Starting phenix.real_space_refine on Sat Aug 8 09:31:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r6r_18959/08_2026/8r6r_18959.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r6r_18959/08_2026/8r6r_18959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r6r_18959/08_2026/8r6r_18959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r6r_18959/08_2026/8r6r_18959.map" model { file = "/net/cci-nas-00/data/ceres_data/8r6r_18959/08_2026/8r6r_18959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r6r_18959/08_2026/8r6r_18959.cif" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 83 5.49 5 Mg 1 5.21 5 S 91 5.16 5 C 17036 2.51 5 N 4918 2.21 5 O 5492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27623 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1716 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1790 Classifications: {'peptide': 236} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 220} Chain: "C" Number of atoms: 8594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1109, 8594 Classifications: {'peptide': 1109} Link IDs: {'PCIS': 1, 'PTRANS': 58, 'TRANS': 1049} Chain: "D" Number of atoms: 9867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1261, 9867 Classifications: {'peptide': 1261} Link IDs: {'PCIS': 2, 'PTRANS': 55, 'TRANS': 1203} Chain breaks: 1 Chain: "E" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 595 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 69} Chain breaks: 1 Chain: "F" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2530 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 307} Chain: "J" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 804 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 7, 'TRANS': 91} Chain: "O" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 971 Classifications: {'DNA': 47} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 46} Chain breaks: 1 Chain: "P" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 753 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain breaks: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19132 SG CYS D 890 34.334 61.050 68.960 1.00 13.19 S ATOM 19694 SG CYS D 967 37.253 63.317 69.997 1.00 12.90 S ATOM 19736 SG CYS D 974 34.678 62.113 72.556 1.00 9.75 S ATOM 19755 SG CYS D 977 36.996 59.672 71.230 1.00 13.87 S ATOM 12559 SG CYS D 60 36.152 125.789 86.813 1.00 33.58 S ATOM 12577 SG CYS D 62 36.766 129.474 87.310 1.00 29.87 S ATOM 12686 SG CYS D 75 34.440 128.263 84.688 1.00 40.82 S ATOM 12712 SG CYS D 78 37.964 127.455 84.268 1.00 34.04 S Time building chain proxies: 5.60, per 1000 atoms: 0.20 Number of scatterers: 27623 At special positions: 0 Unit cell: (127.541, 168.387, 164.219, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 91 16.00 P 83 15.00 Mg 1 11.99 O 5492 8.00 N 4918 7.00 C 17036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 974 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 977 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 890 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 967 " pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 62 " Number of angles added : 12 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6124 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 44 sheets defined 42.8% alpha, 15.5% beta 33 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 3.61 Creating SS restraints... Processing helix chain 'A' and resid 30 through 46 removed outlier: 3.844A pdb=" N SER A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 203 through 224 removed outlier: 3.563A pdb=" N ALA A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 46 removed outlier: 3.844A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.653A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 57 removed outlier: 3.651A pdb=" N SER C 51 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 68 removed outlier: 4.301A pdb=" N ALA C 64 " --> pdb=" O ARG C 60 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP C 67 " --> pdb=" O GLN C 63 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 84 removed outlier: 3.740A pdb=" N LEU C 84 " --> pdb=" O VAL C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 116 Processing helix chain 'C' and resid 225 through 231 Processing helix chain 'C' and resid 238 through 243 removed outlier: 4.428A pdb=" N ARG C 242 " --> pdb=" O GLN C 238 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 238 through 243' Processing helix chain 'C' and resid 247 through 256 removed outlier: 3.991A pdb=" N GLU C 254 " --> pdb=" O MET C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 281 through 289 removed outlier: 3.657A pdb=" N LEU C 287 " --> pdb=" O ALA C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 312 Processing helix chain 'C' and resid 325 through 342 removed outlier: 3.513A pdb=" N VAL C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 395 removed outlier: 3.622A pdb=" N GLN C 379 " --> pdb=" O LEU C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 Processing helix chain 'C' and resid 411 through 425 removed outlier: 3.549A pdb=" N GLY C 423 " --> pdb=" O LYS C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 444 removed outlier: 3.678A pdb=" N ARG C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 465 removed outlier: 3.664A pdb=" N ARG C 464 " --> pdb=" O LEU C 461 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP C 465 " --> pdb=" O GLU C 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 461 through 465' Processing helix chain 'C' and resid 467 through 471 removed outlier: 3.949A pdb=" N TYR C 471 " --> pdb=" O PRO C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 529 removed outlier: 3.782A pdb=" N ARG C 529 " --> pdb=" O ASP C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 578 removed outlier: 4.240A pdb=" N MET C 577 " --> pdb=" O PRO C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 584 Processing helix chain 'C' and resid 587 through 591 Processing helix chain 'C' and resid 592 through 604 removed outlier: 3.883A pdb=" N ARG C 604 " --> pdb=" O ALA C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 628 removed outlier: 3.700A pdb=" N ALA C 626 " --> pdb=" O GLU C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 725 removed outlier: 3.750A pdb=" N ASP C 724 " --> pdb=" O ASN C 721 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 768 through 773 Processing helix chain 'C' and resid 806 through 816 Processing helix chain 'C' and resid 847 through 849 No H-bonds generated for 'chain 'C' and resid 847 through 849' Processing helix chain 'C' and resid 891 through 895 removed outlier: 3.594A pdb=" N MET C 895 " --> pdb=" O VAL C 892 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 917 removed outlier: 4.146A pdb=" N ARG C 915 " --> pdb=" O HIS C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 933 removed outlier: 3.540A pdb=" N LEU C 923 " --> pdb=" O ILE C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 948 Processing helix chain 'C' and resid 951 through 955 Processing helix chain 'C' and resid 972 through 982 Processing helix chain 'C' and resid 1060 through 1071 removed outlier: 3.582A pdb=" N CYS C1064 " --> pdb=" O GLY C1060 " (cutoff:3.500A) Processing helix chain 'C' and resid 1072 through 1081 Processing helix chain 'C' and resid 1086 through 1100 removed outlier: 4.125A pdb=" N VAL C1091 " --> pdb=" O THR C1087 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS C1092 " --> pdb=" O VAL C1088 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1122 Processing helix chain 'D' and resid 16 through 23 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 141 through 144 Processing helix chain 'D' and resid 148 through 151 Processing helix chain 'D' and resid 152 through 184 removed outlier: 3.538A pdb=" N VAL D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU D 158 " --> pdb=" O GLU D 154 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP D 167 " --> pdb=" O GLU D 163 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA D 168 " --> pdb=" O ASP D 164 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA D 172 " --> pdb=" O ALA D 168 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG D 173 " --> pdb=" O ASP D 169 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA D 174 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA D 179 " --> pdb=" O GLN D 175 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA D 182 " --> pdb=" O GLU D 178 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU D 184 " --> pdb=" O ASP D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 195 removed outlier: 3.711A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG D 195 " --> pdb=" O SER D 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 190 through 195' Processing helix chain 'D' and resid 195 through 227 removed outlier: 4.232A pdb=" N ARG D 203 " --> pdb=" O ASP D 199 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG D 206 " --> pdb=" O GLU D 202 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP D 210 " --> pdb=" O ARG D 206 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU D 219 " --> pdb=" O GLU D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 249 removed outlier: 3.634A pdb=" N GLU D 243 " --> pdb=" O VAL D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 268 Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.964A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU D 275 " --> pdb=" O ASP D 271 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER D 276 " --> pdb=" O ALA D 272 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG D 282 " --> pdb=" O ARG D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 300 removed outlier: 3.813A pdb=" N LEU D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.554A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 331 through 333 No H-bonds generated for 'chain 'D' and resid 331 through 333' Processing helix chain 'D' and resid 338 through 361 removed outlier: 4.171A pdb=" N ASP D 342 " --> pdb=" O SER D 338 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 445 through 463 Proline residue: D 454 - end of helix Processing helix chain 'D' and resid 468 through 478 removed outlier: 3.708A pdb=" N ARG D 478 " --> pdb=" O ARG D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 482 No H-bonds generated for 'chain 'D' and resid 480 through 482' Processing helix chain 'D' and resid 483 through 492 removed outlier: 3.982A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 579 through 590 removed outlier: 3.501A pdb=" N LEU D 585 " --> pdb=" O MET D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 removed outlier: 4.066A pdb=" N ALA D 648 " --> pdb=" O THR D 644 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN D 649 " --> pdb=" O ASP D 645 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 674 Processing helix chain 'D' and resid 688 through 703 removed outlier: 3.511A pdb=" N ARG D 702 " --> pdb=" O ASP D 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 704 through 724 removed outlier: 3.597A pdb=" N VAL D 708 " --> pdb=" O PRO D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 761 removed outlier: 3.579A pdb=" N GLU D 746 " --> pdb=" O GLN D 742 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA D 750 " --> pdb=" O GLU D 746 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU D 751 " --> pdb=" O ARG D 747 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN D 760 " --> pdb=" O GLU D 756 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG D 761 " --> pdb=" O ARG D 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 765 through 792 Processing helix chain 'D' and resid 796 through 804 Processing helix chain 'D' and resid 809 through 818 removed outlier: 3.558A pdb=" N THR D 813 " --> pdb=" O ASN D 809 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 880 removed outlier: 3.606A pdb=" N THR D 852 " --> pdb=" O TYR D 848 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N HIS D 853 " --> pdb=" O PHE D 849 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N GLY D 854 " --> pdb=" O ILE D 850 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA D 855 " --> pdb=" O ASN D 851 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR D 862 " --> pdb=" O GLY D 858 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ALA D 863 " --> pdb=" O LEU D 859 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU D 864 " --> pdb=" O ALA D 860 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 919 Processing helix chain 'D' and resid 944 through 954 Processing helix chain 'D' and resid 975 through 979 Processing helix chain 'D' and resid 993 through 1004 Processing helix chain 'D' and resid 1028 through 1037 Processing helix chain 'D' and resid 1118 through 1126 Processing helix chain 'D' and resid 