9990 chunk 175 optimal weight: 7.9990 chunk 204 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 250 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 157 ASN C 465 GLN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 ASN ** D 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1101 HIS ** H 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.167174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.130405 restraints weight = 32659.882| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.64 r_work: 0.3242 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27891 Z= 0.172 Angle : 0.566 24.039 38020 Z= 0.297 Chirality : 0.044 0.229 4285 Planarity : 0.005 0.189 4689 Dihedral : 16.299 134.986 4443 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.40 % Favored : 97.57 % Rotamer: Outliers : 2.56 % Allowed : 17.47 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.15), residues: 3214 helix: 1.28 (0.14), residues: 1272 sheet: 0.18 (0.26), residues: 381 loop : 0.12 (0.16), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 644 TYR 0.042 0.002 TYR D1050 PHE 0.019 0.002 PHE D 155 TRP 0.013 0.001 TRP C 765 HIS 0.007 0.001 HIS D1101 Details of bonding type rmsd covalent geometry : bond 0.00415 (27891) covalent geometry : angle 0.56574 (38020) hydrogen bonds : bond 0.03948 ( 1256) hydrogen bonds : angle 4.69908 ( 3465) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 295 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7298 (pt0) REVERT: A 174 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7486 (mm-30) REVERT: B 132 LYS cc_start: 0.7795 (ttmm) cc_final: 0.7463 (tttt) REVERT: C 263 LYS cc_start: 0.7569 (mmmt) cc_final: 0.7274 (mmmm) REVERT: C 500 MET cc_start: 0.4681 (tpt) cc_final: 0.3930 (mmm) REVERT: C 504 ASP cc_start: 0.8163 (m-30) cc_final: 0.7643 (m-30) REVERT: C 590 GLU cc_start: 0.6720 (pm20) cc_final: 0.6318 (tt0) REVERT: C 638 MET cc_start: 0.7601 (mtt) cc_final: 0.7356 (mtt) REVERT: C 748 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8106 (tt0) REVERT: C 752 MET cc_start: 0.8254 (tpp) cc_final: 0.7884 (tpp) REVERT: C 793 GLU cc_start: 0.7679 (pt0) cc_final: 0.7338 (pt0) REVERT: C 839 ASP cc_start: 0.7681 (m-30) cc_final: 0.7392 (m-30) REVERT: C 852 GLU cc_start: 0.3876 (OUTLIER) cc_final: 0.3196 (pm20) REVERT: C 1045 ASP cc_start: 0.6900 (m-30) cc_final: 0.6497 (t0) REVERT: C 1145 MET cc_start: 0.7585 (mmm) cc_final: 0.7378 (mmt) REVERT: D 56 LYS cc_start: 0.8304 (tptp) cc_final: 0.7562 (ptpp) REVERT: D 162 TYR cc_start: 0.5978 (m-80) cc_final: 0.5722 (m-80) REVERT: D 169 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7750 (mtpp) REVERT: D 260 ARG cc_start: 0.8228 (ttm170) cc_final: 0.7888 (mtp85) REVERT: D 303 ARG cc_start: 0.8095 (tpt170) cc_final: 0.7309 (tpp80) REVERT: D 351 LYS cc_start: 0.8554 (mmtt) cc_final: 0.8203 (mptt) REVERT: D 432 GLU cc_start: 0.7410 (mm-30) cc_final: 0.7038 (mp0) REVERT: D 471 MET cc_start: 0.8665 (mmm) cc_final: 0.8345 (mmp) REVERT: D 693 ARG cc_start: 0.5026 (OUTLIER) cc_final: 0.4286 (ptm160) REVERT: D 754 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6615 (pp) REVERT: D 789 LYS cc_start: 0.7425 (tttt) cc_final: 0.7114 (ttmm) REVERT: D 1020 GLN cc_start: 0.5392 (tm-30) cc_final: 0.5125 (tm-30) REVERT: D 1053 LYS cc_start: 0.8487 (tttt) cc_final: 0.7888 (ttmm) REVERT: F 32 GLU cc_start: 0.7313 (tt0) cc_final: 0.6916 (tt0) REVERT: G 27 GLU cc_start: 0.8037 (tp30) cc_final: 0.7789 (tp30) REVERT: G 29 GLN cc_start: 0.7753 (mm-40) cc_final: 0.7434 (mm110) REVERT: H 52 LYS cc_start: 0.7171 (mttt) cc_final: 0.4910 (ttpt) REVERT: H 56 HIS cc_start: 0.7063 (p90) cc_final: 0.6444 (p90) REVERT: H 77 MET cc_start: 0.7291 (ptm) cc_final: 0.6820 (ptm) REVERT: H 94 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7514 (mm-30) REVERT: H 123 SER cc_start: 0.8901 (t) cc_final: 0.8613 (p) REVERT: H 144 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7178 (tt0) REVERT: H 156 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.6472 (mpt) REVERT: H 182 ASP cc_start: 0.7946 (m-30) cc_final: 0.7648 (m-30) REVERT: H 198 MET cc_start: 0.8122 (mtp) cc_final: 0.7605 (mtp) REVERT: H 237 MET cc_start: 0.7557 (tpt) cc_final: 0.7260 (tpt) outliers start: 72 outliers final: 61 residues processed: 356 average time/residue: 0.1710 time to fit residues: 95.9285 Evaluate side-chains 356 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 289 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 23 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 280 HIS Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 401 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 529 SER Chi-restraints excluded: chain C residue 650 MET Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 797 GLU Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 852 GLU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1132 MET Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 693 ARG Chi-restraints excluded: chain D residue 730 ILE Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 824 THR Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1044 LEU Chi-restraints excluded: chain D residue 1064 VAL Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 158 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 210 optimal weight: 3.9990 chunk 208 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 310 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 168 optimal weight: 0.0970 chunk 6 optimal weight: 9.9990 chunk 327 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 465 GLN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 ASN D1101 HIS G 62 ASN ** H 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.168204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.131635 restraints weight = 32641.771| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.62 r_work: 0.3284 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27891 Z= 0.146 Angle : 0.545 24.988 38020 Z= 0.286 Chirality : 0.043 0.231 4285 Planarity : 0.005 0.192 4689 Dihedral : 16.217 134.971 4443 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.27 % Favored : 97.70 % Rotamer: Outliers : 2.49 % Allowed : 17.76 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.15), residues: 3214 helix: 1.40 (0.14), residues: 1269 sheet: 0.24 (0.26), residues: 381 loop : 0.18 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 644 TYR 0.045 0.002 TYR D1050 PHE 0.019 0.001 PHE D 155 TRP 0.014 0.001 TRP C 765 HIS 0.008 0.001 HIS D1101 Details of bonding type rmsd covalent geometry : bond 0.00348 (27891) covalent geometry : angle 0.54545 (38020) hydrogen bonds : bond 0.03746 ( 1256) hydrogen bonds : angle 4.60354 ( 3465) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7278.58 seconds wall clock time: 125 minutes 28.07 seconds (7528.07 seconds total)