Starting phenix.real_space_refine on Sun May 25 21:01:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r6r_18959/05_2025/8r6r_18959.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r6r_18959/05_2025/8r6r_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_18959/05_2025/8r6r_18959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r6r_18959/05_2025/8r6r_18959.map" model { file = "/net/cci-nas-00/data/ceres_data/8r6r_18959/05_2025/8r6r_18959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r6r_18959/05_2025/8r6r_18959.cif" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 13.97, per 1000 atoms: 0.51 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: 6.10 Conformation dependent library (CDL) restraints added in 3.1 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: 8.50 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: 12.06 Time building geometry restraints manager: 7.25 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=" N PHE D 6 " pdb=" CA PHE D 6 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.20e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N ARG F 151 " pdb=" CA ARG F 151 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N LEU J 6 " pdb=" CA LEU J 6 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 ... (remaining 28247 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 37792 1.46 - 2.91: 644 2.91 - 4.37: 153 4.37 - 5.83: 11 5.83 - 7.29: 2 Bond angle restraints: 38602 Sorted by residual: angle pdb=" C ARG D 247 " pdb=" N TYR D 248 " pdb=" CA TYR D 248 " ideal model delta sigma weight residual 122.54 117.25 5.29 1.82e+00 3.02e-01 8.44e+00 angle pdb=" CA TYR E 53 " pdb=" CB TYR E 53 " pdb=" CG TYR E 53 " ideal model delta sigma weight residual 113.90 118.87 -4.97 1.80e+00 3.09e-01 7.63e+00 angle pdb=" C SER C 85 " pdb=" N PRO C 86 " pdb=" CD PRO C 86 " ideal model delta sigma weight residual 120.60 114.54 6.06 2.20e+00 2.07e-01 7.60e+00 angle pdb=" N PHE D 226 " pdb=" CA PHE D 226 " pdb=" CB PHE D 226 " ideal model delta sigma weight residual 110.01 113.79 -3.78 1.45e+00 4.76e-01 6.81e+00 angle pdb=" CA PRO D 573 " pdb=" N PRO D 573 " pdb=" CD PRO D 573 " ideal model delta sigma weight residual 112.00 108.55 3.45 1.40e+00 5.10e-01 6.08e+00 ... (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 - 0.030: 2824 0.030 - 0.059: 992 0.059 - 0.089: 312 0.089 - 0.118: 214 0.118 - 0.148: 48 Chirality restraints: 4390 Sorted by residual: chirality pdb=" CA ILE D 509 " pdb=" N ILE D 509 " pdb=" C ILE D 509 " pdb=" CB ILE D 509 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA ILE C 131 " pdb=" N ILE C 131 " pdb=" C ILE C 131 " pdb=" CB ILE C 131 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE B 193 " pdb=" N ILE B 193 " pdb=" C ILE B 193 " pdb=" CB ILE B 193 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.94e-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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.210 Set scattering table: 0.220 Process input model: 66.480 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6229 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= 0.114 Angle : 0.506 7.287 38614 Z= 0.275 Chirality : 0.040 0.148 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (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 TRP 0.020 0.001 TRP D 223 HIS 0.005 0.001 HIS C 470 PHE 0.078 0.001 PHE D 226 TYR 0.033 0.001 TYR D 248 ARG 0.019 0.000 ARG D 387 Details of bonding type rmsd hydrogen bonds : bond 0.15179 ( 1154) hydrogen bonds : angle 6.00178 ( 3162) metal coordination : bond 0.06161 ( 8) metal coordination : angle 2.61123 ( 12) covalent geometry : bond 0.00240 (28252) covalent geometry : angle 0.50371 (38602) *********************** 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 : 2.877 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: 0.6841 (mp) REVERT: C 992 MET cc_start: 0.8513 (mmp) cc_final: 0.8287 (mmm) REVERT: C 1037 THR cc_start: 0.7449 (m) cc_final: 0.7092 (m) REVERT: D 137 THR cc_start: 0.7118 (p) cc_final: 0.6911 (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: 0.4284 (mtm) REVERT: D 499 ASN cc_start: 0.8640 (t0) cc_final: 0.7570 (t0) REVERT: D 509 ILE cc_start: 0.8145 (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: 0.7969 (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: 0.7936 (mt) outliers start: 0 outliers final: 0 residues processed: 900 average time/residue: 0.4676 time to fit residues: 626.4134 Evaluate side-chains 601 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 601 time to evaluate : 2.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 282 optimal weight: 8.9990 chunk 253 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 171 optimal weight: 20.0000 chunk 135 optimal weight: 2.9990 chunk 262 optimal weight: 30.0000 chunk 101 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 304 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 HIS B 231 HIS D 213 GLN D 349 ASN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 914 HIS D1000 GLN E 97 HIS F 231 ASN F 232 HIS F 352 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.122214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.085641 restraints weight = 74350.