1127 through 1146 removed outlier: 3.653A pdb=" N GLN D1132 " --> pdb=" O PRO D1128 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE D1133 " --> pdb=" O ARG D1129 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL D1142 " --> pdb=" O GLU D1138 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR D1143 " --> pdb=" O VAL D1139 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN D1146 " --> pdb=" O VAL D1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 1151 through 1161 removed outlier: 4.324A pdb=" N ILE D1155 " --> pdb=" O HIS D1151 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN D1161 " --> pdb=" O VAL D1157 " (cutoff:3.500A) Processing helix chain 'D' and resid 1184 through 1198 removed outlier: 3.533A pdb=" N VAL D1195 " --> pdb=" O ASN D1191 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ALA D1196 " --> pdb=" O ARG D1192 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU D1197 " --> pdb=" O ARG D1193 " (cutoff:3.500A) Processing helix chain 'D' and resid 1210 through 1217 Processing helix chain 'D' and resid 1220 through 1228 Processing helix chain 'D' and resid 1229 through 1241 Processing helix chain 'D' and resid 1248 through 1256 removed outlier: 3.849A pdb=" N ASN D1252 " --> pdb=" O GLY D1248 " (cutoff:3.500A) Processing helix chain 'D' and resid 1261 through 1264 Processing helix chain 'D' and resid 1265 through 1270 Processing helix chain 'D' and resid 1276 through 1281 Processing helix chain 'E' and resid 30 through 34 Processing helix chain 'E' and resid 36 through 42 removed outlier: 3.829A pdb=" N SER E 42 " --> pdb=" O ASP E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 66 Processing helix chain 'E' and resid 87 through 98 removed outlier: 3.739A pdb=" N GLY E 98 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 160 removed outlier: 4.729A pdb=" N ALA F 157 " --> pdb=" O ALA F 153 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLU F 158 " --> pdb=" O ARG F 154 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR F 160 " --> pdb=" O ASP F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 163 No H-bonds generated for 'chain 'F' and resid 161 through 163' Processing helix chain 'F' and resid 164 through 173 removed outlier: 3.956A pdb=" N LEU F 170 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS F 171 " --> pdb=" O ARG F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 183 Processing helix chain 'F' and resid 184 through 206 removed outlier: 3.716A pdb=" N ALA F 202 " --> pdb=" O THR F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 236 removed outlier: 3.595A pdb=" N GLN F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 246 Processing helix chain 'F' and resid 247 through 249 No H-bonds generated for 'chain 'F' and resid 247 through 249' Processing helix chain 'F' and resid 254 through 271 Processing helix chain 'F' and resid 274 through 278 Processing helix chain 'F' and resid 280 through 300 removed outlier: 4.322A pdb=" N TRP F 287 " --> pdb=" O THR F 283 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TRP F 288 " --> pdb=" O TYR F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 329 removed outlier: 3.519A pdb=" N VAL F 313 " --> pdb=" O HIS F 309 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU F 325 " --> pdb=" O GLN F 321 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLN F 326 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ASP F 327 " --> pdb=" O GLU F 323 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU F 328 " --> pdb=" O LEU F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 342 removed outlier: 3.624A pdb=" N GLU F 340 " --> pdb=" O GLU F 336 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP F 342 " --> pdb=" O ALA F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 355 Processing helix chain 'F' and resid 384 through 398 removed outlier: 3.723A pdb=" N THR F 392 " --> pdb=" O ALA F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 417 removed outlier: 3.568A pdb=" N VAL F 412 " --> pdb=" O ARG F 408 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL F 413 " --> pdb=" O GLU F 409 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG F 414 " --> pdb=" O ALA F 410 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU F 415 " --> pdb=" O GLY F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 432 Processing helix chain 'F' and resid 437 through 454 removed outlier: 3.678A pdb=" N HIS F 454 " --> pdb=" O SER F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 463 removed outlier: 5.514A pdb=" N VAL F 460 " --> pdb=" O SER F 456 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU F 461 " --> pdb=" O ARG F 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASP F 463 " --> pdb=" O GLN F 459 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 87 Processing helix chain 'J' and resid 90 through 101 removed outlier: 3.505A pdb=" N LEU J 94 " --> pdb=" O SER J 90 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 6.365A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.397A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 removed outlier: 3.652A pdb=" N VAL A 147 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 15 removed outlier: 6.350A pdb=" N ARG B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ARG B 18 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR B 198 " --> pdb=" O ARG B 18 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ARG B 20 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL B 196 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N VAL B 22 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE B 194 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N GLU B 24 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU B 192 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B 188 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N THR B 181 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASP B 190 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLU B 179 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU B 192 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LYS B 177 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE B 194 " --> pdb=" O THR B 175 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR B 175 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL B 196 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS B 173 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR B 198 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL B 171 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 100 removed outlier: 4.044A pdb=" N SER B 53 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLU B 141 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL B 51 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLY B 143 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ALA B 49 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 30 through 31 removed outlier: 6.659A pdb=" N VAL C 30 " --> pdb=" O ALA C 964 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 94 through 103 removed outlier: 6.317A pdb=" N PHE C 125 " --> pdb=" O PRO C 101 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N PHE C 103 " --> pdb=" O PRO C 123 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ALA C 122 " --> pdb=" O ASP C 147 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ASP C 147 " --> pdb=" O ALA C 122 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LEU C 124 " --> pdb=" O MET C 145 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 157 through 159 Processing sheet with id=AB5, first strand: chain 'C' and resid 367 through 370 removed outlier: 3.819A pdb=" N SER C 168 " --> pdb=" O ARG C 445 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 175 through 182 removed outlier: 4.039A pdb=" N GLY C 175 " --> pdb=" O ILE C 196 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE C 196 " --> pdb=" O GLY C 175 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL C 193 " --> pdb=" O PHE C 205 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 214 through 215 Processing sheet with id=AB8, first strand: chain 'C' and resid 345 through 347 Processing sheet with id=AB9, first strand: chain 'C' and resid 496 through 497 removed outlier: 3.564A pdb=" N ARG C 496 " --> pdb=" O GLU C 504 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N GLN C 518 " --> pdb=" O LYS C 509 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 496 through 497 removed outlier: 3.564A pdb=" N ARG C 496 " --> pdb=" O GLU C 504 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL C 532 " --> pdb=" O ARG C 553 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 633 through 634 removed outlier: 6.470A pdb=" N VAL C 633 " --> pdb=" O ILE C 693 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 658 through 662 removed outlier: 7.109A pdb=" N TYR C 648 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N VAL C 644 " --> pdb=" O TYR C 648 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR C 650 " --> pdb=" O GLU C 642 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 699 through 700 Processing sheet with id=AC5, first strand: chain 'C' and resid 998 through 999 removed outlier: 3.796A pdb=" N ALA C 877 " --> pdb=" O LEU C1022 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE C 726 " --> pdb=" O LYS C 888 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N LEU C 890 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU C 728 " --> pdb=" O LEU C 890 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE C 727 " --> pdb=" O ILE C 907 " (cutoff:3.500A) removed outlier: 9.385A pdb=" N ILE C 906 " --> pdb=" O ASN C 709 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU C 711 " --> pdb=" O ILE C 906 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LEU C 908 " --> pdb=" O LEU C 711 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA C 713 " --> pdb=" O LEU C 908 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N THR C1015 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 740 through 750 removed outlier: 6.741A pdb=" N LEU C 859 " --> pdb=" O VAL C 843 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL C 843 " --> pdb=" O LEU C 859 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG C 861 " --> pdb=" O ILE C 841 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE C 841 " --> pdb=" O ARG C 861 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TYR C 863 " --> pdb=" O ILE C 839 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 759 through 760 Processing sheet with id=AC8, first strand: chain 'C' and resid 792 through 794 removed outlier: 3.533A pdb=" N VAL C 794 " --> pdb=" O LEU C 828 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1033 through 1035 removed outlier: 6.090A pdb=" N CYS D 441 " --> pdb=" O GLN D 515 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL D 517 " --> pdb=" O CYS D 441 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1057 through 1059 removed outlier: 3.616A pdb=" N GLN C1057 " --> pdb=" O VAL D 422 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1124 through 1129 Processing sheet with id=AD3, first strand: chain 'D' and resid 24 through 27 removed outlier: 4.471A pdb=" N SER D 24 " --> pdb=" O MET D 92 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N HIS D 94 " --> pdb=" O SER D 24 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLY D 26 " --> pdb=" O HIS D 94 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N GLU D 96 " --> pdb=" O GLY D 26 " (cutoff:3.500A) removed outlier: 10.282A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 234 through 235 removed outlier: 6.998A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 327 through 329 Processing sheet with id=AD6, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AD7, first strand: chain 'D' and resid 885 through 887 Processing sheet with id=AD8, first strand: chain 'D' and resid 896 through 899 Processing sheet with id=AD9, first strand: chain 'D' and resid 901 through 902 Processing sheet with id=AE1, first strand: chain 'D' and resid 928 through 929 removed outlier: 6.499A pdb=" N ALA D 928 " --> pdb=" O ILE D 936 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1044 through 1045 removed outlier: 3.569A pdb=" N ALA D1045 " --> pdb=" O ALA D1116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'D' and resid 1077 through 1078 Processing sheet with id=AE4, first strand: chain 'D' and resid 1089 through 1090 Processing sheet with id=AE5, first strand: chain 'D' and resid 1181 through 1183 removed outlier: 6.211A pdb=" N ALA D1203 " --> pdb=" O ILE D1169 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1272 through 1275 removed outlier: 3.824A pdb=" N GLU E 102 " --> pdb=" O GLN D1274 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 378 through 379 removed outlier: 6.231A pdb=" N GLU F 378 " --> pdb=" O GLY J 8 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'J' and resid 39 through 44 1074 hydrogen bonds defined for protein. 