Starting phenix.real_space_refine on Sun May 25 17:29:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x6g_38088/05_2025/8x6g_38088.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x6g_38088/05_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_38088/05_2025/8x6g_38088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x6g_38088/05_2025/8x6g_38088.map" model { file = "/net/cci-nas-00/data/ceres_data/8x6g_38088/05_2025/8x6g_38088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x6g_38088/05_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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 15.99, per 1000 atoms: 0.59 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: 7.71 Conformation dependent library (CDL) restraints added in 3.6 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: 9.52 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: 13.16 Time building geometry restraints manager: 8.84 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.210 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 70.200 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.110 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: 0.000 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.660 ------------------------------------------------------------------------------- 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 : 2.898 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: 0.4764 time to fit residues: 435.1806 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 : 2.997 ------------------------------------------------------------------------------- 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 = 0.157597 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 = 33185.781| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.84 r_work: 0.3190 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 : 2.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7363 (pt0) REVERT: A 103 ASP cc_start: 0.6385 (p0) cc_final: 0.5486 (p0) REVERT: A 106 GLU cc_start: 0.6423 (mp0) cc_final: 0.6097 (tp30) REVERT: A 107 VAL cc_start: 0.7456 (p) cc_final: 0.6612 (p) REVERT: A 126 LYS cc_start: 0.6763 (tttt) cc_final: 0.6283 (tttm) REVERT: A 172 PRO cc_start: 0.8415 (Cg_endo) cc_final: 0.8138 (Cg_endo) REVERT: B 74 ASP cc_start: 0.8581 (p0) cc_final: 0.8256 (p0) REVERT: B 121 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8106 (mm) REVERT: B 132 LYS cc_start: 0.7894 (ttmm) cc_final: 0.7514 (tttt) REVERT: B 146 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.8037 (mtp85) REVERT: B 153 GLN cc_start: 0.6884 (tm-30) cc_final: 0.6585 (mm-40) REVERT: B 217 MET cc_start: 0.8576 (tpt) cc_final: 0.8366 (tpt) REVERT: C 38 GLU cc_start: 0.8738 (tt0) cc_final: 0.8489 (mt-10) REVERT: C 109 GLN cc_start: 0.5186 (tt0) cc_final: 0.4859 (tt0) REVERT: C 113 MET cc_start: 0.8195 (tpp) cc_final: 0.7623 (tpp) REVERT: C 116 PHE cc_start: 0.7624 (t80) cc_final: 0.7324 (t80) REVERT: C 178 ASP cc_start: 0.5601 (m-30) cc_final: 0.5234 (t0) REVERT: C 263 LYS cc_start: 0.7651 (mmmt) cc_final: 0.6353 (mmmt) REVERT: C 458 LYS cc_start: 0.7765 (tttt) cc_final: 0.7551 (tttp) REVERT: C 470 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7893 (tpp) REVERT: C 528 ASN cc_start: 0.8667 (OUTLIER) cc_final: 0.8448 (m-40) REVERT: C 579 LYS cc_start: 0.6761 (mtpt) cc_final: 0.6434 (mmtm) REVERT: C 589 ASP cc_start: 0.6481 (m-30) cc_final: 0.5956 (t70) REVERT: C 763 MET cc_start: 0.8147 (ptm) cc_final: 0.7871 (ptm) REVERT: C 814 ASN cc_start: 0.6779 (m-40) cc_final: 0.6451 (t0) REVERT: C 839 ASP cc_start: 0.7631 (m-30) cc_final: 0.7381 (m-30) REVERT: C 852 GLU cc_start: 0.3336 (OUTLIER) cc_final: 0.2813 (pm20) REVERT: C 956 MET cc_start: 0.8616 (mtm) cc_final: 0.8324 (mtp) REVERT: C 1045 ASP cc_start: 0.7037 (m-30) cc_final: 0.6468 (t0) REVERT: C 1117 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8224 (mt-10) REVERT: C 1120 SER cc_start: 0.8586 (t) cc_final: 0.8187 (m) REVERT: C 1143 LYS cc_start: 0.8075 (mtmm) cc_final: 0.7777 (mttt) REVERT: C 1154 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7471 (ttm) REVERT: D 137 VAL cc_start: 0.8173 (t) cc_final: 0.7910 (m) REVERT: