Starting phenix.real_space_refine on Mon Jun 23 11:32:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x6g_38088/06_2025/8x6g_38088.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x6g_38088/06_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_38088/06_2025/8x6g_38088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x6g_38088/06_2025/8x6g_38088.map" model { file = "/net/cci-nas-00/data/ceres_data/8x6g_38088/06_2025/8x6g_38088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x6g_38088/06_2025/8x6g_38088.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.89, per 1000 atoms: 0.55 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: 6.91 Conformation dependent library (CDL) restraints added in 3.5 seconds 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: 10.37 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: 15.76 Time building geometry restraints manager: 8.11 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: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.200 Check model and map are aligned: 0.230 Set scattering table: 0.220 Process input model: 72.780 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.140 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.850 ------------------------------------------------------------------------------- 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 : 8.79 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (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 TRP 0.012 0.001 TRP C 765 HIS 0.005 0.001 HIS H 238 PHE 0.022 0.001 PHE B 65 TYR 0.014 0.001 TYR C1098 ARG 0.009 0.001 ARG F 61 Details of bonding type rmsd hydrogen bonds : bond 0.14395 ( 1256) hydrogen bonds : angle 6.37236 ( 3465) covalent geometry : bond 0.00356 (27891) covalent geometry : angle 0.60467 (38020) *********************** 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 : 3.172 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: 0.4867 time to fit residues: 445.0212 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 : 3.167 ------------------------------------------------------------------------------- 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 276 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 167 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 257 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 297 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 724 ASN C 970 GLN C1042 HIS D 385 ASN D 675 GLN D 703 ASN D 897 ASN D1062 GLN D1101 HIS E 57 GLN G 42 ASN ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.157598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.119260 restraints weight = 33185.770| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.84 r_work: 0.3192 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.101 27891 Z= 0.402 Angle : 0.819 23.054 38020 Z= 0.435 Chirality : 0.054 0.283 4285 Planarity : 0.007 0.191 4689 Dihedral : 17.109 146.809 4453 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.49 % Favored : 97.48 % Rotamer: Outliers : 3.66 % Allowed : 12.93 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.14), residues: 3214 helix: 0.49 (0.14), residues: 1267 sheet: 0.10 (0.25), residues: 417 loop : -0.06 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 199 HIS 0.013 0.002 HIS D 540 PHE 0.037 0.003 PHE G 47 TYR 0.038 0.003 TYR E 34 ARG 0.011 0.001 ARG D 959 Details of bonding type rmsd hydrogen bonds : bond 0.06216 ( 1256) hydrogen bonds : angle 5.59119 ( 3465) covalent geometry : bond 0.00978 (27891) covalent geometry : angle 0.81932 (38020) *********************** 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 464 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 361 time to evaluate : 3.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7368 (pt0) REVERT: A 103 ASP cc_start: 0.6364 (p0) cc_final: 0.5469 (p0) REVERT: A 106 GLU cc_start: 0.6423 (mp0) cc_final: 0.6101 (tp30) REVERT: A 107 VAL cc_start: 0.7459 (p) cc_final: 0.6615 (p) REVERT: A 126 LYS cc_start: 0.6754 (tttt) cc_final: 0.6277 (tttm) REVERT: A 172 PRO cc_start: 0.8411 (Cg_endo) cc_final: 0.8134 (Cg_endo) REVERT: B 74 ASP cc_start: 0.8573 (p0) cc_final: 0.8251 (p0) REVERT: B 121 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8103 (mm) REVERT: B 132 LYS cc_start: 0.7888 (ttmm) cc_final: 0.7513 (tttt) REVERT: B 146 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.8040 (mtp85) REVERT: B 153 GLN cc_start: 0.6887 (tm-30) cc_final: 0.6590 (mm-40) REVERT: B 217 MET cc_start: 0.8579 (tpt) cc_final: 0.8369 (tpt) REVERT: C 38 GLU cc_start: 0.8743 (tt0) cc_final: 0.8495 (mt-10) REVERT: C 109 GLN cc_start: 0.5185 (tt0) cc_final: 0.4859 (tt0) REVERT: C 113 MET cc_start: 0.8199 (tpp) cc_final: 0.7627 (tpp) REVERT: C 116 PHE cc_start: 0.7630 (t80) cc_final: 0.7328 (t80) REVERT: C 178 ASP cc_start: 0.5609 (m-30) cc_final: 0.5240 (t0) REVERT: C 263 LYS cc_start: 0.7655 (mmmt) cc_final: 0.6354 (mmmt) REVERT: C 458 LYS cc_start: 0.7763 (tttt) cc_final: 0.7549 (tttp) REVERT: C 470 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7891 (tpp) REVERT: C 528 ASN cc_start: 0.8672 (OUTLIER) cc_final: 0.8450 (m-40) REVERT: C 579 LYS cc_start: 0.6770 (mtpt) cc_final: 0.6446 (mmtm) REVERT: C 589 ASP cc_start: 0.6470 (m-30) cc_final: 0.5967 (t70) REVERT: C 763 MET cc_start: 0.8138 (ptm) cc_final: 0.7862 (ptm) REVERT: C 814 ASN cc_start: 0.6765 (m-40) cc_final: 0.6449 (t0) REVERT: C 839 ASP cc_start: 0.7637 (m-30) cc_final: 0.7386 (m-30) REVERT: C 852 GLU cc_start: 0.3347 (OUTLIER) cc_final: 0.2819 (pm20) REVERT: C 956 MET cc_start: 0.8625 (mtm) cc_final: 0.8335 (mtp) REVERT: C 1045 ASP cc_start: 0.7004 (m-30) cc_final: 0.6457 (t0) REVERT: C 1117 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8229 (mt-10) REVERT: C 1120 SER cc_start: 0.8576 (t) cc_final: 0.8177 (m) REVERT: C 1143 LYS cc_start: 0.8070 (mtmm) cc_final: 0.7774 (mttt) REVERT: C 1154 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7464 (ttm) REVERT: D 137 VAL cc_start: 0.8171 (t) cc_final: 0.7910 (m) REVERT: D 248 ARG cc_start: 0.6913 (ptm160) cc_final: 0.6665 (ttm-80) REVERT: D 260 ARG cc_start: 0.8442 (ttm170) cc_final: 0.7956 (mtp85) REVERT: D 303 ARG cc_start: 0.7688 (mmt180) cc_final: 0.7292 (ttm-80) REVERT: D 319 MET cc_start: 0.8400 (mtp) cc_final: 0.8028 (mtp) REVERT: D 351 LYS cc_start: 0.8655 (mmtt) cc_final: 0.8364 (mptt) REVERT: D 432 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7346 (mp0) REVERT: D 471 MET cc_start: 0.8730 (mmm) cc_final: 0.8478 (mmp) REVERT: D 690 GLN cc_start: 0.5256 (OUTLIER) cc_final: 0.4976 (tm-30) REVERT: D 835 GLU cc_start: 0.6752 (tp30) cc_final: 0.6281 (pt0) REVERT: D 977 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6436 (mt-10) REVERT: D 1053 LYS cc_start: 0.8539 (tttt) cc_final: 0.8326 (tttm) REVERT: D 1065 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7452 (pt0) REVERT: D 1101 HIS cc_start: 0.7318 (p-80) cc_final: 0.7078 (p90) REVERT: D 1109 GLU cc_start: 0.6066 (tp30) cc_final: 0.5341 (tm-30) REVERT: D 1129 LYS cc_start: 0.8156 (tttt) cc_final: 0.7847 (tptp) REVERT: D 1181 MET cc_start: 0.9062 (mmm) cc_final: 0.8798 (mmm) REVERT: D 1188 LYS cc_start: 0.8292 (mttt) cc_final: 0.7867 (mtpp) REVERT: E 57 GLN cc_start: 0.4157 (OUTLIER) cc_final: 0.2946 (mm110) REVERT: E 78 LEU cc_start: 0.6310 (OUTLIER) cc_final: 0.6069 (mp) REVERT: F 25 LYS cc_start: 0.8284 (mttm) cc_final: 0.7723 (mmtt) REVERT: F 32 GLU cc_start: 0.7270 (tt0) cc_final: 0.6869 (tt0) REVERT: G 27 GLU cc_start: 0.8084 (tp30) cc_final: 0.7802 (tp30) REVERT: G 29 GLN cc_start: 0.7572 (mm-40) cc_final: 0.7280 (mp10) REVERT: G 50 LYS cc_start: 0.8114 (tptt) cc_final: 0.7765 (tptp) REVERT: H 52 LYS cc_start: 0.7045 (mttt) cc_final: 0.5016 (ttpt) REVERT: H 56 HIS cc_start: 0.7199 (p90) cc_final: 0.6793 (p90) REVERT: H 144 GLU cc_start: 0.7410 (mt-10) cc_final: 0.6844 (tt0) REVERT: H 186 GLN cc_start: 0.6818 (tp40) cc_final: 0.6549 (tp40) REVERT: H 195 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7594 (mt-10) REVERT: H 198 MET cc_start: 0.8204 (mtp) cc_final: 0.7778 (mtp) REVERT: H 237 MET cc_start: 0.7189 (tpt) cc_final: 0.6986 (tpt) REVERT: H 239 VAL cc_start: 0.7201 (OUTLIER) cc_final: 0.6907 (t) outliers start: 103 outliers final: 60 residues processed: 445 average time/residue: 0.4419 time to fit residues: 301.4284 Evaluate side-chains 376 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 305 time to evaluate : 3.