3000 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 7.88 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8933 1.34 - 1.45: 3556 1.45 - 1.57: 15438 1.57 - 1.69: 163 1.69 - 1.81: 162 Bond restraints: 28252 Sorted by residual: bond pdb=" C3' DC O 2 " pdb=" C2' DC O 2 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DT O 47 " pdb=" C2' DT O 47 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.61e+00 bond pdb=" C3' DC P 3 " pdb=" C2' DC P 3 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.11e+00 bond pdb=" C3' DG P 26 " pdb=" C2' DG P 26 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.78e+00 bond pdb=" C1' DT P 5 " pdb=" N1 DT P 5 " ideal model delta sigma weight residual 1.468 1.505 -0.037 1.40e-02 5.10e+03 7.06e+00 ... (remaining 28247 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 37613 1.46 - 2.91: 777 2.91 - 4.37: 199 4.37 - 5.83: 11 5.83 - 7.29: 2 Bond angle restraints: 38602 Sorted by residual: angle pdb=" O4' DG P 49 " pdb=" C1' DG P 49 " pdb=" N9 DG P 49 " ideal model delta sigma weight residual 108.00 111.80 -3.80 7.00e-01 2.04e+00 2.94e+01 angle pdb=" N3 DT O 15 " pdb=" C4 DT O 15 " pdb=" O4 DT O 15 " ideal model delta sigma weight residual 119.90 122.66 -2.76 6.00e-01 2.78e+00 2.12e+01 angle pdb=" N3 DT P 34 " pdb=" C4 DT P 34 " pdb=" O4 DT P 34 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.03e+01 angle pdb=" O4 DT O 15 " pdb=" C4 DT O 15 " pdb=" C5 DT O 15 " ideal model delta sigma weight residual 124.90 121.86 3.04 7.00e-01 2.04e+00 1.89e+01 angle pdb=" N3 DT P 9 " pdb=" C4 DT P 9 " pdb=" O4 DT P 9 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 ... (remaining 38597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.05: 16354 32.05 - 64.09: 701 64.09 - 96.14: 51 96.14 - 128.18: 0 128.18 - 160.23: 1 Dihedral angle restraints: 17107 sinusoidal: 7593 harmonic: 9514 Sorted by residual: dihedral pdb=" CA PHE D 226 " pdb=" C PHE D 226 " pdb=" N THR D 227 " pdb=" CA THR D 227 " ideal model delta harmonic sigma weight residual -180.00 -157.31 -22.69 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ARG B 182 " pdb=" C ARG B 182 " pdb=" N VAL B 183 " pdb=" CA VAL B 183 " ideal model delta harmonic sigma weight residual 180.00 159.04 20.96 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" C4' DA O 19 " pdb=" C3' DA O 19 " pdb=" O3' DA O 19 " pdb=" P DT O 20 " ideal model delta sinusoidal sigma weight residual 220.00 59.77 160.23 1 3.50e+01 8.16e-04 1.52e+01 ... (remaining 17104 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2972 0.033 - 0.066: 891 0.066 - 0.099: 257 0.099 - 0.131: 223 0.131 - 0.164: 47 Chirality restraints: 4390 Sorted by residual: chirality pdb=" C3' DC O 43 " pdb=" C4' DC O 43 " pdb=" O3' DC O 43 " pdb=" C2' DC O 43 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.74e-01 chirality pdb=" C3' DA O 19 " pdb=" C4' DA O 19 " pdb=" O3' DA O 19 " pdb=" C2' DA O 19 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.41e-01 chirality pdb=" C3' DA P 28 " pdb=" C4' DA P 28 " pdb=" O3' DA P 28 " pdb=" C2' DA P 28 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.40e-01 ... (remaining 4387 not shown) Planarity restraints: 4789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 226 " -0.036 2.00e-02 2.50e+03 3.44e-02 2.07e+01 pdb=" CG PHE D 226 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 PHE D 226 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE D 226 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE D 226 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE D 226 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE D 226 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 572 " 0.054 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PRO D 573 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO D 573 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 573 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 27 " -0.051 5.00e-02 4.00e+02 7.70e-02 9.49e+00 pdb=" N PRO B 28 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 28 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 28 " -0.042 5.00e-02 4.00e+02 ... (remaining 4786 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 164 2.55 - 3.14: 21919 3.14 - 3.73: 41191 3.73 - 4.31: 56469 4.31 - 4.90: 94991 Nonbonded interactions: 214734 Sorted by model distance: nonbonded pdb=" OG1 THR F 344 " pdb=" OE2 GLU F 346 " model vdw 1.966 3.040 nonbonded pdb=" OH TYR D 36 " pdb=" OP1 DT O 21 " model vdw 2.044 3.040 nonbonded pdb=" O ILE D 320 " pdb=" NH1 ARG D 325 " model vdw 2.061 3.120 nonbonded pdb=" OD1 ASP D 539 " pdb="MG MG D2003 " model vdw 2.067 2.170 nonbonded pdb=" NH2 ARG C 304 " pdb=" O THR C 323 " model vdw 2.080 3.120 ... (remaining 214729 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' selection = (chain 'B' and resid 1 through 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 33.390 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.070 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6167 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 : 0.003 0.094 28260 Z= 0.208 Angle : 0.537 7.287 38614 Z= 0.349 Chirality : 0.043 0.164 4390 Planarity : 0.004 0.081 4789 Dihedral : 16.197 160.229 10983 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.15), residues: 3305 helix: 0.65 (0.15), residues: 1193 sheet: -0.61 (0.25), residues: 423 loop : -0.29 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG D 387 TYR 0.033 0.001 TYR D 248 PHE 0.078 0.001 PHE D 226 TRP 0.020 0.001 TRP D 223 HIS 0.005 0.001 HIS C 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.20 (28252) covalent geometry : angle 0.53523 / 0.35 (38602) hydrogen bonds : bond 0.15179 / 10.76 ( 1154) hydrogen bonds : angle 6.00178 / 4.18 ( 3162) metal coordination : bond 0.06161 / 3.00 ( 8) metal coordination : angle 2.61123 / 1.32 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 900 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ILE cc_start: 0.8322 (mt) cc_final: 0.6842 (mp) REVERT: C 992 MET cc_start: 0.8513 (mmp) cc_final: 0.8287 (mmm) REVERT: C 1037 THR cc_start: 0.7450 (m) cc_final: 0.7092 (m) REVERT: D 137 THR cc_start: 0.7118 (p) cc_final: 0.6910 (p) REVERT: D 312 MET cc_start: 0.5241 (ptp) cc_final: 0.4904 (ptp) REVERT: D 373 MET cc_start: 0.5315 (mtm) cc_final: 0.4287 (mtm) REVERT: D 499 ASN cc_start: 0.8640 (t0) cc_final: 0.7570 (t0) REVERT: D 509 ILE cc_start: 0.8144 (mt) cc_final: 0.7927 (mt) REVERT: D 524 LEU cc_start: 0.7636 (tp) cc_final: 0.7412 (tp) REVERT: D 835 ILE cc_start: 0.5246 (mt) cc_final: 0.4541 (mm) REVERT: D 1133 ILE cc_start: 0.8782 (mm) cc_final: 0.8095 (mm) REVERT: D 1155 ILE cc_start: 0.8261 (mt) cc_final: 0.8058 (mt) REVERT: E 96 ILE cc_start: 0.8276 (mt) cc_final: 0.8000 (tp) REVERT: E 104 THR cc_start: 0.7026 (p) cc_final: 0.6734 (p) REVERT: F 237 ASN cc_start: 0.5139 (m-40) cc_final: 0.4731 (m110) REVERT: F 351 ILE cc_start: 0.8237 (mt) cc_final: 0.7967 (mt) REVERT: J 58 ASN cc_start: 0.7320 (p0) cc_final: 0.7006 (p0) REVERT: J 97 LEU cc_start: 0.8289 (mt) cc_final: 0.7939 (mt) outliers start: 0 outliers final: 0 residues processed: 900 average time/residue: 0.2222 time to fit residues: 300.3572 Evaluate side-chains 600 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 600 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 9.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 HIS B 231 HIS D 213 GLN D 349 ASN ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 914 HIS D1240 ASN E 97 HIS F 231 ASN F 232 HIS F 237 ASN F 352 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.123789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.087084 restraints weight = 74488.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.090206 restraints weight = 41636.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.092273 restraints weight = 28510.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.093645 restraints weight = 22207.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.094552 restraints weight = 18841.383| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 28260 Z= 0.225 Angle : 0.746 9.388 38614 Z= 0.395 Chirality : 0.048 0.291 4390 Planarity : 0.006 0.064 4789 Dihedral : 14.728 162.078 4567 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.78 % Allowed : 13.34 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.14), residues: 3305 helix: 0.34 (0.15), residues: 1236 sheet: -0.64 (0.26), residues: 395 loop : -0.33 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 68 TYR 0.032 0.002 TYR E 53 PHE 0.019 0.002 PHE C 98 TRP 0.025 0.002 TRP F 288 HIS 0.012 0.002 HIS D 766 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.23 (28252) covalent geometry : angle 0.74405 / 0.39 (38602) hydrogen bonds : bond 0.05358 / 3.69 ( 1154) hydrogen bonds : angle 5.25747 / 3.62 ( 3162) metal coordination : bond 0.01442 / 0.70 ( 8) metal coordination : angle 3.09334 / 1.53 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 604 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 HIS cc_start: 0.8228 (p90) cc_final: 0.7813 (p90) REVERT: A 77 ILE cc_start: 0.8364 (mt) cc_final: 0.7943 (mt) REVERT: A 81 LYS cc_start: 0.8947 (mmtp) cc_final: 0.8546 (mmtp) REVERT: A 99 LYS cc_start: 0.8458 (tptt) cc_final: 0.8184 (tptt) REVERT: A 177 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.7007 (ptmm) REVERT: B 17 ASN cc_start: 0.8972 (m-40) cc_final: 0.8709 (m-40) REVERT: B 43 LEU cc_start: 0.8895 (tt) cc_final: 0.8622 (tp) REVERT: B 123 MET cc_start: 0.7764 (tmm) cc_final: 0.7507 (tmm) REVERT: B 128 LEU cc_start: 0.7944 (tp) cc_final: 0.7528 (tp) REVERT: B 131 LYS cc_start: 0.8900 (mmmt) cc_final: 0.8659 (mmmt) REVERT: B 172 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8716 (mm) REVERT: B 173 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8565 (pptt) REVERT: B 179 GLU cc_start: 0.7473 (mp0) cc_final: 0.7101 (mp0) REVERT: B 191 LYS cc_start: 0.8592 (ptmm) cc_final: 0.7848 (ptmm) REVERT: B 199 LYS cc_start: 0.8365 (mttt) cc_final: 0.8120 (mttt) REVERT: B 225 LEU cc_start: 0.8999 (mm) cc_final: 0.8593 (mp) REVERT: B 226 ASN cc_start: 0.8691 (t0) cc_final: 0.8459 (t0) REVERT: C 72 ASN cc_start: 0.8245 (p0) cc_final: 0.7806 (p0) REVERT: C 118 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.7316 (ptt) REVERT: C 151 MET cc_start: 0.7248 (ttm) cc_final: 0.6877 (ttm) REVERT: C 412 ARG cc_start: 0.7908 (tpp-160) cc_final: 0.7619 (tpm170) REVERT: C 481 GLU cc_start: 0.7755 (pm20) cc_final: 0.7336 (mp0) REVERT: C 548 ASP cc_start: 0.7988 (p0) cc_final: 0.7634 (p0) REVERT: C 598 MET cc_start: 0.8331 (mmm) cc_final: 0.8051 (mmm) REVERT: C 703 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7655 (tt0) REVERT: C 704 MET cc_start: 0.8161 (tpp) cc_final: 0.7848 (mpp) REVERT: C 724 ASP cc_start: 0.7383 (t0) cc_final: 0.6938 (t0) REVERT: C 915 ARG cc_start: 0.8141 (tmm-80) cc_final: 0.7911 (tmm-80) REVERT: C 1110 GLU cc_start: 0.7846 (tp30) cc_final: 0.7352 (tp30) REVERT: D 27 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7399 (pp20) REVERT: D 43 LYS cc_start: 0.8381 (tppt) cc_final: 0.7815 (tppt) REVERT: D 158 GLU cc_start: 0.9290 (tp30) cc_final: 0.8928 (tm-30) REVERT: D 350 ARG cc_start: 0.8375 (mtt180) cc_final: 0.7965 (mtt180) REVERT: D 373 MET cc_start: 0.7080 (mtm) cc_final: 0.6798 (mtm) REVERT: D 457 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8313 (mtt) REVERT: D 518 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7265 (mm-30) REVERT: D 552 GLN cc_start: 0.8689 (mt0) cc_final: 0.8342 (mp10) REVERT: D 634 LYS cc_start: 0.9007 (ttmt) cc_final: 0.8758 (tptt) REVERT: D 841 GLU cc_start: 0.8209 (tt0) cc_final: 0.7855 (tm-30) REVERT: D 859 LEU cc_start: 0.9229 (mm) cc_final: 0.8978 (mm) REVERT: D 864 LEU cc_start: 0.9060 (mt) cc_final: 0.8841 (pp) REVERT: D 992 GLU cc_start: 0.8164 (tp30) cc_final: 0.7928 (tp30) REVERT: D 1036 PHE cc_start: 0.9203 (m-80) cc_final: 0.9003 (m-80) REVERT: D 1152 ASP cc_start: 0.8637 (m-30) cc_final: 0.8187 (m-30) REVERT: D 1236 ASP cc_start: 0.8953 (t0) cc_final: 0.8667 (m-30) REVERT: E 94 ARG cc_start: 0.7878 (ttt-90) cc_final: 0.7519 (ttt180) REVERT: F 192 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8217 (pt0) REVERT: F 221 TRP cc_start: 0.8653 (t-100) cc_final: 0.8419 (t-100) REVERT: F 256 LEU cc_start: 0.7959 (tp) cc_final: 0.7598 (tp) REVERT: F 268 ARG cc_start: 0.8812 (tpp80) cc_final: 0.8569 (tpp80) REVERT: F 279 TYR cc_start: 0.7057 (m-80) cc_final: 0.6834 (m-80) REVERT: F 310 MET cc_start: 0.8709 (tpp) cc_final: 0.8278 (tpp) outliers start: 78 outliers final: 45 residues processed: 642 average time/residue: 0.2149 time to fit residues: 210.2740 Evaluate side-chains 591 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 540 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 794 VAL Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain C residue 859 LEU Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 1080 LEU Chi-restraints excluded: chain C residue 1115 LEU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 349 ASN Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 732 MET Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 994 VAL Chi-restraints excluded: chain D residue 1032 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1254 ILE Chi-restraints excluded: chain F residue 447 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 334 optimal weight: 20.0000 chunk 314 optimal weight: 9.9990 chunk 318 optimal weight: 0.9990 chunk 242 optimal weight: 5.9990 chunk 304 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 251 optimal weight: 0.5980 chunk 236 optimal weight: 5.9990 chunk 272 optimal weight: 0.3980 chunk 66 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN D 349 ASN D 494 HIS ** D 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 853 HIS D1000 GLN ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.123261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.086106 restraints weight = 74837.