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.088696 restraints weight = 42222.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.090695 restraints weight = 29059.979| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 28260 Z= 0.246 Angle : 0.739 9.286 38614 Z= 0.387 Chirality : 0.047 0.236 4390 Planarity : 0.006 0.060 4789 Dihedral : 14.692 158.755 4567 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.68 % Allowed : 13.52 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.14), residues: 3305 helix: 0.38 (0.15), residues: 1228 sheet: -0.57 (0.25), residues: 407 loop : -0.31 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 23 HIS 0.010 0.002 HIS D 914 PHE 0.019 0.002 PHE C 98 TYR 0.031 0.003 TYR E 53 ARG 0.011 0.001 ARG F 268 Details of bonding type rmsd hydrogen bonds : bond 0.04955 ( 1154) hydrogen bonds : angle 5.17783 ( 3162) metal coordination : bond 0.01610 ( 8) metal coordination : angle 3.75212 ( 12) covalent geometry : bond 0.00538 (28252) covalent geometry : angle 0.73643 (38602) *********************** 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 678 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 603 time to evaluate : 2.808 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: A 61 HIS cc_start: 0.8319 (p90) cc_final: 0.8090 (p90) REVERT: A 81 LYS cc_start: 0.9010 (mmtp) cc_final: 0.8711 (mmmt) REVERT: A 99 LYS cc_start: 0.8535 (tptt) cc_final: 0.8214 (tptt) REVERT: A 125 ILE cc_start: 0.9379 (mt) cc_final: 0.9085 (mm) REVERT: A 191 LYS cc_start: 0.7848 (ptpp) cc_final: 0.7595 (ptpp) REVERT: B 17 ASN cc_start: 0.8890 (m-40) cc_final: 0.8634 (m-40) REVERT: B 43 LEU cc_start: 0.8949 (tt) cc_final: 0.8675 (tp) REVERT: B 123 MET cc_start: 0.7876 (tmm) cc_final: 0.7673 (tmm) REVERT: B 128 LEU cc_start: 0.8017 (tp) cc_final: 0.7612 (tp) REVERT: B 131 LYS cc_start: 0.9003 (mmmt) cc_final: 0.8745 (mmmt) REVERT: B 173 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8645 (pptt) REVERT: B 179 GLU cc_start: 0.7581 (mp0) cc_final: 0.7166 (mp0) REVERT: B 191 LYS cc_start: 0.8574 (ptmm) cc_final: 0.7946 (ptmm) REVERT: B 199 LYS cc_start: 0.8441 (mttt) cc_final: 0.8118 (mttp) REVERT: B 226 ASN cc_start: 0.8744 (t0) cc_final: 0.8533 (t0) REVERT: C 72 ASN cc_start: 0.8351 (p0) cc_final: 0.7932 (p0) REVERT: C 151 MET cc_start: 0.7390 (ttm) cc_final: 0.6706 (mtm) REVERT: C 163 GLU cc_start: 0.8381 (tt0) cc_final: 0.8111 (tt0) REVERT: C 304 ARG cc_start: 0.9001 (tpp-160) cc_final: 0.8551 (tpp80) REVERT: C 374 GLU cc_start: 0.8238 (mp0) cc_final: 0.7995 (tp30) REVERT: C 394 ARG cc_start: 0.8884 (ttm170) cc_final: 0.8548 (ptm160) REVERT: C 412 ARG cc_start: 0.8032 (tpp-160) cc_final: 0.7757 (tpm170) REVERT: C 481 GLU cc_start: 0.7903 (pm20) cc_final: 0.7455 (mp0) REVERT: C 548 ASP cc_start: 0.8134 (p0) cc_final: 0.7743 (p0) REVERT: C 664 ARG cc_start: 0.8336 (mtp-110) cc_final: 0.8121 (mtp-110) REVERT: C 704 MET cc_start: 0.8162 (tpp) cc_final: 0.7881 (mpp) REVERT: C 724 ASP cc_start: 0.7512 (t0) cc_final: 0.7113 (t0) REVERT: C 811 LEU cc_start: 0.9050 (mt) cc_final: 0.8833 (mt) REVERT: C 813 ARG cc_start: 0.8564 (mmm160) cc_final: 0.8228 (mtp180) REVERT: C 1110 GLU cc_start: 0.7897 (tp30) cc_final: 0.7398 (tp30) REVERT: D 27 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7419 (pp20) REVERT: D 43 LYS cc_start: 0.8350 (tppt) cc_final: 0.7781 (tppt) REVERT: D 86 LYS cc_start: 0.8929 (pttm) cc_final: 0.8434 (pttm) REVERT: D 134 TYR cc_start: 0.8186 (m-10) cc_final: 0.7039 (m-10) REVERT: D 158 GLU cc_start: 0.9301 (tp30) cc_final: 0.8973 (tm-30) REVERT: D 226 PHE cc_start: 0.6426 (m-80) cc_final: 0.6054 (m-80) REVERT: D 233 GLN cc_start: 0.7686 (tm-30) cc_final: 0.7453 (tm-30) REVERT: D 235 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7615 (mp) REVERT: D 247 ARG cc_start: 0.7127 (mtm110) cc_final: 0.6900 (mtm110) REVERT: D 312 MET cc_start: 0.8159 (ptp) cc_final: 0.7798 (ptp) REVERT: D 457 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8396 (mtt) REVERT: D 469 ILE cc_start: 0.9282 (mm) cc_final: 0.9068 (mm) REVERT: D 493 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6353 (pt0) REVERT: D 518 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7425 (mm-30) REVERT: D 552 GLN cc_start: 0.8760 (mt0) cc_final: 0.8381 (mp10) REVERT: D 634 LYS cc_start: 0.9056 (ttmt) cc_final: 0.8793 (tptt) REVERT: D 685 GLU cc_start: 0.7866 (tp30) cc_final: 0.7607 (tp30) REVERT: D 741 LYS cc_start: 0.9367 (pptt) cc_final: 0.8852 (mmmt) REVERT: D 742 GLN cc_start: 0.8380 (mp10) cc_final: 0.7764 (pm20) REVERT: D 841 GLU cc_start: 0.8302 (tt0) cc_final: 0.7978 (tm-30) REVERT: D 859 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8998 (mm) REVERT: D 864 LEU cc_start: 0.9063 (mt) cc_final: 0.8791 (pp) REVERT: D 941 HIS cc_start: 0.7254 (t-170) cc_final: 0.6991 (t-170) REVERT: D 980 ARG cc_start: 0.8152 (ptm160) cc_final: 0.7873 (ptm160) REVERT: D 1236 ASP cc_start: 0.8996 (t0) cc_final: 0.8693 (m-30) REVERT: E 65 TYR cc_start: 0.7924 (m-80) cc_final: 0.7719 (m-80) REVERT: E 87 LYS cc_start: 0.8322 (mmtp) cc_final: 0.8058 (mptt) REVERT: E 94 ARG cc_start: 0.8021 (ttt-90) cc_final: 0.7651 (ttt180) REVERT: E 95 