D 248 ARG cc_start: 0.6912 (ptm160) cc_final: 0.6662 (ttm-80) REVERT: D 260 ARG cc_start: 0.8442 (ttm170) cc_final: 0.7955 (mtp85) REVERT: D 303 ARG cc_start: 0.7705 (mmt180) cc_final: 0.7302 (ttm-80) REVERT: D 319 MET cc_start: 0.8403 (mtp) cc_final: 0.8028 (mtp) REVERT: D 351 LYS cc_start: 0.8650 (mmtt) cc_final: 0.8359 (mptt) REVERT: D 432 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7347 (mp0) REVERT: D 471 MET cc_start: 0.8728 (mmm) cc_final: 0.8473 (mmp) REVERT: D 690 GLN cc_start: 0.5256 (OUTLIER) cc_final: 0.4975 (tm-30) REVERT: D 835 GLU cc_start: 0.6741 (tp30) cc_final: 0.6267 (pt0) REVERT: D 977 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6436 (mt-10) REVERT: D 1053 LYS cc_start: 0.8543 (tttt) cc_final: 0.8328 (tttm) REVERT: D 1065 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7451 (pt0) REVERT: D 1101 HIS cc_start: 0.7304 (p-80) cc_final: 0.7066 (p90) REVERT: D 1109 GLU cc_start: 0.6069 (tp30) cc_final: 0.5342 (tm-30) REVERT: D 1129 LYS cc_start: 0.8149 (tttt) cc_final: 0.7840 (tptp) REVERT: D 1181 MET cc_start: 0.9061 (mmm) cc_final: 0.8798 (mmm) REVERT: D 1188 LYS cc_start: 0.8297 (mttt) cc_final: 0.7869 (mtpp) REVERT: E 57 GLN cc_start: 0.4159 (OUTLIER) cc_final: 0.2947 (mm110) REVERT: E 78 LEU cc_start: 0.6299 (OUTLIER) cc_final: 0.6058 (mp) REVERT: F 25 LYS cc_start: 0.8288 (mttm) cc_final: 0.7721 (mmtt) REVERT: F 32 GLU cc_start: 0.7258 (tt0) cc_final: 0.6853 (tt0) REVERT: G 27 GLU cc_start: 0.8079 (tp30) cc_final: 0.7798 (tp30) REVERT: G 29 GLN cc_start: 0.7565 (mm-40) cc_final: 0.7273 (mp10) REVERT: G 50 LYS cc_start: 0.8118 (tptt) cc_final: 0.7766 (tptp) REVERT: H 52 LYS cc_start: 0.7035 (mttt) cc_final: 0.5007 (ttpt) REVERT: H 56 HIS cc_start: 0.7205 (p90) cc_final: 0.6799 (p90) REVERT: H 144 GLU cc_start: 0.7405 (mt-10) cc_final: 0.6839 (tt0) REVERT: H 186 GLN cc_start: 0.6822 (tp40) cc_final: 0.6555 (tp40) REVERT: H 195 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7594 (mt-10) REVERT: H 198 MET cc_start: 0.8213 (mtp) cc_final: 0.7786 (mtp) REVERT: H 237 MET cc_start: 0.7208 (tpt) cc_final: 0.7004 (tpt) REVERT: H 239 VAL cc_start: 0.7215 (OUTLIER) cc_final: 0.6918 (t) outliers start: 103 outliers final: 60 residues processed: 445 average time/residue: 0.4229 time to fit residues: 289.1679 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 : 2.888 ------------------------------------------------------------------------------- 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: 3.9990 chunk 120 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 302 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 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: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.168423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.130175 restraints weight = 32311.151| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.72 r_work: 0.3233 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 27891 Z= 0.134 Angle : 0.539 13.496 38020 Z= 0.291 Chirality : 0.043 0.247 4285 Planarity : 0.005 0.165 4689 Dihedral : 16.806 141.241 4446 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.59 % Favored : 98.38 % Rotamer: Outliers : 2.24 % Allowed : 15.34 % Favored : 82.42 % 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: 0.81 (0.15), residues: 3214 helix: 1.18 (0.14), residues: 1270 sheet: 0.26 (0.26), residues: 389 loop : 0.21 (0.16), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 0.007 0.000 ARG C 644 Details of bonding type rmsd hydrogen bonds : bond 0.04133 ( 1256) hydrogen bonds : angle 4.87485 ( 3465) covalent geometry : bond 0.00311 (27891) covalent geometry : angle 0.53934 (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 415 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 352 time to evaluate : 3.