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.089229 restraints weight = 42050.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.091295 restraints weight = 28957.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.092640 restraints weight = 22630.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.093527 restraints weight = 19285.691| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28260 Z= 0.177 Angle : 0.702 10.087 38614 Z= 0.369 Chirality : 0.046 0.272 4390 Planarity : 0.006 0.123 4789 Dihedral : 14.846 163.456 4567 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.43 % Allowed : 16.77 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.14), residues: 3305 helix: 0.40 (0.15), residues: 1234 sheet: -0.68 (0.25), residues: 419 loop : -0.33 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG D 69 TYR 0.034 0.002 TYR B 168 PHE 0.025 0.002 PHE D 70 TRP 0.019 0.002 TRP F 288 HIS 0.026 0.002 HIS B 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.18 (28252) covalent geometry : angle 0.69928 / 0.37 (38602) hydrogen bonds : bond 0.04662 / 3.17 ( 1154) hydrogen bonds : angle 5.04017 / 3.48 ( 3162) metal coordination : bond 0.01018 / 0.50 ( 8) metal coordination : angle 3.25854 / 1.66 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 555 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.8434 (tptt) cc_final: 0.8109 (tptt) REVERT: A 177 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7137 (ptmm) REVERT: A 191 LYS cc_start: 0.8705 (ttpp) cc_final: 0.8202 (ptpp) REVERT: A 199 LYS cc_start: 0.8895 (pttt) cc_final: 0.8472 (ptpp) REVERT: B 43 LEU cc_start: 0.8931 (tt) cc_final: 0.8586 (tp) REVERT: B 95 MET cc_start: 0.3748 (mmm) cc_final: 0.3022 (tpt) REVERT: B 123 MET cc_start: 0.7915 (tmm) cc_final: 0.7701 (tmm) REVERT: B 128 LEU cc_start: 0.8025 (tp) cc_final: 0.7515 (tp) REVERT: B 173 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8522 (pptt) REVERT: B 179 GLU cc_start: 0.7606 (mp0) cc_final: 0.7231 (mp0) REVERT: B 191 LYS cc_start: 0.8473 (ptmm) cc_final: 0.7858 (ptmm) REVERT: B 199 LYS cc_start: 0.8364 (mttt) cc_final: 0.8072 (mttp) REVERT: B 226 ASN cc_start: 0.8732 (t0) cc_final: 0.8469 (t0) REVERT: C 62 ARG cc_start: 0.9081 (mtt90) cc_final: 0.8527 (mmt180) REVERT: C 304 ARG cc_start: 0.8766 (tpt-90) cc_final: 0.8329 (tpp-160) REVERT: C 374 GLU cc_start: 0.8256 (mp0) cc_final: 0.7949 (mt-10) REVERT: C 394 ARG cc_start: 0.8899 (ttm170) cc_final: 0.8607 (ptm160) REVERT: C 548 ASP cc_start: 0.8071 (p0) cc_final: 0.7605 (p0) REVERT: C 619 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.7996 (p) REVERT: C 703 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7708 (tt0) REVERT: C 704 MET cc_start: 0.8222 (tpp) cc_final: 0.7823 (mpp) REVERT: C 715 MET cc_start: 0.8863 (ptm) cc_final: 0.8616 (ptm) REVERT: C 724 ASP cc_start: 0.7498 (t0) cc_final: 0.6977 (t0) REVERT: C 774 ASP cc_start: 0.7676 (t0) cc_final: 0.7453 (t0) REVERT: C 813 ARG cc_start: 0.8559 (mmm160) cc_final: 0.8126 (mtp180) REVERT: C 1110 GLU cc_start: 0.7828 (tp30) cc_final: 0.7472 (tp30) REVERT: D 27 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7386 (pp20) REVERT: D 43 LYS cc_start: 0.8416 (tppt) cc_final: 0.7799 (tppt) REVERT: D 84 ARG cc_start: 0.8382 (tpt90) cc_final: 0.7852 (tmt-80) REVERT: D 86 LYS cc_start: 0.8917 (pttm) cc_final: 0.8676 (ptpp) REVERT: D 90 GLU cc_start: 0.8317 (pt0) cc_final: 0.8083 (pt0) REVERT: D 134 TYR cc_start: 0.7751 (m-10) cc_final: 0.7300 (m-10) REVERT: D 136 ILE cc_start: 0.9420 (mm) cc_final: 0.9153 (tp) REVERT: D 143 MET cc_start: 0.8158 (mtm) cc_final: 0.7785 (ptp) REVERT: D 155 MET cc_start: 0.8434 (tmm) cc_final: 0.8003 (ppp) REVERT: D 247 ARG cc_start: 0.6744 (mtm110) cc_final: 0.6381 (ptp90) REVERT: D 256 MET cc_start: 0.5811 (OUTLIER) cc_final: 0.5000 (ttm) REVERT: D 335 PHE cc_start: 0.8171 (m-80) cc_final: 0.7197 (m-10) REVERT: D 346 ARG cc_start: 0.7446 (mmm-85) cc_final: 0.6649 (mmm-85) REVERT: D 373 MET cc_start: 0.7124 (mtm) cc_final: 0.6848 (mtm) REVERT: D 457 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8353 (mtt) REVERT: D 515 GLN cc_start: 0.8195 (pm20) cc_final: 0.7952 (pm20) REVERT: D 518 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7284 (mm-30) REVERT: D 581 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7742 (mtp) REVERT: D 634 LYS cc_start: 0.9083 (ttmt) cc_final: 0.8743 (tppt) REVERT: D 741 LYS cc_start: 0.9380 (pptt) cc_final: 0.8774 (mtpt) REVERT: D 841 GLU cc_start: 0.8246 (tt0) cc_final: 0.7904 (tm-30) REVERT: D 859 LEU cc_start: 0.9305 (mm) cc_final: 0.8900 (mm) REVERT: D 864 LEU cc_start: 0.9074 (mt) cc_final: 0.8774 (pp) REVERT: D 941 HIS cc_start: 0.7473 (t-170) cc_final: 0.7164 (t-170) REVERT: D 976 MET cc_start: 0.8718 (mmm) cc_final: 0.7435 (tpp) REVERT: D 992 GLU cc_start: 0.8199 (tp30) cc_final: 0.7973 (tp30) REVERT: D 1036 PHE cc_start: 0.9229 (m-80) cc_final: 0.9004 (m-80) REVERT: D 1152 ASP cc_start: 0.8621 (m-30) cc_final: 0.8162 (m-30) REVERT: D 1236 ASP cc_start: 0.8964 (t0) cc_final: 0.8741 (t0) REVERT: E 94 ARG cc_start: 0.7999 (ttt-90) cc_final: 0.7581 (ttt180) REVERT: F 192 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8207 (pt0) REVERT: F 196 TYR cc_start: 0.8606 (t80) cc_final: 0.8283 (t80) REVERT: F 219 MET cc_start: 0.9190 (ptp) cc_final: 0.8926 (ptp) REVERT: F 221 TRP cc_start: 0.8621 (t-100) cc_final: 0.8345 (t-100) REVERT: F 231 ASN cc_start: 0.8629 (m110) cc_final: 0.8390 (p0) REVERT: F 261 GLU cc_start: 0.8182 (tp30) cc_final: 0.7941 (tp30) REVERT: F 268 ARG cc_start: 0.8826 (tpp80) cc_final: 0.8522 (tpp80) REVERT: F 279 TYR cc_start: 0.7002 (m-80) cc_final: 0.6701 (m-80) REVERT: F 310 MET cc_start: 0.8709 (tpp) cc_final: 0.7873 (tpp) REVERT: J 101 ARG cc_start: 0.8408 (tpp-160) cc_final: 0.8116 (tpp-160) outliers start: 68 outliers final: 42 residues processed: 584 average time/residue: 0.2091 time to fit residues: 187.3646 Evaluate side-chains 560 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 511 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 619 THR Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain C residue 859 LEU Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 1080 LEU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 349 ASN Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 713 ASP Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 994 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1265 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 301 optimal weight: 3.9990 chunk 198 optimal weight: 0.0030 chunk 304 optimal weight: 0.9990 chunk 291 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 230 optimal weight: 9.9990 chunk 325 optimal weight: 0.9990 chunk 210 optimal weight: 0.7980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS C 594 ASN D 349 ASN ** D 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.124112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.087692 restraints weight = 73676.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.090808 restraints weight = 41886.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.092834 restraints weight = 28905.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.094147 restraints weight = 22652.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.095011 restraints weight = 19354.355| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28260 Z= 0.142 Angle : 0.687 10.608 38614 Z= 0.357 Chirality : 0.045 0.337 4390 Planarity : 0.005 0.086 4789 Dihedral : 14.873 164.102 4567 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.18 % Allowed : 19.02 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.15), residues: 3305 helix: 0.47 (0.15), residues: 1216 sheet: -0.56 (0.25), residues: 427 loop : -0.30 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 216 TYR 0.029 0.002 TYR D 248 PHE 0.023 0.002 PHE C 157 TRP 0.017 0.001 TRP F 288 HIS 0.006 0.001 HIS B 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (28252) covalent geometry : angle 0.68462 / 0.36 (38602) hydrogen bonds : bond 0.04321 / 2.93 ( 1154) hydrogen bonds : angle 4.91425 / 3.40 ( 3162) metal coordination : bond 0.00672 / 0.33 ( 8) metal coordination : angle 2.96392 / 1.49 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 549 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.8395 (tptt) cc_final: 0.8009 (tptt) REVERT: A 123 MET cc_start: 0.8206 (tmm) cc_final: 0.7669 (ttp) REVERT: A 177 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.7120 (ptmm) REVERT: A 191 LYS cc_start: 0.8702 (ttpp) cc_final: 0.8140 (ptpp) REVERT: B 1 MET cc_start: 0.5912 (pmm) cc_final: 0.5554 (pmm) REVERT: B 43 LEU cc_start: 0.8897 (tt) cc_final: 0.8540 (tp) REVERT: B 95 MET cc_start: 0.3505 (mmm) cc_final: 0.2842 (tpt) REVERT: B 128 LEU cc_start: 0.8085 (tp) cc_final: 0.7544 (tp) REVERT: B 141 GLU cc_start: 0.6252 (mp0) cc_final: 0.5973 (mp0) REVERT: B 173 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8545 (pptt) REVERT: B 179 GLU cc_start: 0.7740 (mp0) cc_final: 0.7339 (mp0) REVERT: B 191 LYS cc_start: 0.8459 (ptmm) cc_final: 0.7825 (ptmm) REVERT: B 225 LEU cc_start: 0.9029 (mm) cc_final: 0.8819 (mp) REVERT: B 226 ASN cc_start: 0.8754 (t0) cc_final: 0.8453 (t0) REVERT: C 62 ARG cc_start: 0.9045 (mtt90) cc_final: 0.8586 (mtt-85) REVERT: C 250 MET cc_start: 0.8902 (mmm) cc_final: 0.8671 (mmp) REVERT: C 304 ARG cc_start: 0.8751 (tpt-90) cc_final: 0.8256 (tpp-160) REVERT: C 374 GLU cc_start: 0.8224 (mp0) cc_final: 0.7932 (tp30) REVERT: C 394 ARG cc_start: 0.8911 (ttm170) cc_final: 0.8692 (ptm160) REVERT: C 619 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.7760 (p) REVERT: C 715 MET cc_start: 0.8875 (ptm) cc_final: 0.8631 (ptm) REVERT: C 724 ASP cc_start: 0.7501 (t0) cc_final: 0.6846 (t0) REVERT: C 774 ASP cc_start: 0.7678 (t0) cc_final: 0.7471 (t0) REVERT: C 813 ARG cc_start: 0.8545 (mmm160) cc_final: 0.8267 (mtp180) REVERT: C 867 LYS cc_start: 0.8891 (mtpp) cc_final: 0.8546 (tttp) REVERT: C 1083 LYS cc_start: 0.9226 (mtmt) cc_final: 0.8907 (mttt) REVERT: C 1110 GLU cc_start: 0.8037 (tp30) cc_final: 0.7658 (tp30) REVERT: D 27 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7404 (pp20) REVERT: D 43 LYS cc_start: 0.8405 (tppt) cc_final: 0.7777 (tppt) REVERT: D 58 TRP cc_start: 0.7826 (m-90) cc_final: 0.6617 (m-90) REVERT: D 81 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7908 (tm-30) REVERT: D 84 ARG cc_start: 0.8356 (tpt90) cc_final: 0.7716 (tmt-80) REVERT: D 134 TYR cc_start: 0.7694 (m-10) cc_final: 0.7347 (m-10) REVERT: D 136 ILE cc_start: 0.9441 (mm) cc_final: 0.9177 (tp) REVERT: D 143 MET cc_start: 0.8205 (mtm) cc_final: 0.7721 (ptp) REVERT: D 145 HIS cc_start: 0.7603 (p90) cc_final: 0.7395 (p90) REVERT: D 158 GLU cc_start: 0.9342 (tp30) cc_final: 0.8988 (tm-30) REVERT: D 256 MET cc_start: 0.5777 (OUTLIER) cc_final: 0.5333 (ttm) REVERT: D 335 PHE cc_start: 0.8234 (m-80) cc_final: 0.8022 (m-80) REVERT: D 346 ARG cc_start: 0.7401 (mmm-85) cc_final: 0.6947 (mmm-85) REVERT: D 356 ARG cc_start: 0.8549 (mmp80) cc_final: 0.8271 (mmp80) REVERT: D 457 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8421 (mtt) REVERT: D 515 GLN cc_start: 0.8196 (pm20) cc_final: 0.7904 (pm20) REVERT: D 518 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7233 (mm-30) REVERT: D 530 GLU cc_start: 0.8312 (tt0) cc_final: 0.7980 (tt0) REVERT: D 552 GLN cc_start: 0.8729 (mt0) cc_final: 0.8289 (mp10) REVERT: D 622 MET cc_start: 0.8967 (ptp) cc_final: 0.8621 (ptm) REVERT: D 634 LYS cc_start: 0.9077 (ttmt) cc_final: 0.8725 (tppt) REVERT: D 741 LYS cc_start: 0.9338 (pptt) cc_final: 0.8765 (mmmt) REVERT: D 841 GLU cc_start: 0.8217 (tt0) cc_final: 0.7838 (tm-30) REVERT: D 859 LEU cc_start: 0.9403 (mm) cc_final: 0.9041 (mm) REVERT: D 941 HIS cc_start: 0.7552 (t-170) cc_final: 0.7281 (t-170) REVERT: D 976 MET cc_start: 0.8735 (mmm) cc_final: 0.7465 (tpp) REVERT: D 992 GLU cc_start: 0.8290 (tp30) cc_final: 0.8021 (tp30) REVERT: D 1036 PHE cc_start: 0.9234 (m-80) cc_final: 0.9027 (m-80) REVERT: D 1152 ASP cc_start: 0.8607 (m-30) cc_final: 0.8088 (m-30) REVERT: D 1236 ASP cc_start: 0.8991 (t0) cc_final: 0.8696 (m-30) REVERT: E 94 ARG cc_start: 0.8064 (ttt-90) cc_final: 0.7612 (ttt180) REVERT: F 196 TYR cc_start: 0.8596 (t80) cc_final: 0.8111 (t80) REVERT: F 221 TRP cc_start: 0.8584 (t-100) cc_final: 0.8294 (t-100) REVERT: F 231 ASN cc_start: 0.8613 (m110) cc_final: 0.8321 (p0) REVERT: F 261 GLU cc_start: 0.8179 (tp30) cc_final: 0.7830 (tp30) REVERT: F 268 ARG cc_start: 0.8890 (tpp80) cc_final: 0.8653 (tpp80) REVERT: F 273 PHE cc_start: 0.8788 (t80) cc_final: 0.8533 (t80) REVERT: F 279 TYR cc_start: 0.6850 (m-80) cc_final: 0.6575 (m-80) REVERT: F 310 MET cc_start: 0.8656 (tpp) cc_final: 0.8253 (tpp) REVERT: J 101 ARG cc_start: 0.8366 (tpp-160) cc_final: 0.7990 (tpp-160) outliers start: 61 outliers final: 36 residues processed: 573 average time/residue: 0.2053 time to fit residues: 182.1432 Evaluate side-chains 557 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 515 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 594 ASN Chi-restraints excluded: chain C residue 619 THR Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1043 ILE Chi-restraints excluded: chain C residue 1080 LEU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 226 PHE Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 349 ASN Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 959 VAL Chi-restraints excluded: chain D residue 1216 LEU Chi-restraints excluded: chain D residue 1265 ILE Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 361 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 226 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 170 optimal weight: 9.9990 chunk 309 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 317 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 148 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS C 594 ASN ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1132 GLN F 152 GLN ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.120232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.083346 restraints weight = 75631.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.086333 restraints weight = 43621.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.088304 restraints weight = 30431.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.089611 restraints weight = 23962.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.090392 restraints weight = 20486.746| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 28260 Z= 0.285 Angle : 0.746 14.978 38614 Z= 0.386 Chirality : 0.046 0.238 4390 Planarity : 0.005 0.103 4789 Dihedral : 15.010 164.231 4567 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.28 % Allowed : 19.41 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.15), residues: 3305 helix: 0.35 (0.15), residues: 1234 sheet: -0.68 (0.25), residues: 413 loop : -0.35 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 453 TYR 0.032 0.002 TYR F 354 PHE 0.023 0.002 PHE F 391 TRP 0.017 0.002 TRP D1221 HIS 0.010 0.001 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.29 (28252) covalent geometry : angle 0.74255 / 0.39 (38602) hydrogen bonds : bond 0.04597 / 3.12 ( 1154) hydrogen bonds : angle 5.08285 / 3.52 ( 3162) metal coordination : bond 0.01842 / 0.90 ( 8) metal coordination : angle 3.86386 / 1.93 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 511 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7902 (mmm) cc_final: 0.7568 (mmm) REVERT: A 99 LYS cc_start: 0.8480 (tptt) cc_final: 0.8134 (tptt) REVERT: A 191 LYS cc_start: 0.8729 (ttpp) cc_final: 0.8151 (ptpp) REVERT: B 1 MET cc_start: 0.6288 (pmm) cc_final: 0.6043 (pmm) REVERT: B 95 MET cc_start: 0.3248 (mmm) cc_final: 0.2564 (tpt) REVERT: B 123 MET cc_start: 0.7999 (tmm) cc_final: 0.7443 (tmm) REVERT: B 141 GLU cc_start: 0.6284 (mp0) cc_final: 0.5957 (mp0) REVERT: B 173 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8545 (pptt) REVERT: B 179 GLU cc_start: 0.7796 (mp0) cc_final: 0.7352 (mp0) REVERT: B 191 LYS cc_start: 0.8542 (ptmm) cc_final: 0.7869 (ptmm) REVERT: B 226 ASN cc_start: 0.8802 (t0) cc_final: 0.8572 (t0) REVERT: C 62 ARG cc_start: 0.9084 (mtt90) cc_final: 0.8614 (mtp85) REVERT: C 107 LYS cc_start: 0.8739 (mtmt) cc_final: 0.8399 (ptpp) REVERT: C 124 LEU cc_start: 0.9186 (tp) cc_final: 0.8956 (tt) REVERT: C 304 ARG cc_start: 0.8772 (tpt-90) cc_final: 0.8554 (tpp-160) REVERT: C 374 GLU cc_start: 0.8281 (mp0) cc_final: 0.8011 (tp30) REVERT: C 548 ASP cc_start: 0.8125 (p0) cc_final: 0.7625 (p0) REVERT: C 619 THR cc_start: 0.8582 (OUTLIER) cc_final: 0.8160 (p) REVERT: C 704 MET cc_start: 0.8214 (tpp) cc_final: 0.7974 (mpp) REVERT: C 715 MET cc_start: 0.8923 (ptm) cc_final: 0.8564 (ptm) REVERT: C 724 ASP cc_start: 0.7527 (t0) cc_final: 0.7247 (t0) REVERT: C 774 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7625 (t0) REVERT: C 791 ASP cc_start: 0.8026 (m-30) cc_final: 0.7615 (p0) REVERT: C 813 ARG cc_start: 0.8573 (mmm160) cc_final: 0.8200 (mtp180) REVERT: C 883 LYS cc_start: 0.8890 (pttm) cc_final: 0.8518 (ptmm) REVERT: C 915 ARG cc_start: 0.7846 (tmm-80) cc_final: 0.7640 (tmm-80) REVERT: C 950 LEU cc_start: 0.9150 (mt) cc_final: 0.8900 (mt) REVERT: C 1008 GLU cc_start: 0.8393 (mp0) cc_final: 0.8114 (mp0) REVERT: C 1083 LYS cc_start: 0.9228 (mtmt) cc_final: 0.8897 (mttt) REVERT: C 1110 GLU cc_start: 0.8171 (tp30) cc_final: 0.7751 (tp30) REVERT: D 27 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7377 (pp20) REVERT: D 43 LYS cc_start: 0.8382 (tppt) cc_final: 0.7764 (tppt) REVERT: D 81 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8000 (tm-30) REVERT: D 86 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8734 (pttm) REVERT: D 90 GLU cc_start: 0.8341 (pt0) cc_final: 0.8126 (pp20) REVERT: D 134 TYR cc_start: 0.7668 (m-10) cc_final: 0.7274 (m-10) REVERT: D 136 ILE cc_start: 0.9474 (mm) cc_final: 0.9230 (tp) REVERT: D 143 MET cc_start: 0.8386 (mtm) cc_final: 0.7908 (ptp) REVERT: D 158 GLU cc_start: 0.9329 (tp30) cc_final: 0.8936 (tm-30) REVERT: D 159 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8714 (tptt) REVERT: D 223 TRP cc_start: 0.8622 (t-100) cc_final: 0.8407 (t-100) REVERT: D 233 GLN cc_start: 0.7794 (tm-30) cc_final: 0.7565 (tm-30) REVERT: D 256 MET cc_start: 0.5996 (OUTLIER) cc_final: 0.5541 (ttm) REVERT: D 335 PHE cc_start: 0.8203 (m-80) cc_final: 0.7901 (m-80) REVERT: D 346 ARG cc_start: 0.7452 (mmm-85) cc_final: 0.6927 (mmm-85) REVERT: D 356 ARG cc_start: 0.8611 (mmp80) cc_final: 0.8311 (mmp80) REVERT: D 404 ASP cc_start: 0.8888 (t0) cc_final: 0.8253 (t0) REVERT: D 457 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8256 (mmm) REVERT: D 474 ARG cc_start: 0.7453 (tpt90) cc_final: 0.6988 (tpt170) REVERT: D 515 GLN cc_start: 0.8430 (pm20) cc_final: 0.8095 (pm20) REVERT: D 518 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7389 (mm-30) REVERT: D 552 GLN cc_start: 0.8681 (mt0) cc_final: 0.8258 (mp10) REVERT: D 634 LYS cc_start: 0.9128 (ttmt) cc_final: 0.8833 (tptt) REVERT: D 841 GLU cc_start: 0.8255 (tt0) cc_final: 0.7842 (tm-30) REVERT: D 859 LEU cc_start: 0.9489 (mm) cc_final: 0.9178 (mm) REVERT: D 941 HIS cc_start: 0.7656 (t-170) cc_final: 0.7342 (t-170) REVERT: D 976 MET cc_start: 0.8834 (mmm) cc_final: 0.7534 (tpp) REVERT: D 992 GLU cc_start: 0.8246 (tp30) cc_final: 0.8031 (tp30) REVERT: E 94 ARG cc_start: 0.8117 (ttt-90) cc_final: 0.7844 (ttt-90) REVERT: F 159 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7661 (mt) REVERT: F 192 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8256 (pt0) REVERT: F 196 TYR cc_start: 0.8698 (t80) cc_final: 0.8216 (t80) REVERT: F 219 MET cc_start: 0.9138 (ptp) cc_final: 0.8896 (ptp) REVERT: F 221 TRP cc_start: 0.8580 (t-100) cc_final: 0.8305 (t-100) REVERT: F 261 GLU cc_start: 0.8294 (tp30) cc_final: 0.8046 (tp30) REVERT: F 279 TYR cc_start: 0.7131 (m-80) cc_final: 0.6813 (m-80) REVERT: F 310 MET cc_start: 0.8720 (tpp) cc_final: 0.8383 (tpp) REVERT: F 391 PHE cc_start: 0.8616 (t80) cc_final: 0.8356 (t80) outliers start: 92 outliers final: 61 residues processed: 552 average time/residue: 0.2077 time to fit residues: 176.7461 Evaluate side-chains 564 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 494 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 619 THR Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 648 TYR Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 774 ASP Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1043 ILE Chi-restraints excluded: chain C residue 1080 LEU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 159 LYS Chi-restraints excluded: chain D residue 226 PHE Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 732 MET Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 959 VAL Chi-restraints excluded: chain D residue 961 VAL Chi-restraints excluded: chain D residue 994 VAL Chi-restraints excluded: chain D residue 1132 GLN Chi-restraints excluded: chain D residue 1158 ILE Chi-restraints excluded: chain D residue 1186 GLU Chi-restraints excluded: chain D residue 1216 LEU Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1247 ASN Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 384 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 65 optimal weight: 0.0170 chunk 84 optimal weight: 0.9990 chunk 172 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 332 optimal weight: 40.0000 chunk 309 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 285 optimal weight: 0.5980 chunk 271 optimal weight: 7.9990 chunk 277 optimal weight: 2.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN ** D 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1240 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.122967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.085953 restraints weight = 74961.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.089141 restraints weight = 41989.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.091214 restraints weight = 28745.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.092569 restraints weight = 22444.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.093473 restraints weight = 19122.547| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28260 Z= 0.138 Angle : 0.710 11.421 38614 Z= 0.361 Chirality : 0.045 0.357 4390 Planarity : 0.005 0.068 4789 Dihedral : 14.966 163.928 4567 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.71 % Allowed : 20.69 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.15), residues: 3305 helix: 0.40 (0.15), residues: 1228 sheet: -0.58 (0.25), residues: 415 loop : -0.27 (0.16), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 216 TYR 0.029 0.002 TYR E 53 PHE 0.015 0.001 PHE F 391 TRP 0.035 0.002 TRP F 288 HIS 0.007 0.001 HIS F 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (28252) covalent geometry : angle 0.70719 / 0.36 (38602) hydrogen bonds : bond 0.04147 / 2.81 ( 1154) hydrogen bonds : angle 4.84500 / 3.34 ( 3162) metal coordination : bond 0.00662 / 0.33 ( 8) metal coordination : angle 3.33109 / 1.