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7981 (tm-30) REVERT: F 192 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8354 (pt0) REVERT: F 196 TYR cc_start: 0.8724 (t80) cc_final: 0.8346 (t80) REVERT: F 221 TRP cc_start: 0.8750 (t-100) cc_final: 0.8529 (t-100) REVERT: F 268 ARG cc_start: 0.8887 (tpp80) cc_final: 0.8303 (tpt-90) REVERT: F 310 MET cc_start: 0.8755 (tpp) cc_final: 0.8273 (tpp) REVERT: F 391 PHE cc_start: 0.8723 (t80) cc_final: 0.8506 (t80) REVERT: F 393 LEU cc_start: 0.9545 (mt) cc_final: 0.9243 (tt) REVERT: J 101 ARG cc_start: 0.8671 (mmm160) cc_final: 0.8434 (mmm160) outliers start: 75 outliers final: 42 residues processed: 639 average time/residue: 0.4523 time to fit residues: 433.8081 Evaluate side-chains 592 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 544 time to evaluate : 2.970 ------------------------------------------------------------------------------- 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 138 LEU Chi-restraints excluded: chain A residue 147 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 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 118 MET Chi-restraints excluded: chain C residue 226 THR 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 644 VAL 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 1080 LEU Chi-restraints excluded: chain C residue 1115 LEU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 235 ILE 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 493 GLU 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 613 SER 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 859 LEU Chi-restraints excluded: chain D residue 994 VAL Chi-restraints excluded: chain D residue 1032 VAL Chi-restraints excluded: chain E residue 53 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 157 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 289 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 139 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** D 349 ASN D 494 HIS ** D 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 GLN F 232 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.121725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.085142 restraints weight = 74411.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.088180 restraints weight = 42128.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.090178 restraints weight = 29115.142| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28260 Z= 0.191 Angle : 0.679 9.348 38614 Z= 0.353 Chirality : 0.045 0.241 4390 Planarity : 0.005 0.093 4789 Dihedral : 14.691 160.209 4567 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.03 % Allowed : 16.55 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.14), residues: 3305 helix: 0.43 (0.15), residues: 1228 sheet: -0.68 (0.25), residues: 411 loop : -0.30 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 288 HIS 0.011 0.001 HIS B 231 PHE 0.018 0.002 PHE D 70 TYR 0.039 0.002 TYR E 53 ARG 0.022 0.001 ARG D 69 Details of bonding type rmsd hydrogen bonds : bond 0.04345 ( 1154) hydrogen bonds : angle 4.95501 ( 3162) metal coordination : bond 0.01347 ( 8) metal coordination : angle 3.82623 ( 12) covalent geometry : bond 0.00421 (28252) covalent geometry : angle 0.67561 (38602) *********************** 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 644 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 559 time to evaluate : 2.789 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 77 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.7992 (mt) REVERT: A 123 MET cc_start: 0.8329 (tmm) cc_final: 0.7951 (ttp) REVERT: B 43 LEU cc_start: 0.8965 (tt) cc_final: 0.8625 (tp) REVERT: B 95 MET cc_start: 0.3535 (mmm) cc_final: 0.2961 (tpt) REVERT: B 123 MET cc_start: 0.7947 (tmm) cc_final: 0.7718 (tmm) REVERT: B 128 LEU cc_start: 0.8132 (tp) cc_final: 0.7655 (tp) REVERT: B 173 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8595 (pptt) REVERT: B 179 GLU cc_start: 0.7731 (mp0) cc_final: 0.7326 (mp0) REVERT: B 191 LYS cc_start: 0.8506 (ptmm) cc_final: 0.7956 (ptmm) REVERT: B 199 LYS cc_start: 0.8258 (mttt) cc_final: 0.8018 (mttt) REVERT: B 226 ASN cc_start: 0.8755 (t0) cc_final: 0.8517 (t0) REVERT: C 107 LYS cc_start: 0.8767 (mtmt) cc_final: 0.8413 (ptpp) REVERT: C 304 ARG cc_start: 0.9017 (tpp-160) cc_final: 0.8511 (tpp80) REVERT: C 374 GLU cc_start: 0.8212 (mp0) cc_final: 0.7955 (tp30) REVERT: C 548 ASP cc_start: 0.8197 (p0) cc_final: 0.7730 (p0) REVERT: C 598 MET cc_start: 0.8427 (mmm) cc_final: 0.8222 (mmm) REVERT: C 619 THR cc_start: 0.8732 (OUTLIER) cc_final: 0.8256 (p) REVERT: C 715 MET cc_start: 0.8888 (ptm) cc_final: 0.8636 (ptm) REVERT: C 724 ASP cc_start: 0.7704 (t0) cc_final: 0.7215 (t0) REVERT: C 774 ASP cc_start: 0.7742 (t0) cc_final: 0.7538 (t0) REVERT: C 811 LEU cc_start: 0.8969 (mt) cc_final: 0.8763 (mt) REVERT: C 950 LEU cc_start: 0.9197 (mt) cc_final: 0.8752 (mp) REVERT: C 1110 GLU cc_start: 0.7948 (tp30) cc_final: 0.7585 (tp30) REVERT: D 27 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7421 (pp20) REVERT: D 43 LYS cc_start: 0.8403 (tppt) cc_final: 0.7788 (tppt) REVERT: D 90 GLU cc_start: 0.8341 (pt0) cc_final: 0.8083 (pt0) REVERT: D 134 TYR cc_start: 0.7959 (m-10) cc_final: 0.7477 (m-10) REVERT: D 143 MET cc_start: 0.8354 (mtm) cc_final: 0.7920 (ptp) REVERT: D 145 HIS cc_start: 0.7659 (p90) cc_final: 0.7441 (p90) REVERT: D 158 GLU cc_start: 0.9335 (tp30) cc_final: 0.8934 (tm-30) REVERT: D 235 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7686 (mp) REVERT: D 256 MET cc_start: 0.6011 (OUTLIER) cc_final: 0.5303 (ttm) REVERT: D 356 ARG cc_start: 0.8633 (mmp80) cc_final: 0.8361 (mmp80) REVERT: D 373 MET cc_start: 0.6906 (mtm) cc_final: 0.6598 (mtt) REVERT: D 457 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8458 (mtt) REVERT: D 518 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7391 (mm-30) REVERT: D 530 GLU cc_start: 0.8400 (tt0) cc_final: 0.8080 (tt0) REVERT: D 541 MET cc_start: 0.8526 (tpp) cc_final: 0.8193 (mmm) REVERT: D 552 GLN cc_start: 0.8699 (mt0) cc_final: 0.8279 (mp10) REVERT: D 634 LYS cc_start: 0.9094 (ttmt) cc_final: 0.8739 (tppt) REVERT: D 685 GLU cc_start: 0.7825 (tp30) cc_final: 0.7608 (tp30) REVERT: D 717 ASP cc_start: 0.8579 (m-30) cc_final: 0.8287 (m-30) REVERT: D 741 LYS cc_start: 0.9355 (pptt) cc_final: 0.8814 (mmmt) REVERT: D 742 GLN cc_start: 0.8417 (mp10) cc_final: 0.7855 (pm20) REVERT: D 841 GLU cc_start: 0.8317 (tt0) cc_final: 0.7936 (tm-30) REVERT: D 859 LEU cc_start: 0.9337 (mm) cc_final: 0.9053 (mm) REVERT: D 976 MET cc_start: 0.8445 (mpp) cc_final: 0.8242 (mpp) REVERT: D 980 ARG cc_start: 0.8091 (ptm160) cc_final: 0.7837 (ptm160) REVERT: D 1232 ARG cc_start: 0.8975 (mtm110) cc_final: 0.8547 (mtm110) REVERT: D 1236 ASP cc_start: 0.9004 (t0) cc_final: 0.8698 (m-30) REVERT: E 94 ARG cc_start: 0.8067 (ttt-90) cc_final: 0.7723 (ttt180) REVERT: E 97 HIS cc_start: 0.8670 (t-90) cc_final: 0.8117 (t-170) REVERT: F 192 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8211 (pt0) REVERT: F 196 TYR cc_start: 0.8712 (t80) cc_final: 0.8163 (t80) REVERT: F 219 MET cc_start: 0.9185 (ptp) cc_final: 0.8865 (ptp) REVERT: F 221 TRP cc_start: 0.8620 (t-100) cc_final: 0.8371 (t-100) REVERT: F 231 ASN cc_start: 0.8657 (m110) cc_final: 0.8423 (p0) REVERT: F 261 GLU cc_start: 0.8219 (tp30) cc_final: 0.7870 (tp30) REVERT: F 268 ARG cc_start: 0.8920 (tpp80) cc_final: 0.8627 (tpp80) REVERT: F 279 TYR cc_start: 0.6972 (m-80) cc_final: 0.6431 (m-80) REVERT: F 310 MET cc_start: 0.8735 (tpp) cc_final: 0.8285 (tpp) REVERT: F 391 PHE cc_start: 0.8816 (t80) cc_final: 0.8488 (t80) REVERT: F 393 LEU cc_start: 0.9557 (mt) cc_final: 0.9216 (tt) REVERT: J 101 ARG cc_start: 0.8685 (mmm160) cc_final: 0.8444 (mmm160) outliers start: 85 outliers final: 48 residues processed: 602 average time/residue: 0.4244 time to fit residues: 387.9011 Evaluate side-chains 579 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 524 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 147 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 173 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 148 PHE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 418 ILE 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 648 TYR Chi-restraints excluded: chain C residue 692 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 979 LEU Chi-restraints excluded: chain C residue 980 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 92 MET Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 244 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 432 VAL Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 493 GLU Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 613 SER 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 823 VAL Chi-restraints excluded: chain D residue 959 VAL Chi-restraints excluded: chain D residue 994 VAL Chi-restraints excluded: chain D residue 1216 LEU 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 115 optimal weight: 2.9990 chunk 219 optimal weight: 0.0370 chunk 212 optimal weight: 3.9990 chunk 304 optimal weight: 0.4980 chunk 276 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 50 optimal weight: 0.0870 chunk 129 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS C 134 ASN ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 853 HIS ** 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** ** F 454 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 = 0.3954 r_free = 0.3954 target = 0.123923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.087294 restraints weight = 74698.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.090495 restraints weight = 41814.