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 156 THR 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 82 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 129 THR 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 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 344 ILE 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 470 MET Chi-restraints excluded: chain C residue 528 ASN Chi-restraints excluded: chain C residue 529 SER 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 1104 VAL Chi-restraints excluded: chain C residue 1127 SER Chi-restraints excluded: chain C residue 1132 MET Chi-restraints excluded: chain C residue 1154 MET Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 552 GLU Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain D residue 690 GLN Chi-restraints excluded: chain D residue 730 ILE Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 860 GLU Chi-restraints excluded: chain D residue 977 GLU Chi-restraints excluded: chain D residue 1100 ILE Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 57 GLN Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 188 ASP Chi-restraints excluded: chain H residue 202 LYS Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain H residue 239 VAL 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 317 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 284 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 302 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 275 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 chunk 281 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN C 465 GLN C 575 GLN C 651 ASN C 724 ASN C 907 GLN D 218 ASN D 744 ASN D 785 HIS E 63 ASN ** H 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.168622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.130320 restraints weight = 32304.031| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.74 r_work: 0.3236 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 27891 Z= 0.131 Angle : 0.538 13.480 38020 Z= 0.290 Chirality : 0.043 0.249 4285 Planarity : 0.005 0.165 4689 Dihedral : 16.802 141.120 4446 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.56 % Favored : 98.41 % Rotamer: Outliers : 2.20 % Allowed : 15.52 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.15), residues: 3214 helix: 1.19 (0.14), residues: 1266 sheet: 0.26 (0.26), residues: 387 loop : 0.21 (0.16), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 199 HIS 0.004 0.001 HIS D 532 PHE 0.019 0.001 PHE G 47 TYR 0.019 0.001 TYR A 178 ARG 0.006 0.000 ARG C 644 Details of bonding type rmsd hydrogen bonds : bond 0.04090 ( 1256) hydrogen bonds : angle 4.86181 ( 3465) covalent geometry : bond 0.00304 (27891) covalent geometry : angle 0.53780 (38020) *********************** 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 414 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 352 time to evaluate : 3.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7155 (pt0) REVERT: A 103 ASP cc_start: 0.6279 (p0) cc_final: 0.5306 (p0) REVERT: A 107 VAL cc_start: 0.7048 (OUTLIER) cc_final: 0.6472 (p) REVERT: A 126 LYS cc_start: 0.6633 (tttt) cc_final: 0.5929 (pttp) REVERT: A 174 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7479 (mm-30) REVERT: B 132 LYS cc_start: 0.7822 (ttmm) cc_final: 0.7370 (tttt) REVERT: B 153 GLN cc_start: 0.7053 (tm-30) cc_final: 0.6810 (mm-40) REVERT: B 182 ASN cc_start: 0.7782 (t0) cc_final: 0.7542 (t0) REVERT: B 217 MET cc_start: 0.8523 (tpt) cc_final: 0.8237 (tpt) REVERT: C 47 GLU cc_start: 0.8015 (tt0) cc_final: 0.7760 (tt0) REVERT: C 51 ASP cc_start: 0.6427 (m-30) cc_final: 0.6016 (m-30) REVERT: C 98 LEU cc_start: 0.7911 (tp) cc_final: 0.7365 (tp) REVERT: C 113 MET cc_start: 0.8244 (tpp) cc_final: 0.7643 (tpp) REVERT: C 116 PHE cc_start: 0.7418 (t80) cc_final: 0.7154 (t80) REVERT: C 178 ASP cc_start: 0.5495 (m-30) cc_final: 0.5151 (t70) REVERT: C 263 LYS cc_start: 0.7648 (mmmt) cc_final: 0.6153 (mmmt) REVERT: C 458 LYS cc_start: 0.7842 (tttt) cc_final: 0.7542 (tttp) REVERT: C 589 ASP cc_start: 0.6265 (m-30) cc_final: 0.5879 (t70) REVERT: C 602 MET cc_start: 0.7862 (mtt) cc_final: 0.7403 (mtt) REVERT: C 638 MET cc_start: 0.7723 (mtt) cc_final: 0.7492 (mtt) REVERT: C 684 VAL cc_start: 0.8496 (t) cc_final: 0.8179 (p) REVERT: C 752 MET cc_start: 0.8277 (tpp) cc_final: 0.8002 (tpp) REVERT: C 763 MET cc_start: 0.8123 (ptm) cc_final: 0.7787 (ptm) REVERT: C 786 TYR cc_start: 0.8651 (m-80) cc_final: 0.8369 (m-80) REVERT: C 814 ASN cc_start: 0.6647 (m-40) cc_final: 0.6193 (t0) REVERT: C 839 ASP cc_start: 0.7648 (m-30) cc_final: 0.7364 (m-30) REVERT: C 956 MET cc_start: 0.8474 (mtm) cc_final: 0.7941 (mtp) REVERT: C 1043 MET cc_start: 0.5495 (ptt) cc_final: 0.5190 (ptt) REVERT: C 1045 ASP cc_start: 0.7048 (m-30) cc_final: 0.6460 (t0) REVERT: C 1070 PHE cc_start: 0.6890 (t80) cc_final: 0.6650 (t80) REVERT: D 10 MET cc_start: 0.8012 (ttm) cc_final: 0.7781 (ttt) REVERT: D 11 LYS cc_start: 0.8428 (tttt) cc_final: 0.7903 (tttt) REVERT: D 260 ARG cc_start: 0.8331 (ttm170) cc_final: 0.7947 (mtp85) REVERT: D 303 ARG cc_start: 0.7663 (mmt180) cc_final: 0.7252 (ttm-80) REVERT: D 351 LYS cc_start: 0.8529 (mmtt) cc_final: 0.8144 (mptt) REVERT: D 432 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7008 (mp0) REVERT: D 451 ASP cc_start: 0.8175 (p0) cc_final: 0.7851 (p0) REVERT: D 471 MET cc_start: 0.8631 (mmm) cc_final: 0.8286 (mmp) REVERT: D 507 LYS cc_start: 0.8514 (mmmt) cc_final: 0.8257 (mmmt) REVERT: D 826 ARG cc_start: 0.7041 (mtm180) cc_final: 0.6811 (mtp180) REVERT: D 933 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7523 (tm-30) REVERT: D 957 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.7001 (mt) REVERT: D 1053 LYS cc_start: 0.8436 (tttt) cc_final: 0.7818 (ttmm) REVERT: D 1109 GLU cc_start: 0.6151 (tp30) cc_final: 0.5430 (tm-30) REVERT: D 1129 LYS cc_start: 0.7995 (tttt) cc_final: 0.7710 (tptp) REVERT: D 1181 MET cc_start: 0.8973 (mmm) cc_final: 0.8656 (mmm) REVERT: E 78 LEU cc_start: 0.5960 (OUTLIER) cc_final: 0.5699 (mm) REVERT: F 25 LYS cc_start: 0.8067 (mttm) cc_final: 0.7790 (mttt) REVERT: F 31 ASP cc_start: 0.7677 (t70) cc_final: 0.7351 (t70) REVERT: F 32 GLU cc_start: 0.7195 (tt0) cc_final: 0.6800 (tt0) REVERT: G 27 GLU cc_start: 0.7918 (tp30) cc_final: 0.7637 (tp30) REVERT: G 29 GLN cc_start: 0.7403 (mm-40) cc_final: 0.7150 (mp10) REVERT: H 17 ASN cc_start: 0.6193 (m-40) cc_final: 0.5961 (m-40) REVERT: H 52 LYS cc_start: 0.6812 (mttt) cc_final: 0.4715 (ttpt) REVERT: H 56 HIS cc_start: 0.7144 (p90) cc_final: 0.6709 (p90) REVERT: H 77 MET cc_start: 0.7171 (ptm) cc_final: 0.6643 (ptm) REVERT: H 144 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6839 (tt0) REVERT: H 198 MET cc_start: 0.8212 (mtp) cc_final: 0.7573 (mtt) REVERT: H 206 ILE cc_start: 0.7231 (mm) cc_final: 0.7013 (tt) REVERT: H 237 MET cc_start: 0.7534 (tpt) cc_final: 0.7237 (tpt) REVERT: H 239 VAL cc_start: 0.7178 (t) cc_final: 0.6915 (t) REVERT: H 251 GLN cc_start: 0.5625 (mt0) cc_final: 0.5251 (mt0) outliers start: 62 outliers final: 37 residues processed: 401 average time/residue: 0.5339 time to fit residues: 333.3104 Evaluate side-chains 339 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 299 time to evaluate : 3.