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 533 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 HIS cc_start: 0.8408 (p90) cc_final: 0.7972 (p90) REVERT: A 99 LYS cc_start: 0.8550 (tptt) cc_final: 0.8107 (tptt) REVERT: A 123 MET cc_start: 0.8262 (tmm) cc_final: 0.7696 (ttp) REVERT: A 191 LYS cc_start: 0.8699 (ttpp) cc_final: 0.8194 (ptpp) REVERT: B 1 MET cc_start: 0.6401 (pmm) cc_final: 0.6178 (pmm) REVERT: B 43 LEU cc_start: 0.8887 (tt) cc_final: 0.8477 (tp) REVERT: B 95 MET cc_start: 0.3369 (mmm) cc_final: 0.2720 (tpt) REVERT: B 128 LEU cc_start: 0.8167 (tp) cc_final: 0.7584 (tp) REVERT: B 141 GLU cc_start: 0.6266 (mp0) cc_final: 0.6037 (mp0) REVERT: B 173 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8563 (pptt) REVERT: B 179 GLU cc_start: 0.7829 (mp0) cc_final: 0.7389 (mp0) REVERT: B 191 LYS cc_start: 0.8576 (ptmm) cc_final: 0.7997 (ptmm) REVERT: B 225 LEU cc_start: 0.9061 (mm) cc_final: 0.8649 (mp) REVERT: B 226 ASN cc_start: 0.8776 (t0) cc_final: 0.8476 (t0) REVERT: C 62 ARG cc_start: 0.9036 (mtt90) cc_final: 0.8543 (mtp85) REVERT: C 107 LYS cc_start: 0.8699 (mtmt) cc_final: 0.8366 (ptpp) REVERT: C 124 LEU cc_start: 0.9127 (tp) cc_final: 0.8898 (tt) REVERT: C 172 ARG cc_start: 0.7955 (mmt90) cc_final: 0.7665 (mmt90) REVERT: C 304 ARG cc_start: 0.8736 (tpt-90) cc_final: 0.8454 (tpp-160) REVERT: C 374 GLU cc_start: 0.8208 (mp0) cc_final: 0.7837 (mt-10) REVERT: C 412 ARG cc_start: 0.8008 (tpp-160) cc_final: 0.7718 (tpm170) REVERT: C 478 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7948 (tp30) REVERT: C 619 THR cc_start: 0.8507 (OUTLIER) cc_final: 0.8054 (p) REVERT: C 652 MET cc_start: 0.8966 (tpp) cc_final: 0.8711 (tpp) REVERT: C 724 ASP cc_start: 0.7528 (t0) cc_final: 0.7205 (t0) REVERT: C 791 ASP cc_start: 0.8106 (m-30) cc_final: 0.7695 (p0) REVERT: C 867 LYS cc_start: 0.8850 (mtpp) cc_final: 0.8609 (tttp) REVERT: C 883 LYS cc_start: 0.8840 (pttm) cc_final: 0.8437 (ptmm) REVERT: C 915 ARG cc_start: 0.7811 (tmm-80) cc_final: 0.7528 (tmm-80) REVERT: C 1008 GLU cc_start: 0.8377 (mp0) cc_final: 0.8026 (mp0) REVERT: C 1083 LYS cc_start: 0.9201 (mtmt) cc_final: 0.8941 (mttt) REVERT: C 1110 GLU cc_start: 0.8070 (tp30) cc_final: 0.7677 (tp30) REVERT: C 1124 LEU cc_start: 0.8781 (mt) cc_final: 0.8525 (mp) REVERT: D 27 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7291 (pp20) REVERT: D 43 LYS cc_start: 0.8428 (tppt) cc_final: 0.7741 (tppt) REVERT: D 58 TRP cc_start: 0.7612 (m-90) cc_final: 0.7001 (m-90) REVERT: D 81 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7900 (tm-30) REVERT: D 84 ARG cc_start: 0.8316 (tmt-80) cc_final: 0.7998 (tmt-80) REVERT: D 86 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8653 (ptpp) REVERT: D 134 TYR cc_start: 0.7710 (m-10) cc_final: 0.7337 (m-10) REVERT: D 136 ILE cc_start: 0.9445 (mm) cc_final: 0.9229 (tp) REVERT: D 158 GLU cc_start: 0.9330 (tp30) cc_final: 0.9044 (tm-30) REVERT: D 223 TRP cc_start: 0.8494 (t-100) cc_final: 0.8292 (t-100) REVERT: D 256 MET cc_start: 0.6207 (OUTLIER) cc_final: 0.5794 (ttm) REVERT: D 335 PHE cc_start: 0.8167 (m-80) cc_final: 0.7906 (m-80) REVERT: D 356 ARG cc_start: 0.8567 (mmp80) cc_final: 0.8243 (mmp80) REVERT: D 404 ASP cc_start: 0.8659 (t0) cc_final: 0.8436 (t0) REVERT: D 409 LYS cc_start: 0.9090 (ttpp) cc_final: 0.8791 (tmmt) REVERT: D 457 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8183 (mmm) REVERT: D 474 ARG cc_start: 0.7354 (tpt90) cc_final: 0.6859 (tpt170) REVERT: D 515 GLN cc_start: 0.8257 (pm20) cc_final: 0.7940 (pm20) REVERT: D 541 MET cc_start: 0.8717 (tpp) cc_final: 0.8226 (mmm) REVERT: D 552 GLN cc_start: 0.8690 (mt0) cc_final: 0.8266 (mp10) REVERT: D 558 LEU cc_start: 0.9325 (mm) cc_final: 0.9108 (mm) REVERT: D 634 LYS cc_start: 0.9062 (ttmt) cc_final: 0.8699 (tppt) REVERT: D 717 ASP cc_start: 0.8472 (m-30) cc_final: 0.8209 (m-30) REVERT: D 741 LYS cc_start: 0.9355 (pptt) cc_final: 0.8797 (mmmt) REVERT: D 859 LEU cc_start: 0.9441 (mm) cc_final: 0.9090 (mm) REVERT: D 868 ASP cc_start: 0.7843 (t0) cc_final: 0.7475 (p0) REVERT: D 941 HIS cc_start: 0.7550 (t-170) cc_final: 0.7227 (t-170) REVERT: D 951 LEU cc_start: 0.8715 (mt) cc_final: 0.8016 (pp) REVERT: D 976 MET cc_start: 0.8778 (mmm) cc_final: 0.7396 (tpp) REVERT: D 1254 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7673 (mm) REVERT: E 94 ARG cc_start: 0.8104 (ttt-90) cc_final: 0.7848 (ttt-90) REVERT: E 97 HIS cc_start: 0.8535 (t-90) cc_final: 0.7978 (t-170) REVERT: F 159 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7633 (mt) REVERT: F 219 MET cc_start: 0.9084 (ptp) cc_final: 0.8868 (ptt) REVERT: F 221 TRP cc_start: 0.8582 (t-100) cc_final: 0.8288 (t-100) REVERT: F 261 GLU cc_start: 0.8227 (tp30) cc_final: 0.7873 (tp30) REVERT: F 279 TYR cc_start: 0.6905 (m-80) cc_final: 0.6597 (m-80) REVERT: F 310 MET cc_start: 0.8648 (tpp) cc_final: 0.8295 (tpp) REVERT: F 391 PHE cc_start: 0.8526 (t80) cc_final: 0.8240 (t80) REVERT: J 82 TRP cc_start: 0.9116 (t-100) cc_final: 0.8472 (t-100) REVERT: J 101 ARG cc_start: 0.8405 (tpp-160) cc_final: 0.8156 (tpp-160) outliers start: 76 outliers final: 50 residues processed: 574 average time/residue: 0.2015 time to fit residues: 179.2520 Evaluate side-chains 557 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 499 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 594 ASN Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 619 THR Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain C residue 859 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1043 ILE Chi-restraints excluded: chain C residue 1080 LEU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 226 PHE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 871 TYR Chi-restraints excluded: chain D residue 959 VAL Chi-restraints excluded: chain D residue 961 VAL Chi-restraints excluded: chain D residue 1169 ILE Chi-restraints excluded: chain D residue 1216 LEU Chi-restraints excluded: chain D residue 1254 ILE Chi-restraints excluded: chain D residue 1265 ILE Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 384 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 283 optimal weight: 4.9990 chunk 199 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 5 optimal weight: 0.0980 chunk 293 optimal weight: 9.9990 chunk 298 optimal weight: 8.9990 chunk 50 optimal weight: 0.0000 chunk 205 optimal weight: 3.9990 chunk 238 optimal weight: 8.9990 chunk 256 optimal weight: 0.9990 overall best weight: 1.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 692 GLN ** D 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1132 GLN F 231 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.121475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.084266 restraints weight = 75207.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.087357 restraints weight = 42531.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.089407 restraints weight = 29363.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.090757 restraints weight = 22989.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.091577 restraints weight = 19605.447| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28260 Z= 0.171 Angle : 0.709 12.339 38614 Z= 0.361 Chirality : 0.044 0.292 4390 Planarity : 0.005 0.076 4789 Dihedral : 15.019 164.313 4567 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.14 % Allowed : 21.55 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.15), residues: 3305 helix: 0.40 (0.15), residues: 1234 sheet: -0.63 (0.25), residues: 415 loop : -0.25 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 56 TYR 0.033 0.002 TYR E 53 PHE 0.026 0.002 PHE C 561 TRP 0.037 0.002 TRP F 288 HIS 0.006 0.001 HIS F 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (28252) covalent geometry : angle 0.70689 / 0.36 (38602) hydrogen bonds : bond 0.04143 / 2.79 ( 1154) hydrogen bonds : angle 4.85937 / 3.35 ( 3162) metal coordination : bond 0.01090 / 0.54 ( 8) metal coordination : angle 3.42640 / 1.69 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 508 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.8563 (tptt) cc_final: 0.8166 (tptt) REVERT: A 191 LYS cc_start: 0.8725 (ttpp) cc_final: 0.8193 (ptpp) REVERT: B 1 MET cc_start: 0.6491 (pmm) cc_final: 0.6244 (pmm) REVERT: B 95 MET cc_start: 0.3136 (mmm) cc_final: 0.2533 (tpt) REVERT: B 141 GLU cc_start: 0.6210 (mp0) cc_final: 0.6000 (mp0) REVERT: B 173 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8570 (pptt) REVERT: B 179 GLU cc_start: 0.7859 (mp0) cc_final: 0.7404 (mp0) REVERT: B 191 LYS cc_start: 0.8606 (ptmm) cc_final: 0.8022 (ptmm) REVERT: B 226 ASN cc_start: 0.8867 (t0) cc_final: 0.8594 (t0) REVERT: C 62 ARG cc_start: 0.9072 (mtt90) cc_final: 0.8577 (mtp85) REVERT: C 79 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8594 (mm-30) REVERT: C 107 LYS cc_start: 0.8745 (mtmt) cc_final: 0.8280 (ptpp) REVERT: C 172 ARG cc_start: 0.8000 (mmt90) cc_final: 0.7725 (mmt90) REVERT: C 304 ARG cc_start: 0.8769 (tpt-90) cc_final: 0.8439 (tpp-160) REVERT: C 374 GLU cc_start: 0.8251 (mp0) cc_final: 0.7988 (tp30) REVERT: C 548 ASP cc_start: 0.8154 (p0) cc_final: 0.7621 (p0) REVERT: C 594 ASN cc_start: 0.9012 (OUTLIER) cc_final: 0.8584 (p0) REVERT: C 619 THR cc_start: 0.8486 (OUTLIER) cc_final: 0.8008 (p) REVERT: C 724 ASP cc_start: 0.7549 (t0) cc_final: 0.7285 (t0) REVERT: C 791 ASP cc_start: 0.8013 (m-30) cc_final: 0.7747 (p0) REVERT: C 813 ARG cc_start: 0.8612 (mmm160) cc_final: 0.8262 (mtp180) REVERT: C 883 LYS cc_start: 0.8869 (pttm) cc_final: 0.8466 (ptmm) REVERT: C 915 ARG cc_start: 0.7866 (tmm-80) cc_final: 0.7623 (tmm-80) REVERT: C 950 LEU cc_start: 0.9145 (mt) cc_final: 0.8877 (mt) REVERT: C 1008 GLU cc_start: 0.8403 (mp0) cc_final: 0.8040 (mp0) REVERT: C 1083 LYS cc_start: 0.9190 (mtmt) cc_final: 0.8940 (mttt) REVERT: C 1110 GLU cc_start: 0.8091 (tp30) cc_final: 0.7704 (tp30) REVERT: D 27 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7281 (pp20) REVERT: D 43 LYS cc_start: 0.8403 (tppt) cc_final: 0.7714 (tppt) REVERT: D 56 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.6848 (mmm160) REVERT: D 58 TRP cc_start: 0.7661 (m-90) cc_final: 0.7109 (m-90) REVERT: D 81 GLU cc_start: 0.8362 (tm-30) cc_final: 0.7912 (tm-30) REVERT: D 86 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8592 (pttm) REVERT: D 134 TYR cc_start: 0.7730 (m-10) cc_final: 0.7285 (m-10) REVERT: D 143 MET cc_start: 0.8418 (mtm) cc_final: 0.7995 (ptp) REVERT: D 158 GLU cc_start: 0.9316 (tp30) cc_final: 0.9002 (tm-30) REVERT: D 233 GLN cc_start: 0.7860 (tm-30) cc_final: 0.7620 (tm-30) REVERT: D 256 MET cc_start: 0.6284 (OUTLIER) cc_final: 0.5827 (ttm) REVERT: D 295 ARG cc_start: 0.8724 (ttm170) cc_final: 0.7976 (mtp-110) REVERT: D 335 PHE cc_start: 0.8168 (m-80) cc_final: 0.7891 (m-10) REVERT: D 356 ARG cc_start: 0.8592 (mmp80) cc_final: 0.8235 (mmp80) REVERT: D 457 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8224 (mmm) REVERT: D 474 ARG cc_start: 0.7418 (tpt90) cc_final: 0.6759 (tpt90) REVERT: D 515 GLN cc_start: 0.8344 (pm20) cc_final: 0.8008 (pm20) REVERT: D 518 GLU cc_start: 0.7393 (mm-30) cc_final: 0.6920 (mm-30) REVERT: D 552 GLN cc_start: 0.8686 (mt0) cc_final: 0.8286 (mp10) REVERT: D 634 LYS cc_start: 0.9096 (ttmt) cc_final: 0.8792 (tptt) REVERT: D 717 ASP cc_start: 0.8526 (m-30) cc_final: 0.8285 (m-30) REVERT: D 741 LYS cc_start: 0.9354 (pptt) cc_final: 0.8806 (mmmt) REVERT: D 803 LYS cc_start: 0.8872 (mmtm) cc_final: 0.8651 (mmtm) REVERT: D 859 LEU cc_start: 0.9440 (mm) cc_final: 0.9186 (mm) REVERT: D 864 LEU cc_start: 0.9208 (pp) cc_final: 0.8492 (pt) REVERT: D 868 ASP cc_start: 0.7837 (t0) cc_final: 0.7477 (p0) REVERT: D 941 HIS cc_start: 0.7561 (t-170) cc_final: 0.7327 (t-170) REVERT: D 976 MET cc_start: 0.8821 (mmm) cc_final: 0.7426 (tpp) REVERT: D 1254 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7712 (mm) REVERT: E 94 ARG cc_start: 0.8138 (ttt-90) cc_final: 0.7866 (ttt-90) REVERT: E 97 HIS cc_start: 0.8523 (t-90) cc_final: 0.7976 (t-170) REVERT: F 192 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8146 (pt0) REVERT: F 219 MET cc_start: 0.9082 (ptp) cc_final: 0.8699 (ptt) REVERT: F 221 TRP cc_start: 0.8624 (t-100) cc_final: 0.8332 (t-100) REVERT: F 231 ASN cc_start: 0.8625 (m110) cc_final: 0.8349 (p0) REVERT: F 261 GLU cc_start: 0.8286 (tp30) cc_final: 0.7946 (tp30) REVERT: F 279 TYR cc_start: 0.6938 (m-80) cc_final: 0.6616 (m-80) REVERT: F 310 MET cc_start: 0.8693 (tpp) cc_final: 0.8353 (tpp) REVERT: F 361 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8676 (mt) REVERT: F 391 PHE cc_start: 0.8625 (t80) cc_final: 0.8301 (t80) REVERT: J 101 ARG cc_start: 0.8533 (tpp-160) cc_final: 0.8272 (tpp-160) outliers start: 88 outliers final: 62 residues processed: 557 average time/residue: 0.2030 time to fit residues: 175.0950 Evaluate side-chains 558 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 486 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 594 ASN Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 619 THR Chi-restraints excluded: chain C residue 648 TYR Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain C residue 859 LEU Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1043 ILE Chi-restraints excluded: chain C residue 1080 LEU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 226 PHE Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 732 MET Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 959 VAL Chi-restraints excluded: chain D residue 961 VAL Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 1132 GLN Chi-restraints excluded: chain D residue 1169 ILE Chi-restraints excluded: chain D residue 1186 GLU Chi-restraints excluded: chain D residue 1216 LEU Chi-restraints excluded: chain D residue 1247 ASN Chi-restraints excluded: chain D residue 1254 ILE Chi-restraints excluded: chain D residue 1265 ILE Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 440 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 330 optimal weight: 20.0000 chunk 220 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 245 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 231 optimal weight: 6.9990 chunk 115 optimal weight: 0.4980 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS C 918 ASN ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.120479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.083670 restraints weight = 75717.