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.092574 restraints weight = 28562.800| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4198 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= 0.131 Angle : 0.665 13.670 38614 Z= 0.339 Chirality : 0.044 0.238 4390 Planarity : 0.005 0.084 4789 Dihedral : 14.650 160.074 4567 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.10 % Allowed : 18.59 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.14), residues: 3305 helix: 0.51 (0.15), residues: 1223 sheet: -0.54 (0.26), residues: 397 loop : -0.29 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 82 HIS 0.013 0.001 HIS D 941 PHE 0.046 0.001 PHE D 226 TYR 0.042 0.002 TYR E 53 ARG 0.012 0.001 ARG F 216 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 1154) hydrogen bonds : angle 4.79028 ( 3162) metal coordination : bond 0.00632 ( 8) metal coordination : angle 3.04190 ( 12) covalent geometry : bond 0.00288 (28252) covalent geometry : angle 0.66294 (38602) *********************** 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 616 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 557 time to evaluate : 2.827 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: A 99 LYS cc_start: 0.8564 (tptt) cc_final: 0.8043 (tptt) REVERT: A 191 LYS cc_start: 0.8796 (ttpp) cc_final: 0.8299 (ptpp) REVERT: B 1 MET cc_start: 0.6425 (pmm) cc_final: 0.5974 (pmm) REVERT: B 43 LEU cc_start: 0.8906 (tt) cc_final: 0.8568 (tp) REVERT: B 128 LEU cc_start: 0.8236 (tp) cc_final: 0.7700 (tp) REVERT: B 179 GLU cc_start: 0.7839 (mp0) cc_final: 0.7412 (mp0) REVERT: B 191 LYS cc_start: 0.8553 (ptmm) cc_final: 0.8055 (ptmm) REVERT: B 225 LEU cc_start: 0.9079 (mm) cc_final: 0.8852 (mp) REVERT: B 226 ASN cc_start: 0.8827 (t0) cc_final: 0.8567 (t0) REVERT: C 107 LYS cc_start: 0.8760 (mtmt) cc_final: 0.8390 (ptpp) REVERT: C 304 ARG cc_start: 0.8960 (tpp-160) cc_final: 0.8735 (tpp-160) REVERT: C 374 GLU cc_start: 0.8198 (mp0) cc_final: 0.7926 (tp30) REVERT: C 619 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.7872 (p) REVERT: C 622 GLU cc_start: 0.8620 (mp0) cc_final: 0.8368 (mp0) REVERT: C 652 MET cc_start: 0.8990 (tpp) cc_final: 0.8740 (tpp) REVERT: C 703 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7332 (mp0) REVERT: C 715 MET cc_start: 0.8799 (ptm) cc_final: 0.8570 (ptm) REVERT: C 724 ASP cc_start: 0.7639 (t0) cc_final: 0.6950 (t0) REVERT: C 788 ARG cc_start: 0.7269 (mmp80) cc_final: 0.7027 (mmp80) REVERT: C 791 ASP cc_start: 0.8114 (m-30) cc_final: 0.7691 (p0) REVERT: C 811 LEU cc_start: 0.9005 (mt) cc_final: 0.8805 (mt) REVERT: C 867 LYS cc_start: 0.8875 (mtpp) cc_final: 0.8628 (tttp) REVERT: C 950 LEU cc_start: 0.9189 (mt) cc_final: 0.8764 (mp) REVERT: C 1008 GLU cc_start: 0.8415 (mp0) cc_final: 0.8035 (mp0) REVERT: C 1083 LYS cc_start: 0.9177 (mtmt) cc_final: 0.8865 (mttt) REVERT: C 1110 GLU cc_start: 0.8062 (tp30) cc_final: 0.7693 (tp30) REVERT: D 21 ARG cc_start: 0.8477 (mpt180) cc_final: 0.7916 (mmt180) REVERT: D 27 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7249 (pp20) REVERT: D 43 LYS cc_start: 0.8419 (tppt) cc_final: 0.7719 (tppt) REVERT: D 86 LYS cc_start: 0.8944 (pttm) cc_final: 0.8398 (ptmt) REVERT: D 134 TYR cc_start: 0.7858 (m-10) cc_final: 0.7416 (m-10) REVERT: D 158 GLU cc_start: 0.9322 (tp30) cc_final: 0.8955 (tm-30) REVERT: D 233 GLN cc_start: 0.7794 (tm-30) cc_final: 0.7496 (tm-30) REVERT: D 235 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7647 (mp) REVERT: D 247 ARG cc_start: 0.7363 (ptp-170) cc_final: 0.7070 (mtm180) REVERT: D 256 MET cc_start: 0.6080 (OUTLIER) cc_final: 0.5739 (ttm) REVERT: D 356 ARG cc_start: 0.8591 (mmp80) cc_final: 0.8303 (mmp80) REVERT: D 373 MET cc_start: 0.6667 (mtm) cc_final: 0.6375 (mtt) REVERT: D 457 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8168 (mmm) REVERT: D 530 GLU cc_start: 0.8318 (tt0) cc_final: 0.8027 (tt0) REVERT: D 541 MET cc_start: 0.8534 (tpp) cc_final: 0.8075 (mmm) REVERT: D 552 GLN cc_start: 0.8694 (mt0) cc_final: 0.8278 (mp10) REVERT: D 634 LYS cc_start: 0.9076 (ttmt) cc_final: 0.8689 (tppt) REVERT: D 685 GLU cc_start: 0.7853 (tp30) cc_final: 0.7623 (tp30) REVERT: D 717 ASP cc_start: 0.8504 (m-30) cc_final: 0.8221 (m-30) REVERT: D 741 LYS cc_start: 0.9312 (pptt) cc_final: 0.8793 (mmmt) REVERT: D 742 GLN cc_start: 0.8382 (mp10) cc_final: 0.7849 (pm20) REVERT: D 841 GLU cc_start: 0.8296 (tt0) cc_final: 0.7941 (tm-30) REVERT: D 859 LEU cc_start: 0.9389 (mm) cc_final: 0.9091 (mm) REVERT: D 864 LEU cc_start: 0.9046 (pp) cc_final: 0.8311 (pp) REVERT: D 868 ASP cc_start: 0.7923 (t0) cc_final: 0.7496 (p0) REVERT: D 941 HIS cc_start: 0.7431 (t-170) cc_final: 0.7220 (t-170) REVERT: D 976 MET cc_start: 0.8389 (mpp) cc_final: 0.7580 (tpp) REVERT: D 1129 ARG cc_start: 0.8876 (tpm170) cc_final: 0.8670 (tpm170) REVERT: D 1152 ASP cc_start: 0.8569 (m-30) cc_final: 0.8161 (m-30) REVERT: D 1232 ARG cc_start: 0.8936 (mtm110) cc_final: 0.8492 (mtm110) REVERT: D 1236 ASP cc_start: 0.8996 (t0) cc_final: 0.8696 (m-30) REVERT: E 60 GLN cc_start: 0.9047 (mt0) cc_final: 0.8825 (mm110) REVERT: E 94 ARG cc_start: 0.8093 (ttt-90) cc_final: 0.7766 (ttt-90) REVERT: E 97 HIS cc_start: 0.8554 (t-90) cc_final: 0.8087 (t-170) REVERT: F 196 TYR cc_start: 0.8655 (t80) cc_final: 0.8158 (t80) REVERT: F 219 MET cc_start: 0.9163 (ptp) cc_final: 0.8835 (ptp) REVERT: F 221 TRP cc_start: 0.8563 (t-100) cc_final: 0.8300 (t-100) REVERT: F 231 ASN cc_start: 0.8620 (m110) cc_final: 0.8378 (p0) REVERT: F 261 GLU cc_start: 0.8194 (tp30) cc_final: 0.7879 (tp30) REVERT: F 268 ARG cc_start: 0.8950 (tpp80) cc_final: 0.8690 (tpp80) REVERT: F 310 MET cc_start: 0.8597 (tpp) cc_final: 0.8206 (tpp) REVERT: F 391 PHE cc_start: 0.8804 (t80) cc_final: 0.8412 (t80) REVERT: F 393 LEU cc_start: 0.9567 (mt) cc_final: 0.9232 (tt) REVERT: J 101 ARG cc_start: 0.8693 (mmm160) cc_final: 0.8472 (mmm160) outliers start: 59 outliers final: 36 residues processed: 588 average