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7156 (pt0) REVERT: A 103 ASP cc_start: 0.6278 (p0) cc_final: 0.5303 (p0) REVERT: A 107 VAL cc_start: 0.7054 (OUTLIER) cc_final: 0.6479 (p) REVERT: A 126 LYS cc_start: 0.6643 (tttt) cc_final: 0.5935 (pttp) REVERT: A 174 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7485 (mm-30) REVERT: B 132 LYS cc_start: 0.7825 (ttmm) cc_final: 0.7371 (tttt) REVERT: B 153 GLN cc_start: 0.7052 (tm-30) cc_final: 0.6817 (mm-40) REVERT: B 182 ASN cc_start: 0.7782 (t0) cc_final: 0.7542 (t0) REVERT: B 217 MET cc_start: 0.8493 (tpt) cc_final: 0.8184 (tpt) REVERT: C 47 GLU cc_start: 0.8007 (tt0) cc_final: 0.7751 (tt0) REVERT: C 51 ASP cc_start: 0.6429 (m-30) cc_final: 0.6019 (m-30) REVERT: C 98 LEU cc_start: 0.7914 (tp) cc_final: 0.7372 (tp) REVERT: C 113 MET cc_start: 0.8241 (tpp) cc_final: 0.7639 (tpp) REVERT: C 116 PHE cc_start: 0.7428 (t80) cc_final: 0.7161 (t80) REVERT: C 178 ASP cc_start: 0.5507 (m-30) cc_final: 0.5158 (t70) REVERT: C 263 LYS cc_start: 0.7649 (mmmt) cc_final: 0.6153 (mmmt) REVERT: C 458 LYS cc_start: 0.7840 (tttt) cc_final: 0.7546 (tttp) REVERT: C 589 ASP cc_start: 0.6302 (m-30) cc_final: 0.5925 (t70) REVERT: C 602 MET cc_start: 0.7884 (mtt) cc_final: 0.7444 (mtt) REVERT: C 638 MET cc_start: 0.7733 (mtt) cc_final: 0.7502 (mtt) REVERT: C 684 VAL cc_start: 0.8539 (t) cc_final: 0.8224 (p) REVERT: C 763 MET cc_start: 0.8132 (ptm) cc_final: 0.7801 (ptm) REVERT: C 786 TYR cc_start: 0.8654 (m-80) cc_final: 0.8373 (m-80) REVERT: C 814 ASN cc_start: 0.6632 (m-40) cc_final: 0.6181 (t0) REVERT: C 839 ASP cc_start: 0.7638 (m-30) cc_final: 0.7359 (m-30) REVERT: C 956 MET cc_start: 0.8485 (mtm) cc_final: 0.7956 (mtp) REVERT: C 1043 MET cc_start: 0.5505 (ptt) cc_final: 0.5200 (ptt) REVERT: C 1045 ASP cc_start: 0.7032 (m-30) cc_final: 0.6458 (t0) REVERT: C 1070 PHE cc_start: 0.6901 (t80) cc_final: 0.6659 (t80) REVERT: D 10 MET cc_start: 0.8015 (ttm) cc_final: 0.7783 (ttt) REVERT: D 11 LYS cc_start: 0.8432 (tttt) cc_final: 0.7907 (tttt) REVERT: D 260 ARG cc_start: 0.8335 (ttm170) cc_final: 0.7952 (mtp85) REVERT: D 303 ARG cc_start: 0.7654 (mmt180) cc_final: 0.7249 (ttm-80) REVERT: D 351 LYS cc_start: 0.8533 (mmtt) cc_final: 0.8148 (mptt) REVERT: D 432 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7113 (mp0) REVERT: D 451 ASP cc_start: 0.8182 (p0) cc_final: 0.7846 (p0) REVERT: D 471 MET cc_start: 0.8666 (mmm) cc_final: 0.8332 (mmp) REVERT: D 507 LYS cc_start: 0.8518 (mmmt) cc_final: 0.8255 (mmmt) REVERT: D 826 ARG cc_start: 0.7055 (mtm180) cc_final: 0.6813 (mtp180) REVERT: D 933 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7624 (tm-30) REVERT: D 957 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.7002 (mt) REVERT: D 1053 LYS cc_start: 0.8429 (tttt) cc_final: 0.7813 (ttmm) REVERT: D 1109 GLU cc_start: 0.6153 (tp30) cc_final: 0.5429 (tm-30) REVERT: D 1129 LYS cc_start: 0.7991 (tttt) cc_final: 0.7708 (tptp) REVERT: D 1181 MET cc_start: 0.8982 (mmm) cc_final: 0.8684 (mmm) REVERT: E 78 LEU cc_start: 0.5966 (OUTLIER) cc_final: 0.5349 (mm) REVERT: F 25 LYS cc_start: 0.8072 (mttm) cc_final: 0.7797 (mttt) REVERT: F 31 ASP cc_start: 0.7693 (t70) cc_final: 0.7364 (t70) REVERT: F 32 GLU cc_start: 0.7195 (tt0) cc_final: 0.6792 (tt0) REVERT: G 27 GLU cc_start: 0.7920 (tp30) cc_final: 0.7639 (tp30) REVERT: G 29 GLN cc_start: 0.7405 (mm-40) cc_final: 0.7153 (mp10) REVERT: H 17 ASN cc_start: 0.6196 (m-40) cc_final: 0.5964 (m-40) REVERT: H 52 LYS cc_start: 0.6801 (mttt) cc_final: 0.4695 (ttpt) REVERT: H 56 HIS cc_start: 0.7133 (p90) cc_final: 0.6695 (p90) REVERT: H 77 MET cc_start: 0.7213 (ptm) cc_final: 0.6690 (ptm) REVERT: H 144 GLU cc_start: 0.7403 (mt-10) cc_final: 0.6834 (tt0) REVERT: H 198 MET cc_start: 0.8212 (mtp) cc_final: 0.7576 (mtt) REVERT: H 206 ILE cc_start: 0.7253 (mm) cc_final: 0.7017 (tt) REVERT: H 237 MET cc_start: 0.7439 (tpt) cc_final: 0.7189 (tpt) REVERT: H 239 VAL cc_start: 0.7176 (t) cc_final: 0.6914 (t) REVERT: H 251 GLN cc_start: 0.5787 (mt0) cc_final: 0.5316 (mt0) outliers start: 63 outliers final: 38 residues processed: 402 average time/residue: 0.4427 time to fit residues: 279.0767 Evaluate side-chains 336 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 295 time to evaluate : 3.305 ------------------------------------------------------------------------------- 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 529 SER Chi-restraints excluded: chain C residue 797 GLU Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 852 GLU Chi-restraints excluded: chain C