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 107 VAL 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 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 424 SER Chi-restraints excluded: chain C residue 439 THR 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 1132 MET Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 483 LYS Chi-restraints excluded: chain D residue 552 GLU Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 730 ILE Chi-restraints excluded: chain D residue 864 ILE 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 1099 ASP Chi-restraints excluded: chain D residue 1100 ILE Chi-restraints excluded: chain D residue 1139 SER Chi-restraints excluded: chain E residue 25 ASN Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 243 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 76 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 219 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 150 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 293 optimal weight: 0.9980 chunk 146 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 465 GLN C 472 GLN C 880 HIS D 218 ASN D 703 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.166190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.128392 restraints weight = 32562.587| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.66 r_work: 0.3283 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27891 Z= 0.181 Angle : 0.575 22.799 38020 Z= 0.304 Chirality : 0.044 0.280 4285 Planarity : 0.005 0.189 4689 Dihedral : 16.744 139.933 4443 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.18 % Favored : 97.79 % Rotamer: Outliers : 3.05 % Allowed : 15.66 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.15), residues: 3214 helix: 1.15 (0.14), residues: 1276 sheet: 0.20 (0.26), residues: 387 loop : 0.14 (0.16), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 199 HIS 0.008 0.001 HIS C 920 PHE 0.020 0.002 PHE G 47 TYR 0.021 0.002 TYR C1098 ARG 0.004 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.04311 ( 1256) hydrogen bonds : angle 4.85356 ( 3465) covalent geometry : bond 0.00434 (27891) covalent geometry : angle 0.57461 (38020) *********************** 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 400 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 314 time to evaluate : 3.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7298 (pt0) REVERT: A 54 LYS cc_start: 0.7152 (OUTLIER) cc_final: 0.6809 (mtpt) REVERT: A 88 LYS cc_start: 0.7601 (mtpp) cc_final: 0.6363 (mttm) REVERT: A 103 ASP cc_start: 0.6415 (p0) cc_final: 0.5499 (p0) REVERT: A 107 VAL cc_start: 0.7322 (OUTLIER) cc_final: 0.7069 (p) REVERT: A 126 LYS cc_start: 0.6915 (tttt) cc_final: 0.6264 (pttt) REVERT: A 174 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7489 (mm-30) REVERT: B 132 LYS cc_start: 0.7782 (ttmm) cc_final: 0.7399 (tttt) REVERT: B 153 GLN cc_start: 0.6980 (tm-30) cc_final: 0.6766 (mm-40) REVERT: B 212 LEU cc_start: 0.8655 (tp) cc_final: 0.8330 (mt) REVERT: C 113 MET cc_start: 0.8232 (tpp) cc_final: 0.7580 (tpp) REVERT: C 178 ASP cc_start: 0.5604 (m-30) cc_final: 0.5163 (t0) REVERT: C 263 LYS cc_start: 0.7766 (mmmt) cc_final: 0.6907 (mmmm) REVERT: C 317 GLU cc_start: 0.3809 (mt-10) cc_final: 0.3496 (tt0) REVERT: C 458 LYS cc_start: 0.7942 (tttt) cc_final: 0.7634 (tttp) REVERT: C 589 ASP cc_start: 0.6380 (m-30) cc_final: 0.6006 (t70) REVERT: C 793 GLU cc_start: 0.7509 (pt0) cc_final: 0.7142 (pt0) REVERT: C 814 ASN cc_start: 0.6688 (m-40) cc_final: 0.6176 (t0) REVERT: C 839 ASP cc_start: 0.7670 (m-30) cc_final: 0.7415 (m-30) REVERT: C 852 GLU cc_start: 0.3606 (OUTLIER) cc_final: 0.3080 (pm20) REVERT: C 880 HIS cc_start: 0.7023 (p-80) cc_final: 0.6730 (p90) REVERT: C 1045 ASP cc_start: 0.7054 (m-30) cc_final: 0.6507 (t0) REVERT: C 1070 PHE cc_start: 0.6947 (t80) cc_final: 0.6702 (t80) REVERT: D 260 ARG cc_start: 0.8326 (ttm170) cc_final: 0.7949 (mtp85) REVERT: D 303 ARG cc_start: 0.7700 (mmt180) cc_final: 0.7338 (ttm-80) REVERT: D 351 LYS cc_start: 0.8542 (mmtt) cc_final: 0.8191 (mptt) REVERT: D 432 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7123 (mp0) REVERT: D 471 MET cc_start: 0.8741 (mmm) cc_final: 0.8407 (mmp) REVERT: D 507 LYS cc_start: 0.8578 (mmmt) cc_final: 0.8359 (mmmt) REVERT: D 754 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6611 (pp) REVERT: D 957 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7223 (mt) REVERT: D 1053 LYS cc_start: 0.8473 (tttt) cc_final: 0.7923 (ttmm) REVERT: D 1109 GLU cc_start: 0.6322 (tp30) cc_final: 0.5667 (tm-30) REVERT: D 1129 LYS cc_start: 0.7984 (tttt) cc_final: 0.7739 (tptp) REVERT: D 1181 MET cc_start: 0.9063 (mmm) cc_final: 0.8810 (mmm) REVERT: E 78 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.5911 (mm) REVERT: F 25 LYS cc_start: 0.8161 (mttm) cc_final: 0.7869 (mttt) REVERT: F 32 GLU cc_start: 0.7223 (tt0) cc_final: 0.6872 (tt0) REVERT: F 38 LEU cc_start: 0.8307 (mt) cc_final: 0.8042 (mt) REVERT: G 10 HIS cc_start: 0.8680 (OUTLIER) cc_final: 0.8009 (m-70) REVERT: G 27 GLU cc_start: 0.7952 (tp30) cc_final: 0.7690 (tp30) REVERT: G 29 GLN cc_start: 0.7513 (mm-40) cc_final: 0.7282 (mp10) REVERT: H 52 LYS cc_start: 0.6963 (mttt) cc_final: 0.4755 (ttpt) REVERT: H 56 HIS cc_start: 0.7137 (p90) cc_final: 0.6762 (p90) REVERT: H 77 MET cc_start: 0.7283 (ptm) cc_final: 0.6719 (ptm) REVERT: H 144 GLU cc_start: 0.7476 (mt-10) cc_final: 0.6916 (tt0) REVERT: H 156 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.6146 (mpt) REVERT: H 198 MET cc_start: 0.8271 (mtp) cc_final: 0.7646 (mtt) REVERT: H 206 ILE cc_start: 0.7331 (mm) cc_final: 0.7083 (tt) REVERT: H 237 MET cc_start: 0.7635 (tpt) cc_final: 0.7313 (tpt) REVERT: H 239 VAL cc_start: 0.6795 (t) cc_final: 0.6548 (t) outliers start: 86 outliers final: 58 residues processed: 382 average time/residue: 0.4298 time to fit residues: 257.1346 Evaluate side-chains 355 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 289 time to evaluate : 3.076 ------------------------------------------------------------------------------- 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 54 LYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 129 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 63 HIS 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 198 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 69 TYR 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 439 THR Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 529 SER Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 686 SER Chi-restraints excluded: chain C residue 776 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 1048 LEU Chi-restraints excluded: chain C residue 1103 THR Chi-restraints excluded: chain C residue 1132 MET Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 222 LYS 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 552 GLU Chi-restraints excluded: chain D residue 693 ARG Chi-restraints excluded: chain D residue 721 MET 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 798 THR Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 860 GLU Chi-restraints excluded: chain D residue 864 ILE 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 1100 ILE Chi-restraints excluded: chain D residue 1139 SER Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 65 ASP 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 G residue 10 HIS Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 223 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 251 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 148 optimal weight: 7.9990 chunk 294 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 465 GLN C 920 HIS D 218 ASN ** D 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3962 r_free = 0.3962 target = 