time/residue: 0.4393 time to fit residues: 391.2227 Evaluate side-chains 556 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 515 time to evaluate : 3.130 ------------------------------------------------------------------------------- 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 177 LYS Chi-restraints excluded: chain C residue 77 LEU 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 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 806 THR Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 930 VAL 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 234 LEU Chi-restraints excluded: chain D residue 235 ILE 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 457 MET Chi-restraints excluded: chain D residue 493 GLU Chi-restraints excluded: chain D residue 565 ILE 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 1186 GLU Chi-restraints excluded: chain D residue 1216 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 384 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 64 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 chunk 284 optimal weight: 7.9990 chunk 260 optimal weight: 20.0000 chunk 139 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 277 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 248 optimal weight: 0.0470 chunk 87 optimal weight: 0.6980 chunk 241 optimal weight: 1.9990 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** D 609 GLN ** D 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 881 GLN ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 HIS ** 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 = 0.3935 r_free = 0.3935 target = 0.123116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.086806 restraints weight = 74639.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.089932 restraints weight = 42123.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.091992 restraints weight = 28932.825| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28260 Z= 0.134 Angle : 0.654 10.440 38614 Z= 0.333 Chirality : 0.043 0.285 4390 Planarity : 0.005 0.072 4789 Dihedral : 14.639 159.590 4567 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.68 % Allowed : 19.94 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3305 helix: 0.56 (0.15), residues: 1231 sheet: -0.57 (0.25), residues: 407 loop : -0.27 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 23 HIS 0.006 0.001 HIS D 941 PHE 0.044 0.001 PHE D 226 TYR 0.041 0.002 TYR D 248 ARG 0.019 0.001 ARG D 56 Details of bonding type rmsd hydrogen bonds : bond 0.03742 ( 1154) hydrogen bonds : angle 4.68485 ( 3162) metal coordination : bond 0.00860 ( 8) metal coordination : angle 2.78953 ( 12) covalent geometry : bond 0.00299 (28252) covalent geometry : angle 0.65212 (38602) *********************** 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 608 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 533 time to evaluate : 3.046 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: A 95 MET cc_start: 0.7982 (mmm) cc_final: 0.7393 (mmm) REVERT: A 99 LYS cc_start: 0.8536 (tptt) cc_final: 0.7973 (tptt) REVERT: A 123 MET cc_start: 0.8288 (tmm) cc_final: 0.7856 (ttp) REVERT: A 191 LYS cc_start: 0.8803 (ttpp) cc_final: 0.8300 (pttm) REVERT: B 1 MET cc_start: 0.6482 (pmm) cc_final: 0.6268 (pmm) REVERT: B 98 ARG cc_start: 0.7920 (tpt170) cc_final: 0.7666 (tpm170) REVERT: B 123 MET cc_start: 0.8074 (tmm) cc_final: 0.7520 (tmm) REVERT: B 179 GLU cc_start: 0.7912 (mp0) cc_final: 0.7439 (mp0) REVERT: B 191 LYS cc_start: 0.8637 (ptmm) cc_final: 0.7977 (ptmm) REVERT: B 226 ASN cc_start: 0.8766 (t0) cc_final: 0.8408 (t0) REVERT: C 79 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8579 (mm-30) REVERT: C 107 LYS cc_start: 0.8786 (mtmt) cc_final: 0.8437 (ptpp) REVERT: C 304 ARG cc_start: 0.8950 (tpp-160) cc_final: 0.8727 (tpp-160) REVERT: C 374 GLU cc_start: 0.8207 (mp0) cc_final: 0.7938 (tp30) REVERT: C 530 HIS cc_start: 0.8488 (m-70) cc_final: 0.8061 (m-70) REVERT: C 548 ASP cc_start: 0.8248 (p0) cc_final: 0.7760 (p0) REVERT: C 571 ASP cc_start: 0.8122 (m-30) cc_final: 0.7795 (m-30) REVERT: C 594 ASN cc_start: 0.9094 (OUTLIER) cc_final: 0.8776 (p0) REVERT: C 619 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.7837 (p) REVERT: C 715 MET cc_start: 0.8788 (ptm) cc_final: 0.8531 (ptm) REVERT: C 724 ASP cc_start: 0.7531 (t0) cc_final: 0.7073 (t0) REVERT: C 791 ASP cc_start: 0.8038 (m-30) cc_final: 0.7786 (p0) REVERT: C 915 ARG cc_start: 0.7876 (tmm-80) cc_final: 0.7604 (tmm-80) REVERT: C 1008 GLU cc_start: 0.8425 (mp0) cc_final: 0.8064 (mp0) REVERT: C 1083 LYS cc_start: 0.9156 (mtmt) cc_final: 0.8913 (mttt) REVERT: C 1110 GLU cc_start: 0.8158 (tp30) cc_final: 0.7800 (tp30) REVERT: D 27 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7274 (pp20) REVERT: D 43 LYS cc_start: 0.8409 (tppt) cc_final: 0.7693 (tppt) REVERT: D 69 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.7051 (ptt-90) REVERT: D 84 ARG cc_start: 0.8542 (tpt170) cc_final: 0.8250 (tpt90) REVERT: D 134 TYR cc_start: 0.7965 (m-10) cc_final: 0.7517 (m-10) REVERT: D 143 MET cc_start: 0.8319 (mtm) cc_final: 0.7795 (ptp) REVERT: D 158 GLU cc_start: 0.9318 (tp30) cc_final: 0.8966 (tm-30) REVERT: D 235 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7694 (mp) REVERT: D 247 ARG cc_start: 0.7454 (ptp-170) cc_final: 0.7037 (mtm180) REVERT: D 256 MET cc_start: 0.6445 (OUTLIER) cc_final: 0.5590 (ttm) REVERT: D 356 ARG cc_start: 0.8627 (mmp80) cc_final: 0.8315 (mmp80) REVERT: D 383 ASP cc_start: 0.8858 (t0) cc_final: 0.8355 (p0) REVERT: D 423 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.8061 (t70) REVERT: D 457 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8392 (tpp) REVERT: D 474 ARG cc_start: 0.7390 (tpt90) cc_final: 0.6843 (tpt170) REVERT: D 518 GLU cc_start: 0.7408 (mm-30) cc_final: 0.6803 (mm-30) REVERT: D 541 MET cc_start: 0.8519 (tpp) cc_final: 0.8187 (mmm) REVERT: D 552 GLN cc_start: 0.8674 (mt0) cc_final: 0.8308 (mp10) REVERT: D 634 LYS cc_start: 0.9091 (ttmt) cc_final: 0.8731 (tppt) REVERT: D 685 GLU cc_start: 0.7954 (tp30) cc_final: 0.7743 (tp30) REVERT: D 717 ASP cc_start: 0.8524 (m-30) cc_final: 0.8263 (m-30) REVERT: D 741 LYS cc_start: 0.9302 (pptt) cc_final: 0.8812 (mmmt) REVERT: D 742 GLN cc_start: 0.8399 (mp10) cc_final: 0.7892 (pm20) REVERT: D 841 GLU cc_start: 0.8307 (tt0) cc_final: 0.7880 (tm-30) REVERT: D 859 LEU cc_start: 0.9392 (mm) cc_final: 0.9187 (mm) REVERT: D 864 LEU cc_start: 0.9099 (pp) cc_final: 0.8384 (pp) REVERT: D 868 ASP cc_start: 0.7915 (t0) cc_final: 0.7469 (p0) REVERT: D 941 HIS cc_start: 0.7399 (t-170) cc_final: 0.7174 (t-170) REVERT: D 976 MET cc_start: 0.8385 (mpp) cc_final: 0.7631 (tpp) REVERT: D 1129 ARG cc_start: 0.8886 (tpm170) cc_final: 0.8670 (tpm170) REVERT: D 1232 ARG cc_start: 0.8978 (mtm110) cc_final: 0.8561 (mtm110) REVERT: D 1236 ASP cc_start: 0.9027 (t0) cc_final: 0.8694 (m-30) REVERT: D 1254 ILE cc_start: 0.7880 (mm) cc_final: 0.7669 (mm) REVERT: E 94 ARG cc_start: 0.8141 (ttt-90) cc_final: 0.7784 (ttt180) REVERT: E 97 HIS cc_start: 0.8517 (t-90) cc_final: 0.8071 (t-170) REVERT: F 159 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7635 (mt) REVERT: F 192 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8121 (pt0) REVERT: F 196 TYR cc_start: 0.8690 (t80) cc_final: 0.8167 (t80) REVERT: F 219 MET cc_start: 0.9108 (ptp) cc_final: 0.8845 (ptt) REVERT: F 221 TRP cc_start: 0.8623 (t-100) cc_final: 0.8344 (t-100) REVERT: F 261 GLU cc_start: 0.8199 (tp30) cc_final: 0.7862 (tp30) REVERT: F 268 ARG cc_start: 0.8967 (tpp80) cc_final: 0.8740 (tpp80) REVERT: F 310 MET cc_start: 0.8616 (tpp) cc_final: 0.8247 (tpp) REVERT: F 391 PHE cc_start: 0.8857 (t80) cc_final: 0.8405 (t80) outliers start: 75 outliers final: 53 residues processed: 574 average time/residue: 0.4390 time to fit residues: 382.5513 Evaluate side-chains 560 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 498 time to evaluate : 2.827 ------------------------------------------------------------------------------- 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 65 THR 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 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 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 69 ARG Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 159 LYS Chi-restraints excluded: chain D residue 226 PHE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 244 LEU 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 423 ASP Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 493 GLU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 713 ASP 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 963 SER Chi-restraints excluded: chain D residue 1158 ILE Chi-restraints excluded: chain D residue 1169 ILE Chi-restraints excluded: chain D residue 1216 LEU Chi-restraints excluded: chain D residue 1247 ASN Chi-restraints excluded: chain E residue 101 LEU 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 19 optimal weight: 5.9990 chunk 262 optimal weight: 20.0000 chunk 84 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 214 optimal weight: 6.9990 chunk 321 optimal weight: 20.0000 chunk 280 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 64 optimal weight: 0.0570 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** C 603 GLN D 369 ASN ** D 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 ASN ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 454 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 = 0.3881 r_free = 0.3881 target = 0.119193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.082168 restraints weight = 76841.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.085214 restraints weight = 43626.