residue 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: 2.9990 chunk 121 optimal weight: 1.9990 chunk 219 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 150 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 293 optimal weight: 0.8980 chunk 146 optimal weight: 6.9990 chunk 83 optimal weight: 0.0060 chunk 124 optimal weight: 10.0000 overall best weight: 1.5802 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.168231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.129883 restraints weight = 32392.698| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.72 r_work: 0.3265 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27891 Z= 0.133 Angle : 0.530 21.628 38020 Z= 0.282 Chirality : 0.043 0.302 4285 Planarity : 0.005 0.186 4689 Dihedral : 16.667 138.979 4443 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.74 % Favored : 98.23 % Rotamer: Outliers : 2.73 % Allowed : 15.55 % Favored : 81.71 % 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: 0.97 (0.15), residues: 3214 helix: 1.36 (0.14), residues: 1276 sheet: 0.25 (0.26), residues: 395 loop : 0.28 (0.16), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 199 HIS 0.004 0.001 HIS C 920 PHE 0.017 0.001 PHE G 47 TYR 0.018 0.001 TYR C1098 ARG 0.005 0.000 ARG C 644 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 1256) hydrogen bonds : angle 4.70087 ( 3465) covalent geometry : bond 0.00310 (27891) covalent geometry : angle 0.52979 (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 408 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 331 time to evaluate : 2.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7249 (pt0) REVERT: A 54 LYS cc_start: 0.7111 (OUTLIER) cc_final: 0.6835 (mtpt) REVERT: A 88 LYS cc_start: 0.7578 (mtpp) cc_final: 0.6337 (mttm) REVERT: A 103 ASP cc_start: 0.6393 (p0) cc_final: 0.5514 (p0) REVERT: A 107 VAL cc_start: 0.7366 (OUTLIER) cc_final: 0.7102 (p) REVERT: A 126 LYS cc_start: 0.6724 (tttt) cc_final: 0.6120 (pttt) REVERT: A 174 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7507 (mm-30) REVERT: B 132 LYS cc_start: 0.7776 (ttmm) cc_final: 0.7405 (tttm) REVERT: B 153 GLN cc_start: 0.7014 (tm-30) cc_final: 0.6757 (mm-40) REVERT: B 182 ASN cc_start: 0.7796 (t0) cc_final: 0.7584 (t0) REVERT: B 212 LEU cc_start: 0.8488 (tp) cc_final: 0.8169 (mt) REVERT: B 217 MET cc_start: 0.8412 (tpt) cc_final: 0.8128 (tpt) REVERT: C 51 ASP cc_start: 0.6372 (m-30) cc_final: 0.6159 (m-30) REVERT: C 98 LEU cc_start: 0.8051 (tp) cc_final: 0.7772 (tp) REVERT: C 113 MET cc_start: 0.8305 (tpp) cc_final: 0.7692 (tpp) REVERT: C 116 PHE cc_start: 0.7484 (t80) cc_final: 0.7269 (t80) REVERT: C 178 ASP cc_start: 0.5507 (m-30) cc_final: 0.5137 (t0) REVERT: C 263 LYS cc_start: 0.7741 (mmmt) cc_final: 0.6279 (mmmt) REVERT: C 317 GLU cc_start: 0.3857 (mt-10) cc_final: 0.3556 (tt0) REVERT: C 458 LYS cc_start: 0.7914 (tttt) cc_final: 0.7623 (tttp) REVERT: C 589 ASP cc_start: 0.6281 (m-30) cc_final: 0.5968 (t70) REVERT: C 684 VAL cc_start: 0.8439 (t) cc_final: 0.8230 (p) REVERT: C 752 MET cc_start: 0.8222 (tpp) cc_final: 0.7880 (tpp) REVERT: C 786 TYR cc_start: 0.8652 (m-80) cc_final: 0.8393 (m-80) REVERT: C 793 GLU cc_start: 0.7479 (pt0) cc_final: 0.7116 (pt0) REVERT: C 814 ASN cc_start: 0.6839 (m-40) cc_final: 0.6180 (t0) REVERT: C 839 ASP cc_start: 0.7703 (m-30) cc_final: 0.7448 (m-30) REVERT: C 880 HIS cc_start: 0.6701 (p-80) cc_final: 0.6408 (p90) REVERT: C 1045 ASP cc_start: 0.7059 (m-30) cc_final: 0.6527 (t0) REVERT: C 1070 PHE cc_start: 0.6864 (t80) cc_final: 0.6650 (t80) REVERT: D 260 ARG cc_start: 0.8344 (ttm170) cc_final: 0.7977 (mtp85) REVERT: D 303 ARG cc_start: 0.7683 (mmt180) cc_final: 0.7321 (ttm-80) REVERT: D 351 LYS cc_start: 0.8456 (mmtt) cc_final: 0.8121 (mptt) REVERT: D 432 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7126 (mp0) REVERT: D 451 ASP cc_start: 0.8334 (p0) cc_final: 0.7950 (p0) REVERT: D 471 MET cc_start: 0.8719 (mmm) cc_final: 0.8374 (mmp) REVERT: D 507 LYS cc_start: 0.8540 (mmmt) cc_final: 0.8279 (mmmt) REVERT: D 754 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6770 (pp) REVERT: D 789 LYS cc_start: 0.7321 (tttt) cc_final: 0.7071 (ttmm) REVERT: D 957 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7117 (mt) REVERT: D 1053 LYS cc_start: 0.8468 (tttt) cc_final: 0.7925 (ttmm) REVERT: D 1109 GLU cc_start: 0.6303 (tp30) cc_final: 0.5666 (tm-30) REVERT: D 1129 LYS cc_start: 0.7907 (tttt) cc_final: 0.7689 (tptp) REVERT: D 1181 MET cc_start: 0.9015 (mmm) cc_final: 0.8743 (mmm) REVERT: E 78 LEU cc_start: 0.6084 (OUTLIER) cc_final: 0.5838 (mm) REVERT: F 25 LYS cc_start: 0.8148 (mttm) cc_final: 0.7874 (mttt) REVERT: F 32 GLU cc_start: 0.7091 (tt0) cc_final: 0.6718 (tt0) REVERT: F 38 LEU cc_start: 0.8231 (mt) cc_final: 0.7986 (mt) REVERT: G 10 HIS cc_start: 0.8669 (OUTLIER) cc_final: 0.7977 (m-70) REVERT: G 27 GLU cc_start: 0.7929 (tp30) cc_final: 0.7657 (tp30) REVERT: G 29 GLN cc_start: 0.7412 (mm-40) cc_final: 0.7184 (mp10) REVERT: H 52 LYS cc_start: 0.6897 (mttt) cc_final: 0.4736 (ttpt) REVERT: H 56 HIS cc_start: 0.7089 (p90) cc_final: 0.6735 (p90) REVERT: H 77 MET cc_start: 0.7323 (ptm) cc_final: 0.6693 (ptm) REVERT: H 144 GLU cc_start: 0.7405 (mt-10) cc_final: 0.6962 (tt0) REVERT: H 156 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.6455 (mpt) REVERT: H 198 MET cc_start: 0.8236 (mtp) cc_final: 0.7611 (mtt) REVERT: H 206 ILE cc_start: 0.7258 (mm) cc_final: 0.7035 (tt) REVERT: H 237 MET cc_start: 0.7748 (tpt) cc_final: 0.7450 (tpt) REVERT: H 251 GLN cc_start: 0.5607 (mt0) cc_final: 0.5323 (mt0) outliers start: 77 outliers final: 51 residues processed: 389 average time/residue: 0.4340 time to fit residues: 262.5547 Evaluate side-chains 362 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 304 time to evaluate : 2.852 ------------------------------------------------------------------------------- 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 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 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 439 THR Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 538 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 1132 MET Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 216 PHE 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 811 VAL Chi-restraints excluded: chain D residue 957 LEU Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1044 LEU Chi-restraints excluded: chain D residue 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 251 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 203 optimal weight: 8.9990 chunk 224 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 227 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 294 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 598 ASN C 724 ASN C 725 GLN C 920 HIS D 218 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.164185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.127095 restraints weight = 32813.523| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.68 r_work: 0.3202 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 27891 Z= 0.265 Angle : 0.657 25.011 38020 Z= 0.346 Chirality : 0.047 0.286 4285 Planarity : 0.006 0.194 4689 Dihedral : 16.749 140.204 4443 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.74 % Favored : 97.23 % Rotamer: Outliers : 3.87 % Allowed : 15.84 % Favored : 80.29 % 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: 0.37 (0.14), residues: 3214 helix: 0.83 (0.14), residues: 1276 sheet: 0.07 (0.25), residues: 406 loop : -0.08 (0.16), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 199 HIS 0.010 0.002 HIS C 920 PHE 0.026 0.002 PHE G 47 TYR 0.027 0.002 TYR C1098 ARG 0.011 0.001 ARG C 644 Details of bonding type rmsd hydrogen bonds : bond 0.04897 ( 1256) hydrogen bonds : angle 5.04974 ( 3465) covalent geometry : bond 0.00642 (27891) covalent geometry : angle 0.65671 (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 416 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 307 time to evaluate : 2.