0.166704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.129463 restraints weight = 32581.032| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.63 r_work: 0.3235 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27891 Z= 0.176 Angle : 0.563 22.423 38020 Z= 0.298 Chirality : 0.044 0.290 4285 Planarity : 0.005 0.190 4689 Dihedral : 16.606 138.020 4443 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.24 % Favored : 97.73 % Rotamer: Outliers : 3.55 % Allowed : 16.34 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.15), residues: 3214 helix: 1.15 (0.14), residues: 1275 sheet: 0.12 (0.26), residues: 386 loop : 0.10 (0.16), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 199 HIS 0.007 0.001 HIS C 920 PHE 0.020 0.002 PHE G 47 TYR 0.022 0.002 TYR C1098 ARG 0.011 0.000 ARG C 644 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 1256) hydrogen bonds : angle 4.78741 ( 3465) covalent geometry : bond 0.00421 (27891) covalent geometry : angle 0.56266 (38020) *********************** 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 407 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 307 time to evaluate : 3.598 Fit side-chains revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7320 (pt0) REVERT: A 54 LYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6754 (mtpt) REVERT: A 88 LYS cc_start: 0.7623 (mtpp) cc_final: 0.6352 (mttm) REVERT: A 106 GLU cc_start: 0.5272 (tp30) cc_final: 0.3748 (tp30) REVERT: A 174 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7487 (mm-30) REVERT: B 132 LYS cc_start: 0.7772 (ttmm) cc_final: 0.7421 (tttm) REVERT: B 153 GLN cc_start: 0.7058 (tm-30) cc_final: 0.6788 (mm-40) REVERT: B 175 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7377 (mtp180) REVERT: B 212 LEU cc_start: 0.8671 (tp) cc_final: 0.8368 (mt) REVERT: B 217 MET cc_start: 0.8614 (tpt) cc_final: 0.8378 (tpt) REVERT: C 51 ASP cc_start: 0.6265 (m-30) cc_final: 0.5925 (m-30) REVERT: C 113 MET cc_start: 0.8268 (tpp) cc_final: 0.7633 (tpp) REVERT: C 178 ASP cc_start: 0.5643 (m-30) cc_final: 0.5215 (t0) REVERT: C 263 LYS cc_start: 0.7599 (mmmt) cc_final: 0.6449 (mmmt) REVERT: C 419 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.7561 (m-80) REVERT: C 458 LYS cc_start: 0.7998 (tttt) cc_final: 0.7670 (tttp) REVERT: C 589 ASP cc_start: 0.6287 (m-30) cc_final: 0.6028 (t70) REVERT: C 748 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7979 (tt0) REVERT: C 752 MET cc_start: 0.8232 (tpp) cc_final: 0.7868 (tpp) REVERT: C 793 GLU cc_start: 0.7625 (pt0) cc_final: 0.7281 (pt0) REVERT: C 839 ASP cc_start: 0.7698 (m-30) cc_final: 0.7431 (m-30) REVERT: C 852 GLU cc_start: 0.3746 (OUTLIER) cc_final: 0.3138 (pm20) REVERT: C 1043 MET cc_start: 0.5474 (ptt) cc_final: 0.5270 (ptt) REVERT: C 1045 ASP cc_start: 0.7029 (m-30) cc_final: 0.6529 (t0) REVERT: C 1120 SER cc_start: 0.8450 (t) cc_final: 0.8067 (m) REVERT: D 260 ARG cc_start: 0.8273 (ttm170) cc_final: 0.7913 (mtp85) REVERT: D 303 ARG cc_start: 0.7734 (mmt180) cc_final: 0.7352 (ttm-80) REVERT: D 351 LYS cc_start: 0.8551 (mmtt) cc_final: 0.8189 (mptt) REVERT: D 432 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7000 (mp0) REVERT: D 471 MET cc_start: 0.8730 (mmm) cc_final: 0.8352 (mmp) REVERT: D 507 LYS cc_start: 0.8581 (mmmt) cc_final: 0.8294 (mmmt) REVERT: D 515 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8075 (mt) REVERT: D 622 LYS cc_start: 0.7696 (mttt) cc_final: 0.7467 (mttm) REVERT: D 693 ARG cc_start: 0.4791 (OUTLIER) cc_final: 0.4006 (ptm160) REVERT: D 789 LYS cc_start: 0.7315 (tttt) cc_final: 0.7090 (ttmm) REVERT: D 957 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7104 (mt) REVERT: D 1024 ARG cc_start: 0.6593 (ttt180) cc_final: 0.6390 (ttm170) REVERT: D 1053 LYS cc_start: 0.8473 (tttt) cc_final: 0.7923 (ttmm) REVERT: D 1109 GLU cc_start: 0.6334 (tp30) cc_final: 0.5687 (tm-30) REVERT: D 1181 MET cc_start: 0.9043 (mmm) cc_final: 0.8784 (mmm) REVERT: E 78 LEU cc_start: 0.6509 (OUTLIER) cc_final: 0.6137 (mm) REVERT: F 32 GLU cc_start: 0.7222 (tt0) cc_final: 0.6848 (tt0) REVERT: F 38 LEU cc_start: 0.8340 (mt) cc_final: 0.8044 (mt) REVERT: G 10 HIS cc_start: 0.8695 (OUTLIER) cc_final: 0.8067 (m-70) REVERT: G 27 GLU cc_start: 0.8001 (tp30) cc_final: 0.7730 (tp30) REVERT: G 29 GLN cc_start: 0.7786 (mm-40) cc_final: 0.7472 (mp10) REVERT: H 52 LYS cc_start: 0.7073 (mttt) cc_final: 0.4780 (ttpt) REVERT: H 56 HIS cc_start: 0.7103 (p90) cc_final: 0.6475 (p90) REVERT: H 77 MET cc_start: 0.7312 (ptm) cc_final: 0.6749 (ptm) REVERT: H 144 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7154 (tt0) REVERT: H 156 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.6373 (mpt) REVERT: H 182 ASP cc_start: 0.6845 (t70) cc_final: 0.6625 (m-30) REVERT: H 198 MET cc_start: 0.8127 (mtp) cc_final: 0.7555 (mtt) REVERT: H 206 ILE cc_start: 0.7308 (mm) cc_final: 0.7065 (tt) REVERT: H 237 MET cc_start: 0.7758 (tpt) cc_final: 0.7534 (tpt) REVERT: H 239 VAL cc_start: 0.6866 (t) cc_final: 0.6595 (t) outliers start: 100 outliers final: 67 residues processed: 388 average time/residue: 0.4686 time to fit residues: 284.9812 Evaluate side-chains 364 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 286 time to evaluate : 3.154 ------------------------------------------------------------------------------- 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 54 LYS Chi-restraints excluded: chain A residue 129 THR 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 47 SER Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 181 GLU 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 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 439 THR Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 529 SER Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 776 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 1048 LEU Chi-restraints excluded: chain C residue 1103 THR Chi-restraints excluded: chain C residue 1127 SER Chi-restraints excluded: chain C residue 1132 MET Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 693 ARG Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 730 ILE Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 798 THR Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 860 GLU Chi-restraints excluded: chain D residue 864 ILE 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 D residue 1100 ILE Chi-restraints excluded: chain D residue 1139 SER 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 G residue 6 VAL Chi-restraints excluded: chain G residue 10 HIS Chi-restraints excluded: chain G residue 18 ARG 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 204 LEU Chi-restraints excluded: chain H residue 228 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 66 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 302 optimal weight: 10.0000 chunk 169 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 269 optimal weight: 9.9990 chunk 276 optimal weight: 7.9990 chunk 286 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN C 165 ASN C 465 GLN C 724 ASN C 725 GLN D 218 ASN D 703 ASN ** D 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 26 ASN ** 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 = 0.3923 r_free = 0.3923 target = 0.163259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.126400 restraints weight = 33020.657| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.62 r_work: 0.3210 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 27891 Z= 0.285 Angle : 0.679 26.813 38020 Z= 0.356 Chirality : 0.048 0.284 4285 Planarity : 0.006 0.199 4689 Dihedral : 16.705 139.499 4443 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.24 % Favored : 96.73 % Rotamer: Outliers : 4.40 % Allowed : 16.44 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.14), residues: 3214 helix: 0.69 (0.14), residues: 1275 sheet: -0.06 (0.25), residues: 404 loop : -0.26 (0.16), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 765 HIS 0.007 0.002 HIS H 167 PHE 0.026 0.002 PHE D 654 TYR 0.026 0.002 TYR C1098 ARG 0.008 0.001 ARG D 752 Details of bonding type rmsd hydrogen bonds : bond 0.05012 ( 1256) hydrogen bonds : angle 5.13764 ( 3465) covalent geometry : bond 0.00692 (27891) covalent geometry : angle 0.67862 (38020) *********************** 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 420 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 296 time to evaluate : 3.