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.086680 restraints weight = 42993.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.088693 restraints weight = 29764.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.090035 restraints weight = 23321.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.090863 restraints weight = 19885.716| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 28260 Z= 0.217 Angle : 0.748 13.499 38614 Z= 0.379 Chirality : 0.046 0.339 4390 Planarity : 0.005 0.115 4789 Dihedral : 15.085 163.948 4567 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.03 % Allowed : 22.51 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.15), residues: 3305 helix: 0.36 (0.15), residues: 1230 sheet: -0.47 (0.26), residues: 381 loop : -0.27 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 301 TYR 0.033 0.002 TYR F 354 PHE 0.021 0.002 PHE D 920 TRP 0.055 0.002 TRP F 288 HIS 0.015 0.001 HIS B 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.22 (28252) covalent geometry : angle 0.74539 / 0.38 (38602) hydrogen bonds : bond 0.04196 / 2.84 ( 1154) hydrogen bonds : angle 4.93157 / 3.41 ( 3162) metal coordination : bond 0.01396 / 0.68 ( 8) metal coordination : angle 3.57232 / 1.76 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 487 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 HIS cc_start: 0.8440 (p90) cc_final: 0.8234 (p90) REVERT: A 99 LYS cc_start: 0.8612 (tptt) cc_final: 0.8200 (tptt) REVERT: A 123 MET cc_start: 0.8387 (tmm) cc_final: 0.7756 (ttp) REVERT: A 191 LYS cc_start: 0.8805 (ttpp) cc_final: 0.8278 (ptpp) REVERT: B 95 MET cc_start: 0.3137 (mmm) cc_final: 0.2753 (tpt) REVERT: B 141 GLU cc_start: 0.6166 (mp0) cc_final: 0.5931 (mp0) REVERT: B 173 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8582 (pptt) REVERT: B 179 GLU cc_start: 0.7873 (mp0) cc_final: 0.7519 (mp0) REVERT: B 226 ASN cc_start: 0.8907 (t0) cc_final: 0.8626 (t0) REVERT: C 62 ARG cc_start: 0.9093 (mtt90) cc_final: 0.8586 (mtp85) REVERT: C 79 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8646 (mm-30) REVERT: C 107 LYS cc_start: 0.8769 (mtmt) cc_final: 0.8429 (ptpp) REVERT: C 172 ARG cc_start: 0.7979 (mmt90) cc_final: 0.7714 (mmt90) REVERT: C 346 MET cc_start: 0.7613 (tpt) cc_final: 0.7116 (tmm) REVERT: C 374 GLU cc_start: 0.8262 (mp0) cc_final: 0.7993 (tp30) REVERT: C 594 ASN cc_start: 0.9033 (OUTLIER) cc_final: 0.8622 (p0) REVERT: C 619 THR cc_start: 0.8498 (OUTLIER) cc_final: 0.8009 (p) REVERT: C 704 MET cc_start: 0.8173 (mmt) cc_final: 0.7965 (mpp) REVERT: C 724 ASP cc_start: 0.7554 (t0) cc_final: 0.7291 (t0) REVERT: C 791 ASP cc_start: 0.8026 (m-30) cc_final: 0.7811 (p0) REVERT: C 813 ARG cc_start: 0.8619 (mmm160) cc_final: 0.8272 (mtp180) REVERT: C 915 ARG cc_start: 0.7909 (tmm-80) cc_final: 0.7686 (tmm-80) REVERT: C 918 ASN cc_start: 0.9076 (OUTLIER) cc_final: 0.8139 (p0) REVERT: C 1008 GLU cc_start: 0.8426 (mp0) cc_final: 0.8003 (mp0) REVERT: C 1083 LYS cc_start: 0.9180 (mtmt) cc_final: 0.8913 (mttt) REVERT: C 1110 GLU cc_start: 0.8187 (tp30) cc_final: 0.7772 (tp30) REVERT: D 27 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7295 (pp20) REVERT: D 43 LYS cc_start: 0.8375 (tppt) cc_final: 0.7677 (tppt) REVERT: D 56 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.6863 (mmm160) REVERT: D 58 TRP cc_start: 0.7686 (m-90) cc_final: 0.7071 (m-90) REVERT: D 81 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7920 (tm-30) REVERT: D 86 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8642 (ptpp) REVERT: D 113 ARG cc_start: 0.8211 (mmt-90) cc_final: 0.7895 (mmp80) REVERT: D 134 TYR cc_start: 0.7723 (m-10) cc_final: 0.7300 (m-10) REVERT: D 143 MET cc_start: 0.8426 (mtm) cc_final: 0.7962 (ptp) REVERT: D 158 GLU cc_start: 0.9347 (tp30) cc_final: 0.9012 (tm-30) REVERT: D 233 GLN cc_start: 0.7889 (tm-30) cc_final: 0.7606 (tm-30) REVERT: D 256 MET cc_start: 0.6371 (OUTLIER) cc_final: 0.5905 (ttm) REVERT: D 295 ARG cc_start: 0.8738 (ttm170) cc_final: 0.8047 (mtp-110) REVERT: D 335 PHE cc_start: 0.8156 (m-80) cc_final: 0.7897 (m-10) REVERT: D 356 ARG cc_start: 0.8618 (mmp80) cc_final: 0.8264 (mmp80) REVERT: D 400 LYS cc_start: 0.9044 (tptt) cc_final: 0.8753 (tptp) REVERT: D 457 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8419 (tpp) REVERT: D 474 ARG cc_start: 0.7447 (tpt90) cc_final: 0.6769 (tpt90) REVERT: D 518 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7104 (mm-30) REVERT: D 541 MET cc_start: 0.8675 (tpp) cc_final: 0.8237 (mmm) REVERT: D 552 GLN cc_start: 0.8648 (mt0) cc_final: 0.8239 (mp10) REVERT: D 634 LYS cc_start: 0.9115 (ttmt) cc_final: 0.8814 (tptt) REVERT: D 717 ASP cc_start: 0.8465 (m-30) cc_final: 0.8224 (m-30) REVERT: D 741 LYS cc_start: 0.9363 (pptt) cc_final: 0.8816 (mmmt) REVERT: D 859 LEU cc_start: 0.9429 (mm) cc_final: 0.9183 (mm) REVERT: D 868 ASP cc_start: 0.7868 (t0) cc_final: 0.7484 (p0) REVERT: D 881 GLN cc_start: 0.7957 (tm-30) cc_final: 0.7726 (tm-30) REVERT: D 941 HIS cc_start: 0.7630 (t-90) cc_final: 0.7344 (t-170) REVERT: D 976 MET cc_start: 0.8816 (mmm) cc_final: 0.7386 (tpp) REVERT: D 1254 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7732 (mm) REVERT: E 94 ARG cc_start: 0.8146 (ttt-90) cc_final: 0.7756 (ttt180) REVERT: E 97 HIS cc_start: 0.8514 (t-90) cc_final: 0.7982 (t-170) REVERT: F 192 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8127 (pt0) REVERT: F 219 MET cc_start: 0.9032 (ptp) cc_final: 0.8824 (ptt) REVERT: F 221 TRP cc_start: 0.8633 (t-100) cc_final: 0.8358 (t-100) REVERT: F 231 ASN cc_start: 0.8594 (m110) cc_final: 0.8364 (p0) REVERT: F 261 GLU cc_start: 0.8295 (tp30) cc_final: 0.7983 (tp30) REVERT: F 268 ARG cc_start: 0.9049 (ttm-80) cc_final: 0.8715 (mmm-85) REVERT: F 279 TYR cc_start: 0.6888 (m-80) cc_final: 0.6550 (m-80) REVERT: F 310 MET cc_start: 0.8707 (tpp) cc_final: 0.8373 (tpp) REVERT: J 82 TRP cc_start: 0.9202 (t-100) cc_final: 0.8519 (t-100) REVERT: J 101 ARG cc_start: 0.8565 (tpp-160) cc_final: 0.8234 (tpp-160) outliers start: 85 outliers final: 62 residues processed: 531 average time/residue: 0.2020 time to fit residues: 166.3754 Evaluate side-chains 544 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 472 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 594 ASN Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 619 THR Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 648 TYR Chi-restraints excluded: chain C residue 674 CYS Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 798 THR Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain C residue 859 LEU Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 918 ASN Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1043 ILE Chi-restraints excluded: chain C residue 1080 LEU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 226 PHE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 732 MET Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 959 VAL Chi-restraints excluded: chain D residue 961 VAL Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 1169 ILE Chi-restraints excluded: chain D residue 1186 GLU Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1254 ILE Chi-restraints excluded: chain D residue 1263 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 440 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 159 optimal weight: 0.3980 chunk 295 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 311 optimal weight: 20.0000 chunk 57 optimal weight: 0.0000 chunk 0 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 269 optimal weight: 3.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 918 ASN ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.120702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.084034 restraints weight = 75492.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.087048 restraints weight = 43458.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.089014 restraints weight = 30180.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.090309 restraints weight = 23781.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.091161 restraints weight = 20334.376| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 28260 Z= 0.177 Angle : 0.741 13.342 38614 Z= 0.374 Chirality : 0.046 0.549 4390 Planarity : 0.005 0.087 4789 Dihedral : 15.106 163.827 4567 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.93 % Allowed : 22.58 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.15), residues: 3305 helix: 0.31 (0.15), residues: 1236 sheet: -0.56 (0.25), residues: 393 loop : -0.26 (0.16), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 916 TYR 0.033 0.002 TYR E 53 PHE 0.020 0.002 PHE D 920 TRP 0.046 0.002 TRP F 288 HIS 0.006 0.001 HIS F 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (28252) covalent geometry : angle 0.73864 / 0.37 (38602) hydrogen bonds : bond 0.04122 / 2.79 ( 1154) hydrogen bonds : angle 4.93168 / 3.40 ( 3162) metal coordination : bond 0.01124 / 0.55 ( 8) metal coordination : angle 3.49493 / 1.70 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 486 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.8600 (tptt) cc_final: 0.8192 (tptt) REVERT: A 123 MET cc_start: 0.8376 (tmm) cc_final: 0.7726 (ttp) REVERT: A 191 LYS cc_start: 0.8835 (ttpp) cc_final: 0.8320 (ptpp) REVERT: B 95 MET cc_start: 0.3135 (mmm) cc_final: 0.2086 (tpt) REVERT: B 98 ARG cc_start: 0.7877 (tpt170) cc_final: 0.7372 (tpp-160) REVERT: B 141 GLU cc_start: 0.6215 (mp0) cc_final: 0.5970 (mp0) REVERT: B 173 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8576 (pptt) REVERT: B 179 GLU cc_start: 0.7779 (mp0) cc_final: 0.7459 (mp0) REVERT: B 226 ASN cc_start: 0.8913 (t0) cc_final: 0.8619 (t0) REVERT: C 62 ARG cc_start: 0.9069 (mtt90) cc_final: 0.8562 (mtp85) REVERT: C 79 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8563 (mm-30) REVERT: C 103 PHE cc_start: 0.9035 (m-80) cc_final: 0.8827 (m-10) REVERT: C 107 LYS cc_start: 0.8757 (mtmt) cc_final: 0.8320 (pptt) REVERT: C 118 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.7844 (pmm) REVERT: C 172 ARG cc_start: 0.7961 (mmt90) cc_final: 0.7715 (mmt90) REVERT: C 346 MET cc_start: 0.7706 (tpt) cc_final: 0.7484 (tmm) REVERT: C 548 ASP cc_start: 0.8156 (p0) cc_final: 0.7610 (p0) REVERT: C 594 ASN cc_start: 0.9029 (OUTLIER) cc_final: 0.8623 (p0) REVERT: C 619 THR cc_start: 0.8511 (OUTLIER) cc_final: 0.8024 (p) REVERT: C 704 MET cc_start: 0.8130 (mmt) cc_final: 0.7914 (mpp) REVERT: C 724 ASP cc_start: 0.7517 (t0) cc_final: 0.7294 (t0) REVERT: C 813 ARG cc_start: 0.8624 (mmm160) cc_final: 0.8290 (mtp180) REVERT: C 915 ARG cc_start: 0.7933 (tmm-80) cc_final: 0.7733 (tmm-80) REVERT: C 918 ASN cc_start: 0.9153 (OUTLIER) cc_final: 0.8657 (p0) REVERT: C 1008 GLU cc_start: 0.8413 (mp0) cc_final: 0.8068 (mp0) REVERT: C 1083 LYS cc_start: 0.9153 (mtmt) cc_final: 0.8918 (mttt) REVERT: C 1110 GLU cc_start: 0.8151 (tp30) cc_final: 0.7743 (tp30) REVERT: D 23 TRP cc_start: 0.8266 (m-10) cc_final: 0.8002 (m-10) REVERT: D 27 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7315 (pp20) REVERT: D 43 LYS cc_start: 0.8388 (tppt) cc_final: 0.7643 (tppt) REVERT: D 56 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.6917 (mmm160) REVERT: D 86 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8644 (ptpp) REVERT: D 134 TYR cc_start: 0.7731 (m-10) cc_final: 0.7303 (m-10) REVERT: D 143 MET cc_start: 0.8376 (mtm) cc_final: 0.7896 (ptp) REVERT: D 158 GLU cc_start: 0.9338 (tp30) cc_final: 0.8975 (tm-30) REVERT: D 233 GLN cc_start: 0.7895 (tm-30) cc_final: 0.7615 (tm-30) REVERT: D 256 MET cc_start: 0.6529 (OUTLIER) cc_final: 0.6071 (ttm) REVERT: D 295 ARG cc_start: 0.8743 (ttm170) cc_final: 0.8006 (mtp-110) REVERT: D 335 PHE cc_start: 0.8136 (m-80) cc_final: 0.7906 (m-10) REVERT: D 356 ARG cc_start: 0.8590 (mmp80) cc_final: 0.8254 (mmp80) REVERT: D 400 LYS cc_start: 0.9077 (tptt) cc_final: 0.8867 (tptp) REVERT: D 457 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8400 (tpp) REVERT: D 474 ARG cc_start: 0.7421 (tpt90) cc_final: 0.6740 (tpt90) REVERT: D 518 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6907 (mm-30) REVERT: D 552 GLN cc_start: 0.8610 (mt0) cc_final: 0.8188 (mp10) REVERT: D 576 MET cc_start: 0.8196 (pmm) cc_final: 0.7934 (mpp) REVERT: D 620 MET cc_start: 0.8439 (mpp) cc_final: 0.8094 (mpp) REVERT: D 634 LYS cc_start: 0.9108 (ttmt) cc_final: 0.8819 (tptt) REVERT: D 717 ASP cc_start: 0.8426 (m-30) cc_final: 0.8204 (m-30) REVERT: D 741 LYS cc_start: 0.9350 (pptt) cc_final: 0.8803 (mmmt) REVERT: D 859 LEU cc_start: 0.9419 (mm) cc_final: 0.9180 (mm) REVERT: D 864 LEU cc_start: 0.9247 (pp) cc_final: 0.8459 (pt) REVERT: D 868 ASP cc_start: 0.7803 (t0) cc_final: 