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7311 (pt0) REVERT: A 54 LYS cc_start: 0.7171 (OUTLIER) cc_final: 0.6786 (mtpt) REVERT: A 174 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7555 (mm-30) REVERT: B 132 LYS cc_start: 0.7863 (ttmm) cc_final: 0.7500 (tttt) REVERT: B 153 GLN cc_start: 0.6985 (tm-30) cc_final: 0.6748 (mm-40) REVERT: B 175 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7542 (mtp180) REVERT: B 217 MET cc_start: 0.8558 (tpt) cc_final: 0.8240 (tpt) REVERT: C 113 MET cc_start: 0.8294 (tpp) cc_final: 0.7588 (tpp) REVERT: C 116 PHE cc_start: 0.7552 (t80) cc_final: 0.7255 (t80) REVERT: C 263 LYS cc_start: 0.7815 (mmmt) cc_final: 0.6485 (mmmt) REVERT: C 458 LYS cc_start: 0.7689 (tttt) cc_final: 0.7361 (tttp) REVERT: C 589 ASP cc_start: 0.6334 (m-30) cc_final: 0.6041 (t70) REVERT: C 748 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7984 (tt0) REVERT: C 839 ASP cc_start: 0.7655 (m-30) cc_final: 0.7393 (m-30) REVERT: C 852 GLU cc_start: 0.4004 (OUTLIER) cc_final: 0.3410 (pm20) REVERT: C 1045 ASP cc_start: 0.7005 (m-30) cc_final: 0.6493 (t0) REVERT: D 56 LYS cc_start: 0.8275 (tptp) cc_final: 0.8073 (tttm) REVERT: D 260 ARG cc_start: 0.8324 (ttm170) cc_final: 0.7908 (mtp85) REVERT: D 303 ARG cc_start: 0.7744 (mmt180) cc_final: 0.7343 (ttm-80) REVERT: D 319 MET cc_start: 0.8339 (mtp) cc_final: 0.8003 (mtp) REVERT: D 351 LYS cc_start: 0.8645 (mmtt) cc_final: 0.8296 (mptt) REVERT: D 432 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7034 (mp0) REVERT: D 471 MET cc_start: 0.8711 (mmm) cc_final: 0.8352 (mmp) REVERT: D 515 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8149 (mt) REVERT: D 642 MET cc_start: 0.8131 (mmm) cc_final: 0.7806 (mmm) REVERT: D 693 ARG cc_start: 0.5199 (OUTLIER) cc_final: 0.4336 (ptm160) REVERT: D 754 LEU cc_start: 0.6960 (OUTLIER) cc_final: 0.6512 (pp) REVERT: D 957 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7178 (mt) REVERT: D 1023 GLN cc_start: 0.5600 (OUTLIER) cc_final: 0.5377 (mp10) REVERT: D 1053 LYS cc_start: 0.8496 (tttt) cc_final: 0.7931 (ttmm) REVERT: D 1109 GLU cc_start: 0.6352 (tp30) cc_final: 0.5692 (tm-30) REVERT: D 1129 LYS cc_start: 0.8037 (tttt) cc_final: 0.7805 (tptp) REVERT: D 1181 MET cc_start: 0.9083 (mmm) cc_final: 0.8815 (mmm) REVERT: E 62 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6860 (mp) REVERT: E 78 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.6134 (mp) REVERT: F 32 GLU cc_start: 0.7387 (tt0) cc_final: 0.7016 (tt0) REVERT: F 38 LEU cc_start: 0.8408 (mt) cc_final: 0.8106 (mt) REVERT: G 10 HIS cc_start: 0.8751 (OUTLIER) cc_final: 0.8172 (m-70) REVERT: G 27 GLU cc_start: 0.8034 (tp30) cc_final: 0.7761 (tp30) REVERT: G 29 GLN cc_start: 0.7823 (mm-40) cc_final: 0.7432 (mp10) REVERT: G 39 LYS cc_start: 0.8239 (ttpp) cc_final: 0.7981 (ttpp) REVERT: G 50 LYS cc_start: 0.7976 (tptt) cc_final: 0.7704 (tptp) REVERT: H 52 LYS cc_start: 0.7243 (mttt) cc_final: 0.5032 (ttpt) REVERT: H 56 HIS cc_start: 0.7125 (p90) cc_final: 0.6771 (p90) REVERT: H 77 MET cc_start: 0.7322 (ptm) cc_final: 0.6832 (ptm) REVERT: H 144 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7115 (tt0) REVERT: H 156 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.5929 (mpt) REVERT: H 182 ASP cc_start: 0.6966 (t70) cc_final: 0.6757 (m-30) REVERT: H 198 MET cc_start: 0.8178 (mtp) cc_final: 0.7590 (mtt) REVERT: H 237 MET cc_start: 0.7602 (tpt) cc_final: 0.7357 (tpt) REVERT: H 251 GLN cc_start: 0.5437 (mt0) cc_final: 0.5222 (mt0) outliers start: 109 outliers final: 74 residues processed: 398 average time/residue: 0.3991 time to fit residues: 246.4974 Evaluate side-chains 372 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 285 time to evaluate : 3.252 ------------------------------------------------------------------------------- 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 115 ASP 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 424 SER 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 538 GLU Chi-restraints excluded: chain C residue 599 ASN Chi-restraints excluded: chain C residue 686 SER 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 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 483 LYS 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 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 1023 GLN 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 1139 SER Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 62 LEU 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 