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7155 (OUTLIER) cc_final: 0.6765 (mtpt) REVERT: A 87 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8346 (mp) REVERT: A 106 GLU cc_start: 0.5468 (tp30) cc_final: 0.3876 (tp30) REVERT: A 126 LYS cc_start: 0.6969 (tttt) cc_final: 0.6103 (pttp) REVERT: A 174 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7568 (mm-30) REVERT: B 19 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8650 (ttmm) REVERT: B 132 LYS cc_start: 0.7848 (ttmm) cc_final: 0.7512 (tttt) REVERT: B 146 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7734 (mtp85) REVERT: B 153 GLN cc_start: 0.6931 (tm-30) cc_final: 0.6585 (mm-40) REVERT: B 175 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7515 (mtp180) REVERT: B 217 MET cc_start: 0.8671 (tpt) cc_final: 0.8386 (tpt) REVERT: C 113 MET cc_start: 0.8287 (tpp) cc_final: 0.7580 (tpp) REVERT: C 458 LYS cc_start: 0.7677 (tttt) cc_final: 0.7332 (tttp) REVERT: C 589 ASP cc_start: 0.6356 (m-30) cc_final: 0.6130 (t70) REVERT: C 748 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7968 (tt0) REVERT: C 839 ASP cc_start: 0.7645 (m-30) cc_final: 0.7374 (m-30) REVERT: C 852 GLU cc_start: 0.4102 (OUTLIER) cc_final: 0.3277 (pm20) REVERT: C 1045 ASP cc_start: 0.7117 (m-30) cc_final: 0.6572 (t0) REVERT: C 1120 SER cc_start: 0.8577 (t) cc_final: 0.8220 (m) REVERT: D 56 LYS cc_start: 0.8435 (tptp) cc_final: 0.7624 (ptpp) REVERT: D 73 MET cc_start: -0.0509 (mtm) cc_final: -0.1255 (mpp) REVERT: D 260 ARG cc_start: 0.8393 (ttm170) cc_final: 0.7958 (mtp85) REVERT: D 303 ARG cc_start: 0.7737 (mmt180) cc_final: 0.7337 (ttm-80) REVERT: D 319 MET cc_start: 0.8388 (mtp) cc_final: 0.8002 (mtp) REVERT: D 351 LYS cc_start: 0.8650 (mmtt) cc_final: 0.8318 (mptt) REVERT: D 432 GLU cc_start: 0.7382 (mm-30) cc_final: 0.6988 (mp0) REVERT: D 471 MET cc_start: 0.8695 (mmm) cc_final: 0.8278 (mmp) REVERT: D 515 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8156 (mt) REVERT: D 622 LYS cc_start: 0.7703 (mttt) cc_final: 0.7445 (mttm) REVERT: D 693 ARG cc_start: 0.5257 (OUTLIER) cc_final: 0.4395 (ptm160) REVERT: D 754 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6661 (pp) REVERT: D 957 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7279 (mt) REVERT: D 1053 LYS cc_start: 0.8484 (tttt) cc_final: 0.7935 (ttmm) REVERT: D 1109 GLU cc_start: 0.6478 (tp30) cc_final: 0.5769 (tm-30) REVERT: D 1181 MET cc_start: 0.9085 (mmm) cc_final: 0.8830 (mmm) REVERT: E 78 LEU cc_start: 0.6490 (OUTLIER) cc_final: 0.6089 (mm) REVERT: F 32 GLU cc_start: 0.7248 (tt0) cc_final: 0.6865 (tt0) REVERT: G 10 HIS cc_start: 0.8753 (OUTLIER) cc_final: 0.8221 (m-70) REVERT: G 27 GLU cc_start: 0.8103 (tp30) cc_final: 0.7892 (tp30) REVERT: G 29 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7584 (mm110) REVERT: G 39 LYS cc_start: 0.8151 (ttpp) cc_final: 0.7913 (ttpp) REVERT: H 56 HIS cc_start: 0.7241 (p90) cc_final: 0.6932 (p90) REVERT: H 77 MET cc_start: 0.7324 (ptm) cc_final: 0.6882 (ptm) REVERT: H 144 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7145 (tt0) REVERT: H 156 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.5947 (mpt) REVERT: H 195 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7713 (mt-10) REVERT: H 198 MET cc_start: 0.8142 (mtp) cc_final: 0.7735 (mtp) REVERT: H 237 MET cc_start: 0.7714 (tpt) cc_final: 0.7461 (tpt) REVERT: H 239 VAL cc_start: 0.6834 (t) cc_final: 0.6563 (t) outliers start: 124 outliers final: 82 residues processed: 398 average time/residue: 0.5322 time to fit residues: 332.5253 Evaluate side-chains 374 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 278 time to evaluate : 3.407 ------------------------------------------------------------------------------- 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 54 LYS Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 94 ASP 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 19 LYS Chi-restraints excluded: chain B residue 23 PHE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 175 ARG 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 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 470 MET Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 529 SER Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 599 ASN Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 776 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 925 MET Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1127 SER Chi-restraints excluded: chain C residue 1132 MET Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 222 LYS 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 388 SER Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 552 GLU Chi-restraints excluded: chain D residue 693 ARG Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 730 ILE Chi-restraints excluded: chain D residue 739 ARG Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 798 THR Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 860 GLU Chi-restraints excluded: chain D residue 954 THR 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 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 G residue 6 VAL Chi-restraints excluded: chain G residue 10 HIS Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 68 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 204 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 228 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 18 optimal weight: 7.9990 chunk 189 optimal weight: 0.0570 chunk 24 optimal weight: 7.9990 chunk 302 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 241 optimal weight: 0.0070 chunk 182 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 276 optimal weight: 7.9990 chunk 199 optimal weight: 1.9990 chunk 139 optimal weight: 0.0980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN C 725 GLN D 218 ASN ** D 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 897 ASN ** H 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.169368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.131853 restraints weight = 32586.969| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.65 r_work: 0.3302 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 27891 Z= 0.108 Angle : 0.518 24.698 38020 Z= 0.274 Chirality : 0.042 0.247 4285 Planarity : 0.005 0.194 4689 Dihedral : 16.437 134.885 4443 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.84 % Favored : 98.13 % Rotamer: Outliers : 2.45 % Allowed : 18.64 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.15), residues: 3214 helix: 1.37 (0.14), residues: 1268 sheet: 0.05 (0.26), residues: 388 loop : 0.13 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 765 HIS 0.004 0.001 HIS C 929 PHE 0.020 0.001 PHE D 155 TYR 0.016 0.001 TYR A 178 ARG 0.007 0.000 ARG C 644 Details of bonding type rmsd hydrogen bonds : bond 0.03548 ( 1256) hydrogen bonds : angle 4.61303 ( 3465) covalent geometry : bond 0.00234 (27891) covalent geometry : angle 0.51842 (38020) *********************** 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 392 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 323 time to evaluate : 2.769 Fit side-chains revert: symmetry clash REVERT: A 54 LYS cc_start: 0.6876 (OUTLIER) cc_final: 0.6507 (mtpt) REVERT: A 106 GLU cc_start: 0.5152 (tp30) cc_final: 0.3837 (tp30) REVERT: A 