0.7431 (p0) REVERT: D 881 GLN cc_start: 0.7860 (tm-30) cc_final: 0.7613 (tm-30) REVERT: D 941 HIS cc_start: 0.7579 (t-90) cc_final: 0.7291 (t-170) REVERT: D 951 LEU cc_start: 0.8717 (mt) cc_final: 0.8009 (pp) REVERT: D 976 MET cc_start: 0.8760 (mmm) cc_final: 0.7287 (tpp) REVERT: D 1132 GLN cc_start: 0.9414 (OUTLIER) cc_final: 0.9000 (mp10) REVERT: D 1254 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7727 (mm) REVERT: E 94 ARG cc_start: 0.8109 (ttt-90) cc_final: 0.7886 (ttt-90) REVERT: E 97 HIS cc_start: 0.8495 (t-90) cc_final: 0.7972 (t-170) REVERT: F 192 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8077 (pt0) REVERT: F 196 TYR cc_start: 0.8696 (t80) cc_final: 0.8284 (t80) REVERT: F 221 TRP cc_start: 0.8615 (t-100) cc_final: 0.8343 (t-100) REVERT: F 231 ASN cc_start: 0.8594 (m110) cc_final: 0.8338 (p0) REVERT: F 261 GLU cc_start: 0.8253 (tp30) cc_final: 0.7924 (tp30) REVERT: F 279 TYR cc_start: 0.6855 (m-80) cc_final: 0.6524 (m-80) REVERT: F 310 MET cc_start: 0.8659 (tpp) cc_final: 0.8347 (tpp) REVERT: F 400 SER cc_start: 0.8324 (t) cc_final: 0.8026 (m) REVERT: J 101 ARG cc_start: 0.8574 (tpp-160) cc_final: 0.8182 (tpp-160) outliers start: 82 outliers final: 64 residues processed: 531 average time/residue: 0.2052 time to fit residues: 169.1783 Evaluate side-chains 551 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 475 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 594 ASN Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 619 THR Chi-restraints excluded: chain C residue 648 TYR Chi-restraints excluded: chain C residue 674 CYS Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 798 THR Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain C residue 859 LEU Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 918 ASN Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1043 ILE Chi-restraints excluded: chain C residue 1080 LEU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 226 PHE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 732 MET Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 959 VAL Chi-restraints excluded: chain D residue 961 VAL Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 1132 GLN Chi-restraints excluded: chain D residue 1169 ILE Chi-restraints excluded: chain D residue 1186 GLU Chi-restraints excluded: chain D residue 1216 LEU Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1247 ASN Chi-restraints excluded: chain D residue 1249 LEU Chi-restraints excluded: chain D residue 1254 ILE Chi-restraints excluded: chain D residue 1263 THR Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 440 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 118 optimal weight: 5.9990 chunk 116 optimal weight: 0.6980 chunk 205 optimal weight: 0.5980 chunk 261 optimal weight: 20.0000 chunk 198 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN C 918 ASN C1057 GLN ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1132 GLN F 443 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.121057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.084263 restraints weight = 75401.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.087337 restraints weight = 42688.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.089370 restraints weight = 29430.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.090725 restraints weight = 23036.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.091549 restraints weight = 19598.628| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 28260 Z= 0.166 Angle : 0.750 14.299 38614 Z= 0.377 Chirality : 0.045 0.390 4390 Planarity : 0.005 0.074 4789 Dihedral : 15.124 163.832 4567 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.57 % Allowed : 23.51 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.15), residues: 3305 helix: 0.31 (0.15), residues: 1230 sheet: -0.55 (0.25), residues: 393 loop : -0.27 (0.16), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 412 TYR 0.033 0.002 TYR E 53 PHE 0.020 0.002 PHE D 920 TRP 0.079 0.002 TRP F 288 HIS 0.005 0.001 HIS F 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (28252) covalent geometry : angle 0.74766 / 0.38 (38602) hydrogen bonds : bond 0.04088 / 2.77 ( 1154) hydrogen bonds : angle 4.94663 / 3.42 ( 3162) metal coordination : bond 0.01007 / 0.49 ( 8) metal coordination : angle 3.51048 / 1.64 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 487 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7079 (tmm) cc_final: 0.6789 (tmm) REVERT: A 99 LYS cc_start: 0.8555 (tptt) cc_final: 0.8143 (tptt) REVERT: A 123 MET cc_start: 0.8355 (tmm) cc_final: 0.8078 (tmm) REVERT: A 191 LYS cc_start: 0.8839 (ttpp) cc_final: 0.8325 (ptpp) REVERT: B 95 MET cc_start: 0.3143 (mmm) cc_final: 0.2131 (tpt) REVERT: B 96 TYR cc_start: 0.7526 (m-10) cc_final: 0.7252 (m-10) REVERT: B 98 ARG cc_start: 0.7811 (tpt170) cc_final: 0.7578 (tpm170) REVERT: B 141 GLU cc_start: 0.6069 (mp0) cc_final: 0.5617 (mp0) REVERT: B 173 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8579 (pptt) REVERT: B 179 GLU cc_start: 0.7837 (mp0) cc_final: 0.7578 (mp0) REVERT: B 226 ASN cc_start: 0.8940 (t0) cc_final: 0.8667 (t0) REVERT: C 62 ARG cc_start: 0.9107 (mtt90) cc_final: 0.8618 (mtp85) REVERT: C 79 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8557 (mm-30) REVERT: C 103 PHE cc_start: 0.9026 (m-80) cc_final: 0.8823 (m-10) REVERT: C 107 LYS cc_start: 0.8766 (mtmt) cc_final: 0.8421 (pttp) REVERT: C 118 MET cc_start: 0.8355 (pmm) cc_final: 0.7690 (pmm) REVERT: C 172 ARG cc_start: 0.7981 (mmt90) cc_final: 0.7739 (mmt90) REVERT: C 594 ASN cc_start: 0.9050 (OUTLIER) cc_final: 0.8653 (p0) REVERT: C 619 THR cc_start: 0.8511 (OUTLIER) cc_final: 0.8011 (p) REVERT: C 664 ARG cc_start: 0.8290 (mtp-110) cc_final: 0.8044 (mtp-110) REVERT: C 682 ASP cc_start: 0.8225 (p0) cc_final: 0.8021 (p0) REVERT: C 704 MET cc_start: 0.8158 (mmt) cc_final: 0.7917 (mpp) REVERT: C 724 ASP cc_start: 0.7572 (t0) cc_final: 0.7338 (t0) REVERT: C 813 ARG cc_start: 0.8657 (mmm160) cc_final: 0.8329 (mtp180) REVERT: C 915 ARG cc_start: 0.7987 (tmm-80) cc_final: 0.7775 (tmm-80) REVERT: C 918 ASN cc_start: 0.9105 (OUTLIER) cc_final: 0.8688 (p0) REVERT: C 1008 GLU cc_start: 0.8425 (mp0) cc_final: 0.8064 (mp0) REVERT: C 1070 TYR cc_start: 0.8592 (m-10) cc_final: 0.8172 (m-10) REVERT: C 1083 LYS cc_start: 0.9170 (mtmt) cc_final: 0.8914 (mttt) REVERT: C 1110 GLU cc_start: 0.8159 (tp30) cc_final: 0.7740 (tp30) REVERT: D 27 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7290 (pp20) REVERT: D 43 LYS cc_start: 0.8410 (tppt) cc_final: 0.7641 (tppt) REVERT: D 56 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.6963 (mmm160) REVERT: D 86 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8610 (ptpp) REVERT: D 134 TYR cc_start: 0.7759 (m-10) cc_final: 0.7372 (m-10) REVERT: D 143 MET cc_start: 0.8392 (mtm) cc_final: 0.7910 (ptp) REVERT: D 158 GLU cc_start: 0.9343 (tp30) cc_final: 0.9027 (tm-30) REVERT: D 233 GLN cc_start: 0.7905 (tm-30) cc_final: 0.7616 (tm-30) REVERT: D 256 MET cc_start: 0.6526 (OUTLIER) cc_final: 0.5755 (ttm) REVERT: D 295 ARG cc_start: 0.8743 (ttm170) cc_final: 0.7989 (mtp-110) REVERT: D 335 PHE cc_start: 0.8170 (m-80) cc_final: 0.7925 (m-10) REVERT: D 356 ARG cc_start: 0.8611 (mmp80) cc_final: 0.8269 (mmp80) REVERT: D 453 LYS cc_start: 0.8947 (tttp) cc_final: 0.8563 (tppt) REVERT: D 457 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8414 (tpp) REVERT: D 474 ARG cc_start: 0.7437 (tpt90) cc_final: 0.6991 (tpt170) REVERT: D 475 MET cc_start: 0.7501 (ptm) cc_final: 0.7176 (ptp) REVERT: D 515 GLN cc_start: 0.8341 (pm20) cc_final: 0.8019 (pm20) REVERT: D 518 GLU cc_start: 0.7390 (mm-30) cc_final: 0.6994 (mm-30) REVERT: D 541 MET cc_start: 0.8665 (tpp) cc_final: 0.8283 (mmm) REVERT: D 552 GLN cc_start: 0.8622 (mt0) cc_final: 0.8190 (mp10) REVERT: D 576 MET cc_start: 0.8208 (pmm) cc_final: 0.7976 (mpp) REVERT: D 620 MET cc_start: 0.8473 (mpp) cc_final: 0.8158 (mpp) REVERT: D 634 LYS cc_start: 0.9103 (ttmt) cc_final: 0.8802 (tptt) REVERT: D 717 ASP cc_start: 0.8455 (m-30) cc_final: 0.8252 (m-30) REVERT: D 741 LYS cc_start: 0.9347 (pptt) cc_final: 0.8789 (mmmt) REVERT: D 859 LEU cc_start: 0.9422 (mm) cc_final: 0.9184 (mm) REVERT: D 864 LEU cc_start: 0.9251 (pp) cc_final: 0.8515 (pt) REVERT: D 868 ASP cc_start: 0.7820 (t0) cc_final: 0.7410 (p0) REVERT: D 881 GLN cc_start: 0.7824 (tm-30) cc_final: 0.7592 (tm-30) REVERT: D 941 HIS cc_start: 0.7616 (t-90) cc_final: 0.7317 (t-170) REVERT: D 951 LEU cc_start: 0.8744 (mt) cc_final: 0.7999 (pp) REVERT: D 976 MET cc_start: 0.8787 (mmm) cc_final: 0.7274 (tpp) REVERT: D 1254 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7701 (mm) REVERT: E 94 ARG cc_start: 0.8147 (ttt-90) cc_final: 0.7885 (ttt-90) REVERT: E 97 HIS cc_start: 0.8519 (t-90) cc_final: 0.7995 (t-170) REVERT: F 192 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8086 (pt0) REVERT: F 196 TYR cc_start: 0.8721 (t80) cc_final: 0.8276 (t80) REVERT: F 221 TRP cc_start: 0.8625 (t-100) cc_final: 0.8351 (t-100) REVERT: F 261 GLU cc_start: 0.8256 (tp30) cc_final: 0.7937 (tp30) REVERT: F 279 TYR cc_start: 0.6821 (m-80) cc_final: 0.6479 (m-80) REVERT: F 310 MET cc_start: 0.8665 (tpp) cc_final: 0.8255 (tpp) REVERT: F 315 ASN cc_start: 0.8974 (p0) cc_final: 0.8706 (p0) REVERT: F 361 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8694 (mt) REVERT: F 400 SER cc_start: 0.8353 (t) cc_final: 0.8061 (m) REVERT: J 101 ARG cc_start: 0.8605 (tpp-160) cc_final: 0.8163 (tpp-160) outliers start: 72 outliers final: 58 residues processed: 526 average time/residue: 0.2011 time to fit residues: 164.7924 Evaluate side-chains 545 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 476 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 594 ASN Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 619 THR Chi-restraints excluded: chain C residue 648 TYR Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 798 THR Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain C residue 859 LEU Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 918 ASN Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1043 ILE Chi-restraints excluded: chain C residue 1080 LEU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 226 PHE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 732 MET Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 959 VAL Chi-restraints excluded: chain D residue 961 VAL Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 1132 GLN Chi-restraints excluded: chain D residue 1169 ILE Chi-restraints excluded: chain D residue 1186 GLU Chi-restraints excluded: chain D residue 1216 LEU Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1247 ASN Chi-restraints excluded: chain D residue 1249 LEU Chi-restraints excluded: chain D residue 1254 ILE Chi-restraints excluded: chain D residue 1263 THR Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 440 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 251 optimal weight: 0.2980 chunk 231 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 213 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 136 optimal weight: 6.9990 chunk 163 optimal weight: 0.0040 chunk 20 optimal weight: 0.9980 chunk 281 optimal weight: 6.9990 chunk 250 optimal weight: 3.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1132 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.121666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.085224 restraints weight = 74927.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.088250 restraints weight = 43011.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.090247 restraints weight = 29847.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.091519 restraints weight = 23434.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.092406 restraints weight = 20078.312| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28260 Z= 0.144 Angle : 0.762 14.653 38614 Z= 0.380 Chirality : 0.045 0.391 4390 Planarity : 0.005 0.083 4789 Dihedral : 15.129 163.682 4567 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.50 % Allowed : 23.76 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.15), residues: 3305 helix: 0.32 (0.15), residues: 1229 sheet: -0.53 (0.25), residues: 393 loop : -0.24 (0.16), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D1232 TYR 0.042 0.002 TYR A 168 PHE 0.035 0.002 PHE D 720 TRP 0.018 0.002 TRP F 288 HIS 0.004 0.001 HIS F 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (28252) covalent geometry : angle 0.76009 / 0.38 (38602) hydrogen bonds : bond 0.04025 / 2.73 ( 1154) hydrogen bonds : angle 4.91524 / 3.41 ( 3162) metal coordination : bond 0.00807 / 0.39 ( 8) metal coordination : angle 3.28825 / 1.57 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6272.97 seconds wall clock time: 108 minutes 31.12 seconds (6511.12 seconds total)