Chi-restraints excluded: chain H residue 239 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 66 optimal weight: 20.0000 chunk 76 optimal weight: 0.0040 chunk 96 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 chunk 302 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 269 optimal weight: 3.9990 chunk 276 optimal weight: 10.0000 chunk 286 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 overall best weight: 3.4000 ------------------------------------------------------------------------------- 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 D 218 ASN D 703 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.165295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.127886 restraints weight = 32864.306| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.64 r_work: 0.3240 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 27891 Z= 0.200 Angle : 0.591 25.535 38020 Z= 0.311 Chirality : 0.045 0.274 4285 Planarity : 0.005 0.195 4689 Dihedral : 16.602 137.399 4443 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.46 % Favored : 97.51 % Rotamer: Outliers : 3.87 % Allowed : 16.80 % Favored : 79.33 % 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: 0.46 (0.14), residues: 3214 helix: 0.95 (0.14), residues: 1278 sheet: 0.01 (0.26), residues: 380 loop : -0.06 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 765 HIS 0.005 0.001 HIS C1042 PHE 0.021 0.002 PHE G 47 TYR 0.022 0.002 TYR C1098 ARG 0.009 0.001 ARG D 752 Details of bonding type rmsd hydrogen bonds : bond 0.04330 ( 1256) hydrogen bonds : angle 4.89451 ( 3465) covalent geometry : bond 0.00484 (27891) covalent geometry : angle 0.59083 (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 404 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 295 time to evaluate : 3.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7086 (OUTLIER) cc_final: 0.6662 (mtpt) REVERT: A 87 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8326 (mp) REVERT: A 174 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7523 (mm-30) REVERT: B 19 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8563 (ttmm) REVERT: B 132 LYS cc_start: 0.7844 (ttmm) cc_final: 0.7512 (tttt) REVERT: B 146 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7706 (mtp85) REVERT: B 153 GLN cc_start: 0.7053 (tm-30) cc_final: 0.6672 (mm-40) REVERT: B 212 LEU cc_start: 0.8693 (tp) cc_final: 0.8421 (mt) REVERT: B 217 MET cc_start: 0.8485 (tpt) cc_final: 0.8145 (tpt) REVERT: C 113 MET cc_start: 0.8270 (tpp) cc_final: 0.7614 (tpp) REVERT: C 116 PHE cc_start: 0.7502 (t80) cc_final: 0.7151 (t80) REVERT: C 263 LYS cc_start: 0.7279 (mmmt) cc_final: 0.6340 (mmmt) REVERT: C 458 LYS cc_start: 0.7930 (tttt) cc_final: 0.7583 (tttp) REVERT: C 589 ASP cc_start: 0.6119 (m-30) cc_final: 0.5889 (t70) REVERT: C 748 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7973 (tt0) REVERT: C 839 ASP cc_start: 0.7686 (m-30) cc_final: 0.7419 (m-30) REVERT: C 852 GLU cc_start: 0.3905 (OUTLIER) cc_final: 0.3127 (pm20) REVERT: C 956 MET cc_start: 0.8536 (mtm) cc_final: 0.8208 (mtm) REVERT: C 1045 ASP cc_start: 0.7053 (m-30) cc_final: 0.6520 (t0) REVERT: D 56 LYS cc_start: 0.8498 (tptp) cc_final: 0.7641 (ptpp) REVERT: D 73 MET cc_start: -0.0389 (mtm) cc_final: -0.1363 (mpp) REVERT: D 169 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7833 (mtpp) REVERT: D 260 ARG cc_start: 0.8355 (ttm170) cc_final: 0.7971 (mtp85) REVERT: D 303 ARG cc_start: 0.7716 (mmt180) cc_final: 0.7334 (ttm-80) REVERT: D 319 MET cc_start: 0.8317 (mtp) cc_final: 0.7958 (mtp) REVERT: D 351 LYS cc_start: 0.8602 (mmtt) cc_final: 0.8240 (mptt) REVERT: D 432 GLU cc_start: 0.7333 (mm-30) cc_final: 0.6962 (mp0) REVERT: D 471 MET cc_start: 0.8738 (mmm) cc_final: 0.8329 (mmp) REVERT: D 515 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8052 (mt) REVERT: D 642 MET cc_start: 0.8165 (mmm) cc_final: 0.7812 (mmm) REVERT: D 693 ARG cc_start: 0.5166 (OUTLIER) cc_final: 0.4351 (ptm160) REVERT: D 754 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6501 (pp) REVERT: D 957 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7203 (mt) REVERT: D 1053 LYS cc_start: 0.8451 (tttt) cc_final: 