126 LYS cc_start: 0.6798 (tttt) cc_final: 0.6106 (pttp) REVERT: A 174 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7407 (mm-30) REVERT: B 132 LYS cc_start: 0.7760 (ttmm) cc_final: 0.7420 (tttm) REVERT: B 153 GLN cc_start: 0.6907 (tm-30) cc_final: 0.6579 (mm-40) REVERT: B 217 MET cc_start: 0.8520 (tpt) cc_final: 0.8154 (tpt) REVERT: C 113 MET cc_start: 0.8259 (tpp) cc_final: 0.7784 (tpp) REVERT: C 178 ASP cc_start: 0.5568 (m-30) cc_final: 0.5158 (t0) REVERT: C 419 PHE cc_start: 0.7826 (OUTLIER) cc_final: 0.7510 (m-80) REVERT: C 426 MET cc_start: 0.7584 (ttm) cc_final: 0.7181 (ttp) REVERT: C 602 MET cc_start: 0.7560 (mtt) cc_final: 0.7052 (mtt) REVERT: C 748 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: C 752 MET cc_start: 0.8234 (tpp) cc_final: 0.7840 (tpp) REVERT: C 793 GLU cc_start: 0.7382 (pt0) cc_final: 0.7043 (pt0) REVERT: C 839 ASP cc_start: 0.7661 (m-30) cc_final: 0.7338 (m-30) REVERT: C 852 GLU cc_start: 0.4013 (OUTLIER) cc_final: 0.3342 (pm20) REVERT: C 1043 MET cc_start: 0.5399 (ptt) cc_final: 0.5189 (ptt) REVERT: C 1045 ASP cc_start: 0.7191 (m-30) cc_final: 0.6756 (t0) REVERT: C 1120 SER cc_start: 0.8371 (t) cc_final: 0.8013 (m) REVERT: D 73 MET cc_start: -0.0848 (mtm) cc_final: -0.1667 (mpp) REVERT: D 177 ASP cc_start: 0.7574 (t0) cc_final: 0.6653 (m-30) REVERT: D 260 ARG cc_start: 0.8236 (ttm170) cc_final: 0.7880 (mtp85) REVERT: D 303 ARG cc_start: 0.7711 (mmt180) cc_final: 0.7319 (ttm-80) REVERT: D 351 LYS cc_start: 0.8482 (mmtt) cc_final: 0.8125 (mptt) REVERT: D 387 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7572 (ttmt) REVERT: D 432 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6961 (mp0) REVERT: D 471 MET cc_start: 0.8743 (mmm) cc_final: 0.8341 (mmp) REVERT: D 622 LYS cc_start: 0.7611 (mttt) cc_final: 0.7369 (mttm) REVERT: D 754 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6633 (pp) REVERT: D 933 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7588 (tm-30) REVERT: D 957 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7253 (mt) REVERT: D 1024 ARG cc_start: 0.6704 (ttt180) cc_final: 0.6439 (ttm170) REVERT: D 1053 LYS cc_start: 0.8400 (tttt) cc_final: 0.7872 (ttmm) REVERT: D 1109 GLU cc_start: 0.6636 (tp30) cc_final: 0.5980 (tm-30) REVERT: D 1188 LYS cc_start: 0.8038 (mtmt) cc_final: 0.7768 (mtpp) REVERT: E 78 LEU cc_start: 0.6515 (OUTLIER) cc_final: 0.6310 (mm) REVERT: F 25 LYS cc_start: 0.8066 (mttm) cc_final: 0.7818 (mttt) REVERT: F 31 ASP cc_start: 0.7615 (t70) cc_final: 0.7387 (t70) REVERT: F 32 GLU cc_start: 0.7325 (tt0) cc_final: 0.6914 (tt0) REVERT: G 10 HIS cc_start: 0.8673 (OUTLIER) cc_final: 0.8138 (m-70) REVERT: G 27 GLU cc_start: 0.8089 (tp30) cc_final: 0.7819 (tp30) REVERT: G 29 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7439 (mm110) REVERT: H 22 GLU cc_start: 0.5693 (mm-30) cc_final: 0.5280 (mm-30) REVERT: H 56 HIS cc_start: 0.7096 (p90) cc_final: 0.6487 (p90) REVERT: H 77 MET cc_start: 0.7394 (ptm) cc_final: 0.6989 (ptm) REVERT: H 144 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7136 (tt0) REVERT: H 182 ASP cc_start: 0.7799 (m-30) cc_final: 0.7559 (m-30) REVERT: H 198 MET cc_start: 0.8056 (mtp) cc_final: 0.7444 (mtt) REVERT: H 239 VAL cc_start: 0.6753 (t) cc_final: 0.6477 (t) outliers start: 69 outliers final: 46 residues processed: 378 average time/residue: 0.4135 time to fit residues: 247.4010 Evaluate side-chains 345 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 290 time to evaluate : 3.202 ------------------------------------------------------------------------------- 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 54 LYS Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 23 PHE 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 23 VAL Chi-restraints excluded: chain C residue 69 TYR 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 434 MET Chi-restraints excluded: chain C residue 529 SER Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 776 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 1048 LEU Chi-restraints excluded: chain C residue 1132 MET Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 957 LEU 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 78 LEU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain G residue 10 HIS Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 207 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 68 optimal weight: 0.0040 chunk 61 optimal weight: 6.9990 chunk 232 optimal weight: 9.9990 chunk 285 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 293 optimal weight: 7.9990 chunk 138 optimal weight: 0.6980 chunk 205 optimal weight: 0.9990 chunk 179 optimal weight: 9.9990 chunk 152 optimal weight: 0.6980 chunk 173 optimal weight: 0.6980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 ASN C 280 HIS C 465 GLN D 218 ASN D 318 HIS ** D 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.170376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.133228 restraints weight = 32500.039| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.61 r_work: 0.3320 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 27891 Z= 0.104 Angle : 0.507 25.754 38020 Z= 0.267 Chirality : 0.042 0.263 4285 Planarity : 0.005 0.194 4689 Dihedral : 16.314 135.348 4443 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.96 % Favored : 98.01 % Rotamer: Outliers : 2.27 % Allowed : 19.00 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.15), residues: 3214 helix: 1.63 (0.14), residues: 1264 sheet: 0.31 (0.28), residues: 362 loop : 0.28 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 765 HIS 0.004 0.001 HIS H 238 PHE 0.019 0.001 PHE D 155 TYR 0.022 0.001 TYR A 178 ARG 0.006 0.000 ARG D 752 Details of bonding type rmsd hydrogen bonds : bond 0.03352 ( 1256) hydrogen bonds : angle 4.47296 ( 3465) covalent geometry : bond 0.00232 (27891) covalent geometry : angle 0.50708 (38020) *********************** 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 381 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 317 time to evaluate : 3.097 Fit side-chains revert: symmetry clash REVERT: A 126 LYS cc_start: 0.6706 (tttt) cc_final: 0.6157 (pttt) REVERT: A 174 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7366 (mm-30) REVERT: B 132 LYS cc_start: 0.7817 (ttmm) cc_final: 0.7464 (tttm) REVERT: B 140 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8055 (mt) REVERT: B 153 GLN cc_start: 0.6897 (tm-30) cc_final: 0.6571 (mm-40) REVERT: B 217 MET cc_start: 0.8479 (tpt) cc_final: 0.8167 (tpt) REVERT: C 113 MET cc_start: 0.8292 (tpp) cc_final: 0.7670 (tpp) REVERT: C 178 ASP cc_start: 0.5448 (m-30) cc_final: 0.5160 (t0) REVERT: C 396 TYR cc_start: 0.5949 (OUTLIER) cc_final: 0.5605 (m-80) REVERT: C 535 ARG cc_start: 0.8060 (mtt180) cc_final: 0.7562 (mtm180) REVERT: C 748 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7981 (tt0) REVERT: C 786 TYR cc_start: 0.8539 (m-80) cc_final: 0.8319 (m-80) REVERT: C 793 GLU cc_start: 0.7286 (pt0) cc_final: 0.6972 (pt0) REVERT: C 1045 ASP cc_start: 0.7096 (m-30) cc_final: 0.6715 (t0) REVERT: D 177 ASP cc_start: 0.7644 (t0) cc_final: 0.6666 (m-30) REVERT: D 260 ARG cc_start: 0.8148 (ttm170) cc_final: 0.7819 (mtp85) REVERT: D 303 ARG cc_start: 0.7617 (mmt180) cc_final: 0.7405 (tpt170) REVERT: D 319 MET cc_start: 0.8228 (mtp) cc_final: 0.7925 (mtp) REVERT: D 351 LYS cc_start: 0.8386 (mmtt) cc_final: 0.8031 (mptt) REVERT: D 387 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7783 (ttpt) REVERT: D 432 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6949 (mp0) REVERT: D 471 MET cc_start: 0.8776 (mmm) cc_final: 0.8328 (mmp) REVERT: D 622 LYS cc_start: 0.7594 (mttt) cc_final: 0.7372 (mttm) REVERT: D 741 ASN cc_start: 0.7798 (p0) cc_final: 0.7521 (p0) REVERT: D 754 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6627 (pp) REVERT: D 826 ARG cc_start: 0.6896 (mtm180) cc_final: 0.6649 (mtp-110) REVERT: D 957 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7110 (mt) REVERT: D 1053 LYS cc_start: 0.8376 (tttt) cc_final: 0.7873 (ttmm) REVERT: D 1109 GLU cc_start: 0.6570 (tp30) cc_final: 0.5939 (tm-30) REVERT: D 1188 LYS cc_start: 0.7963 (mtmt) cc_final: 0.7697 (mtpp) REVERT: F 25 LYS cc_start: 0.8049 (mttm) cc_final: 0.7779 (mttt) REVERT: F 32 GLU cc_start: 0.7450 (tt0) cc_final: 0.7083 (tt0) REVERT: G 10 HIS cc_start: 0.8638 (OUTLIER) cc_final: 0.8113 (m-70) REVERT: G 29 GLN cc_start: 0.7756 (mm-40) cc_final: 0.7486 (mm110) REVERT: H 56 HIS cc_start: 0.7064 (p90) cc_final: 0.6488 (p90) REVERT: H 77 MET cc_start: 0.7436 (ptm) cc_final: 0.7011 (ptm) REVERT: H 144 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7160 (tt0) REVERT: H 182 ASP cc_start: 0.7834 (m-30) cc_final: 0.7554 (m-30) REVERT: H 198 MET cc_start: 0.8024 (mtp) cc_final: 0.7452 (mtt) outliers start: 64 outliers final: 44 residues processed: 370 average time/residue: 0.4310 time to fit residues: 250.8635 Evaluate side-chains 339 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 288 time to evaluate : 3.313 ------------------------------------------------------------------------------- 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 156 THR Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 23 PHE 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 C residue 69 TYR Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 254 LEU 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 538 GLU Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 776 MET Chi-restraints excluded: chain C residue 797 GLU Chi-restraints excluded: chain C residue 815 VAL 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 D residue 68 VAL Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 216 PHE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 957 LEU Chi-restraints excluded: chain D residue 1015 ILE 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 F residue 9 LEU Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 10 HIS Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 204 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 303 optimal weight: 0.4980 chunk 112 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 263 optimal weight: 1.9990 chunk 227 optimal weight: 0.8980 chunk 261 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 209 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 465 GLN D 218 ASN D 318 HIS ** 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 = 0.3965 r_free = 0.3965 target = 0.167072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.130850 restraints weight = 32719.085| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.61 r_work: 0.3308 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27891 Z= 0.171 Angle : 0.570 27.178 38020 Z= 0.297 Chirality : 0.044 0.255 4285 Planarity : 0.005 0.197 4689 Dihedral : 16.361 137.251 4443 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.49 % Favored : 97.48 % Rotamer: Outliers : 2.38 % Allowed : 18.68 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.15), residues: 3214 helix: 1.41 (0.14), residues: 1271 sheet: 0.18 (0.26), residues: 392 loop : 0.18 (0.16), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 765 HIS 0.005 0.001 HIS D 785 PHE 0.021 0.002 PHE D 654 TYR 0.039 0.002 TYR D1050 ARG 0.008 0.000 ARG D 752 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 1256) hydrogen bonds : angle 4.62818 ( 3465) covalent geometry : bond 0.00411 (27891) covalent geometry : angle 0.56996 (38020) *********************** 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 367 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 300 time to evaluate : 2.979 Fit side-chains revert: symmetry clash REVERT: A 126 LYS cc_start: 0.6742 (tttt) cc_final: 0.6218 (pttp) REVERT: A 174 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7468 (mm-30) REVERT: B 132 LYS cc_start: 0.7853 (ttmm) cc_final: 0.7531 (tttm) REVERT: B 140 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8156 (mt) REVERT: B 153 GLN cc_start: 0.6840 (tm-30) cc_final: 0.6478 (mm-40) REVERT: C 113 MET cc_start: 0.8298 (tpp) cc_final: 0.7567 (tpp) REVERT: C 119 MET cc_start: 0.8937 (ttm) cc_final: 0.8737 (mtp) REVERT: C 178 ASP cc_start: 0.5566 (m-30) cc_final: 0.5191 (t0) REVERT: C 419 PHE cc_start: 0.7901 (OUTLIER) cc_final: 0.7583 (m-80) REVERT: C 535 ARG cc_start: 0.8066 (mtt180) cc_final: 0.7545 (mtm180) REVERT: C 748 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7954 (tt0) REVERT: C 793 GLU cc_start: 0.7374 (pt0) cc_final: 0.7071 (pt0) REVERT: C 802 LYS cc_start: 0.7334 (ptmm) cc_final: 0.7070 (pttp) REVERT: C 839 ASP cc_start: 0.7644 (m-30) cc_final: 0.7321 (m-30) REVERT: C 840 ILE cc_start: 0.8463 (mm) cc_final: 0.8125 (tp) REVERT: C 852 GLU cc_start: 0.3965 (OUTLIER) cc_final: 0.3245 (pm20) REVERT: C 1045 ASP cc_start: 0.7240 (m-30) cc_final: 0.6808 (t0) REVERT: D 40 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7676 (mttt) REVERT: D 56 LYS cc_start: 0.8463 (tptp) cc_final: 0.7634 (ptpp) REVERT: D 260 ARG cc_start: 0.8263 (ttm170) cc_final: 0.7914 (mtp85) REVERT: D 303 ARG cc_start: 0.7674 (mmt180) cc_final: 0.7418 (tpt170) REVERT: D 319 MET cc_start: 0.8235 (mtp) cc_final: 0.7943 (mtp) REVERT: D 351 LYS cc_start: 0.8521 (mmtt) cc_final: 0.8133 (mptt) REVERT: D 387 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7872 (ttpt) REVERT: D 432 GLU cc_start: 0.7220 (mm-30) cc_final: 0.6928 (mp0) REVERT: D 471 MET cc_start: 0.8708 (mmm) cc_final: 0.8284 (mmp) REVERT: D 622 LYS cc_start: 0.7636 (mttt) cc_final: 0.7400 (mttm) REVERT: D 642 MET cc_start: 0.8113 (mmm) cc_final: 0.7810 (mmm) REVERT: D 693 ARG cc_start: 0.5136 (OUTLIER) cc_final: 0.4301 (ptm160) REVERT: D 741 ASN cc_start: 0.7717 (p0) cc_final: 0.7467 (p0) REVERT: D 754 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6732 (pp) REVERT: D 957 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7388 (mt) REVERT: D 1053 LYS cc_start: 0.8472 (tttt) cc_final: 0.7891 (ttmm) REVERT: D 1109 GLU cc_start: 0.6588 (tp30) cc_final: 0.5945 (tm-30) REVERT: F 32 GLU cc_start: 0.7464 (tt0) cc_final: 0.7100 (tt0) REVERT: F 38 LEU cc_start: 0.8425 (mt) cc_final: 0.8129 (mt) REVERT: G 10 HIS cc_start: 0.8671 (OUTLIER) cc_final: 0.8203 (m-70) REVERT: G 16 ILE cc_start: 0.7975 (mt) cc_final: 0.7687 (tt) REVERT: G 27 GLU cc_start: 0.8080 (tp30) cc_final: 0.7823 (tp30) REVERT: G 29 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7445 (mm110) REVERT: H 56 HIS cc_start: 0.7162 (p90) cc_final: 0.6594 (p90) REVERT: H 77 MET cc_start: 0.7354 (ptm) cc_final: 0.6861 (ptm) REVERT: H 144 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7168 (tt0) REVERT: H 156 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.6357 (mpt) REVERT: H 182 ASP cc_start: 0.7882 (m-30) cc_final: 0.7616 (m-30) REVERT: H 198 MET cc_start: 0.8068 (mtp) cc_final: 0.7489 (mtt) outliers start: 67 outliers final: 49 residues processed: 359 average time/residue: 0.4471 time to fit residues: 254.0047 Evaluate side-chains 348 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 288 time to evaluate : 2.955 ------------------------------------------------------------------------------- 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 156 THR Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 23 PHE 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 198 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 254 LEU 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 434 MET Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 776 MET Chi-restraints excluded: chain C residue 797 GLU Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 852 GLU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 693 ARG Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 864 ILE Chi-restraints excluded: chain D residue 957 LEU Chi-restraints excluded: chain D residue 1015 ILE 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 F residue 9 LEU Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 10 HIS Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 204 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 242 optimal weight: 5.9990 chunk 153 optimal weight: 0.6980 chunk 247 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 chunk 252 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 162 optimal weight: 4.9990 chunk 203 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 chunk 64 optimal weight: 20.