0.7913 (ttmm) REVERT: D 1109 GLU cc_start: 0.6328 (tp30) cc_final: 0.5675 (tm-30) REVERT: D 1129 LYS cc_start: 0.8043 (tttt) cc_final: 0.7806 (tptp) REVERT: D 1181 MET cc_start: 0.9047 (mmm) cc_final: 0.8757 (mmm) REVERT: E 78 LEU cc_start: 0.6482 (OUTLIER) cc_final: 0.6114 (mm) REVERT: F 25 LYS cc_start: 0.8158 (mttm) cc_final: 0.7912 (mttt) REVERT: F 32 GLU cc_start: 0.7195 (tt0) cc_final: 0.6821 (tt0) REVERT: F 38 LEU cc_start: 0.8441 (mt) cc_final: 0.8119 (mt) REVERT: G 10 HIS cc_start: 0.8738 (OUTLIER) cc_final: 0.8181 (m-70) REVERT: G 27 GLU cc_start: 0.8061 (tp30) cc_final: 0.7815 (tp30) REVERT: G 29 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7518 (mm110) REVERT: H 52 LYS cc_start: 0.7126 (mttt) cc_final: 0.4851 (ttpt) REVERT: H 56 HIS cc_start: 0.7185 (p90) cc_final: 0.6552 (p90) REVERT: H 77 MET cc_start: 0.7405 (ptm) cc_final: 0.6914 (ptm) REVERT: H 144 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7156 (tt0) REVERT: H 156 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.6039 (mpt) REVERT: H 182 ASP cc_start: 0.6970 (t70) cc_final: 0.6743 (m-30) REVERT: H 198 MET cc_start: 0.8159 (mtp) cc_final: 0.7582 (mtt) REVERT: H 237 MET cc_start: 0.7799 (tpt) cc_final: 0.7587 (tpt) outliers start: 109 outliers final: 76 residues processed: 384 average time/residue: 0.4077 time to fit residues: 242.7120 Evaluate side-chains 370 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 280 time to evaluate : 2.841 ------------------------------------------------------------------------------- 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 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 197 ASP Chi-restraints excluded: chain A residue 205 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 47 SER Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 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 424 SER 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 686 SER 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 1132 MET Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 169 LYS 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 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 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 888 MET 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 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 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 223 LEU Chi-restraints excluded: chain H residue 239 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.0331 > 50: distance: 21 - 28: 26.906 distance: 28 - 29: 32.440 distance: 29 - 30: 23.820 distance: 30 - 31: 18.532 distance: 30 - 32: 35.872 distance: 32 - 33: 17.504 distance: 33 - 34: 33.287 distance: 33 - 36: 14.961 distance: 34 - 35: 14.252 distance: 34 - 43: 34.597 distance: 36 - 37: 21.522 distance: 37 - 38: 38.947 distance: 38 - 39: 16.569 distance: 39 - 40: 14.267 distance: 40 - 41: 11.258 distance: 40 - 42: 18.746 distance: 43 - 44: 17.666 distance: 43 - 49: 26.275 distance: 44 - 45: 16.253 distance: 44 - 47: 38.400 distance: 45 - 46: 18.128 distance: 45 - 50: 25.602 distance: 47 - 48: 25.218 distance: 48 - 49: 9.454 distance: 50 - 51: 10.418 distance: 51 - 52: 11.786 distance: 51 - 54: 23.526 distance: 52 - 53: 5.357 distance: 52 - 57: 16.117 distance: 54 - 55: 24.332 distance: 54 - 56: 9.031 distance: 58 - 59: 35.312 distance: 59 - 60: 26.507 distance: 59 - 64: 35.030 distance: 61 - 62: 29.416 distance: 61 - 63: 9.069 distance: 66 - 67: 34.901 distance: 66 - 68: 40.176 distance: 68 - 69: 23.267 distance: 69 - 70: 9.282 distance: 69 - 72: 17.269 distance: 70 - 71: 3.713 distance: 70 - 75: 7.071 distance: 73 - 74: 8.088 distance: 75 - 76: 9.233 distance: 76 - 77: 17.483 distance: 77 - 78: 15.683 distance: 77 - 79: 20.034 distance: 80 - 81: 19.549 distance: 80 - 83: 6.914 distance: 81 - 82: 3.979 distance: 81 - 87: 14.915 distance: 84 - 85: 14.359 distance: 84 - 86: 5.308 distance: 87 - 88: 10.296 distance: 88 - 89: 24.581 distance: 88 - 91: 22.189 distance: 89 - 90: 24.287 distance: 89 - 98: 27.160 distance: 91 - 92: 17.234 distance: 92 - 93: 27.267 distance: 93 - 94: 5.656 distance: 94 - 95: 24.494 distance: 95 - 97: 23.961