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 465 GLN D 218 ASN D 282 GLN D 318 HIS ** D 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.166597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.130229 restraints weight = 32688.914| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.61 r_work: 0.3240 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27891 Z= 0.172 Angle : 0.578 26.687 38020 Z= 0.302 Chirality : 0.044 0.241 4285 Planarity : 0.005 0.196 4689 Dihedral : 16.363 138.202 4443 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.58 % Favored : 97.39 % Rotamer: Outliers : 2.41 % Allowed : 19.03 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.15), residues: 3214 helix: 1.26 (0.14), residues: 1277 sheet: 0.17 (0.26), residues: 383 loop : 0.09 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 765 HIS 0.006 0.001 HIS C1042 PHE 0.021 0.002 PHE D 155 TYR 0.034 0.002 TYR D1050 ARG 0.007 0.000 ARG D 752 Details of bonding type rmsd hydrogen bonds : bond 0.03985 ( 1256) hydrogen bonds : angle 4.71543 ( 3465) covalent geometry : bond 0.00414 (27891) covalent geometry : angle 0.57801 (38020) ********************** 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 368 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 300 time to evaluate : 2.919 Fit side-chains revert: symmetry clash REVERT: A 126 LYS cc_start: 0.6831 (tttt) cc_final: 0.6301 (pttp) REVERT: A 174 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7476 (mm-30) REVERT: B 132 LYS cc_start: 0.7905 (ttmm) cc_final: 0.7584 (tttm) REVERT: B 140 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8183 (mt) REVERT: B 153 GLN cc_start: 0.6898 (tm-30) cc_final: 0.6483 (mm-40) REVERT: B 212 LEU cc_start: 0.8589 (tp) cc_final: 0.8262 (mt) REVERT: C 113 MET cc_start: 0.8337 (tpp) cc_final: 0.7611 (tpp) REVERT: C 535 ARG cc_start: 0.8090 (mtt180) cc_final: 0.7559 (mtm180) REVERT: C 602 MET cc_start: 0.7581 (mtt) cc_final: 0.6970 (mtt) REVERT: C 748 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8022 (tt0) REVERT: C 793 GLU cc_start: 0.7570 (pt0) cc_final: 0.7283 (pt0) REVERT: C 802 LYS cc_start: 0.7323 (ptmm) cc_final: 0.7032 (pttp) REVERT: C 839 ASP cc_start: 0.7644 (m-30) cc_final: 0.7318 (m-30) REVERT: C 840 ILE cc_start: 0.8423 (mm) cc_final: 0.8085 (tp) REVERT: C 852 GLU cc_start: 0.4157 (OUTLIER) cc_final: 0.3372 (pm20) REVERT: C 1045 ASP cc_start: 0.7108 (m-30) cc_final: 0.6701 (t0) REVERT: D 40 LYS cc_start: 0.8185 (tmtt) cc_final: 0.7713 (mttt) REVERT: D 56 LYS cc_start: 0.8472 (tptp) cc_final: 0.7681 (ptpp) REVERT: D 260 ARG cc_start: 0.8309 (ttm170) cc_final: 0.7955 (mtp85) REVERT: D 303 ARG cc_start: 0.7652 (mmt180) cc_final: 0.7396 (tpt170) REVERT: D 319 MET cc_start: 0.8231 (mtp) cc_final: 0.7949 (mtp) REVERT: D 351 LYS cc_start: 0.8560 (mmtt) cc_final: 0.8179 (mptt) REVERT: D 387 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7874 (ttpt) REVERT: D 432 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7065 (mp0) REVERT: D 471 MET cc_start: 0.8738 (mmm) cc_final: 0.8374 (mmp) REVERT: D 622 LYS cc_start: 0.7652 (mttt) cc_final: 0.7423 (mttm) REVERT: D 693 ARG cc_start: 0.5149 (OUTLIER) cc_final: 0.4373 (ptm160) REVERT: D 741 ASN cc_start: 0.7747 (p0) cc_final: 0.7546 (p0) REVERT: D 754 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6672 (pp) REVERT: D 957 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7319 (mt) REVERT: D 1053 LYS cc_start: 0.8485 (tttt) cc_final: 0.7930 (ttmm) REVERT: D 1109 GLU cc_start: 0.6631 (tp30) cc_final: 0.5988 (tm-30) REVERT: F 32 GLU cc_start: 0.7478 (tt0) cc_final: 0.7106 (tt0) REVERT: G 10 HIS cc_start: 0.8697 (OUTLIER) cc_final: 0.8252 (m-70) REVERT: G 16 ILE cc_start: 0.7994 (mt) cc_final: 0.7654 (tt) REVERT: G 27 GLU cc_start: 0.8083 (tp30) cc_final: 0.7831 (tp30) REVERT: H 56 HIS cc_start: 0.7159 (p90) cc_final: 0.6597 (p90) REVERT: H 77 MET cc_start: 0.7458 (ptm) cc_final: 0.7037 (ptm) REVERT: H 144 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7197 (tt0) REVERT: H 156 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.6406 (mpt) REVERT: H 182 ASP cc_start: 0.8095 (m-30) cc_final: 0.7829 (m-30) REVERT: H 198 MET cc_start: 0.8091 (mtp) cc_final: 0.7511 (mtt) outliers start: 68 outliers final: 54 residues processed: 360 average time/residue: 0.4149 time to fit residues: 234.8934 Evaluate side-chains 361 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 298 time to evaluate : 3.213 ------------------------------------------------------------------------------- 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 156 THR Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 23 PHE 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 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 98 LEU Chi-restraints excluded: chain C residue 254 LEU 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 538 GLU Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 776 MET Chi-restraints excluded: chain C residue 797 GLU Chi-restraints excluded: chain C residue 815 VAL 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 991 VAL Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 693 ARG Chi-restraints excluded: chain D residue 721 MET 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 864 ILE Chi-restraints excluded: chain D residue 957 LEU Chi-restraints excluded: chain D residue 1015 ILE 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 71 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 10 HIS Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 204 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 197 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 180 optimal weight: 0.6980 chunk 109 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 288 optimal weight: 5.9990 chunk 276 optimal weight: 7.9990 chunk 269 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 465 GLN D 218 ASN D 318 HIS ** D 897 ASN ** 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 = 0.3964 r_free = 0.3964 target = 0.167113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.130704 restraints weight = 32889.258| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.62 r_work: 0.3294 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27891 Z= 0.157 Angle : 0.562 24.119 38020 Z= 0.295 Chirality : 0.044 0.224 4285 Planarity : 0.005 0.189 4689 Dihedral : 16.318 139.339 4443 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.46 % Favored : 97.51 % Rotamer: Outliers : 2.31 % Allowed : 19.35 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.15), residues: 3214 helix: 1.36 (0.14), residues: 1264 sheet: 0.15 (0.26), residues: 388 loop : 0.13 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 765 HIS 0.005 0.001 HIS D 785 PHE 0.020 0.001 PHE D 155 TYR 0.043 0.002 TYR D1050 ARG 0.008 0.000 ARG D 752 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 1256) hydrogen bonds : angle 4.68290 ( 3465) covalent geometry : bond 0.00375 (27891) covalent geometry : angle 0.56238 (38020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16010.49 seconds wall clock time: 282 minutes 35.22 seconds (16955.22 seconds total)