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.087195 restraints weight = 30148.927| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4831 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= 0.250 Angle : 0.712 11.579 38614 Z= 0.366 Chirality : 0.044 0.218 4390 Planarity : 0.005 0.060 4789 Dihedral : 14.761 158.209 4567 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.75 % Allowed : 19.94 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.15), residues: 3305 helix: 0.46 (0.15), residues: 1239 sheet: -0.66 (0.26), residues: 378 loop : -0.29 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP D 23 HIS 0.007 0.001 HIS A 61 PHE 0.042 0.002 PHE D 226 TYR 0.038 0.002 TYR D 248 ARG 0.017 0.001 ARG D 56 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 1154) hydrogen bonds : angle 4.92784 ( 3162) metal coordination : bond 0.01696 ( 8) metal coordination : angle 3.64181 ( 12) covalent geometry : bond 0.00544 (28252) covalent geometry : angle 0.70881 (38602) *********************** 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 619 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 514 time to evaluate : 3.076 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: A 95 MET cc_start: 0.7981 (mmm) cc_final: 0.7667 (mmm) REVERT: A 99 LYS cc_start: 0.8574 (tptt) cc_final: 0.8367 (tptt) REVERT: A 123 MET cc_start: 0.8348 (tmm) cc_final: 0.8091 (tmm) REVERT: A 191 LYS cc_start: 0.8881 (ttpp) cc_final: 0.8308 (ptpp) REVERT: B 1 MET cc_start: 0.6716 (pmm) cc_final: 0.6483 (pmm) REVERT: B 123 MET cc_start: 0.7924 (tmm) cc_final: 0.7622 (tmm) REVERT: B 179 GLU cc_start: 0.7884 (mp0) cc_final: 0.7411 (mp0) REVERT: B 191 LYS cc_start: 0.8631 (ptmm) cc_final: 0.8085 (ptmm) REVERT: B 226 ASN cc_start: 0.8963 (t0) cc_final: 0.8659 (t0) REVERT: C 79 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8595 (mm-30) REVERT: C 107 LYS cc_start: 0.8800 (mtmt) cc_final: 0.8423 (ptpp) REVERT: C 304 ARG cc_start: 0.9002 (tpp-160) cc_final: 0.8756 (tpp-160) REVERT: C 346 MET cc_start: 0.7868 (tmm) cc_final: 0.7144 (tpt) REVERT: C 374 GLU cc_start: 0.8241 (mp0) cc_final: 0.8000 (tp30) REVERT: C 518 GLN cc_start: 0.8590 (tp-100) cc_final: 0.8249 (tp-100) REVERT: C 529 ARG cc_start: 0.8510 (tpt90) cc_final: 0.8287 (tpt90) REVERT: C 530 HIS cc_start: 0.8619 (m-70) cc_final: 0.8202 (m-70) REVERT: C 548 ASP cc_start: 0.8262 (p0) cc_final: 0.7714 (p0) REVERT: C 594 ASN cc_start: 0.9082 (OUTLIER) cc_final: 0.8773 (p0) REVERT: C 619 THR cc_start: 0.8747 (OUTLIER) cc_final: 0.8252 (p) REVERT: C 715 MET cc_start: 0.8867 (ptm) cc_final: 0.8547 (ptm) REVERT: C 724 ASP cc_start: 0.7602 (t0) cc_final: 0.7374 (t0) REVERT: C 734 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: C 788 ARG cc_start: 0.7400 (mmp80) cc_final: 0.7096 (mmp80) REVERT: C 791 ASP cc_start: 0.8077 (m-30) cc_final: 0.7824 (p0) REVERT: C 883 LYS cc_start: 0.8928 (pttm) cc_final: 0.8517 (ptmm) REVERT: C 915 ARG cc_start: 0.7901 (tmm-80) cc_final: 0.7624 (tmm-80) REVERT: C 1110 GLU cc_start: 0.8381 (tp30) cc_final: 0.7943 (tp30) REVERT: D 27 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7506 (pp20) REVERT: D 43 LYS cc_start: 0.8373 (tppt) cc_final: 0.7659 (tppt) REVERT: D 44 ASP cc_start: 0.7820 (t0) cc_final: 0.7187 (t0) REVERT: D 58 TRP cc_start: 0.8107 (m100) cc_final: 0.7856 (m100) REVERT: D 134 TYR cc_start: 0.8001 (m-10) cc_final: 0.7541 (m-10) REVERT: D 143 MET cc_start: 0.8426 (mtm) cc_final: 0.7910 (ptp) REVERT: D 158 GLU cc_start: 0.9334 (tp30) cc_final: 0.8989 (tm-30) REVERT: D 233 GLN cc_start: 0.7866 (tm-30) cc_final: 0.7603 (tm-30) REVERT: D 247 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7080 (mtm180) REVERT: D 256 MET cc_start: 0.6598 (OUTLIER) cc_final: 0.6191 (ttm) REVERT: D 346 ARG cc_start: 0.7955 (mmm-85) cc_final: 0.7446 (mmm-85) REVERT: D 356 ARG cc_start: 0.8674 (mmp80) cc_final: 0.8371 (mmp80) REVERT: D 383 ASP cc_start: 0.8931 (t0) cc_final: 0.8371 (p0) REVERT: D 404 ASP cc_start: 0.8878 (t0) cc_final: 0.8328 (t0) REVERT: D 423 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8040 (t70) REVERT: D 457 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8413 (tpp) REVERT: D 474 ARG cc_start: 0.7485 (tpt90) cc_final: 0.6954 (tpt170) REVERT: D 475 MET cc_start: 0.7612 (ptm) cc_final: 0.7255 (ptp) REVERT: D 518 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7138 (mm-30) REVERT: D 541 MET cc_start: 0.8489 (tpp) cc_final: 0.8193 (mmm) REVERT: D 552 GLN cc_start: 0.8704 (mt0) cc_final: 0.8318 (mp10) REVERT: D 634 LYS cc_start: 0.9124 (ttmt) cc_final: 0.8844 (tptt) REVERT: D 717 ASP cc_start: 0.8589 (m-30) cc_final: 0.8383 (m-30) REVERT: D 741 LYS cc_start: 0.9318 (pptt) cc_final: 0.8846 (mmmt) REVERT: D 742 GLN cc_start: 0.8482 (mp10) cc_final: 0.8031 (pm20) REVERT: D 841 GLU cc_start: 0.8281 (tt0) cc_final: 0.7857 (tm-30) REVERT: D 859 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9205 (mm) REVERT: D 864 LEU cc_start: 0.9134 (pp) cc_final: 0.8475 (pp) REVERT: D 868 ASP cc_start: 0.8006 (t0) cc_final: 0.7517 (p0) REVERT: D 941 HIS cc_start: 0.7579 (t-170) cc_final: 0.7324 (t-170) REVERT: D 976 MET cc_start: 0.8476 (mpp) cc_final: 0.7614 (tpp) REVERT: D 992 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7752 (mp0) REVERT: D 1232 ARG cc_start: 0.8993 (mtm110) cc_final: 0.8591 (mtm110) REVERT: D 1236 ASP cc_start: 0.9060 (t0) cc_final: 0.8720 (m-30) REVERT: D 1254 ILE cc_start: 0.7926 (mm) cc_final: 0.7705 (mm) REVERT: E 94 ARG cc_start: 0.8194 (ttt-90) cc_final: 0.7959 (ttt-90) REVERT: E 97 HIS cc_start: 0.8531 (t-90) cc_final: 0.8114 (t-170) REVERT: F 159 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7773 (mt) REVERT: F 192 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8153 (pt0) REVERT: F 196 TYR cc_start: 0.8719 (t80) cc_final: 0.8205 (t80) REVERT: F 219 MET cc_start: 0.9102 (ptp) cc_final: 0.8848 (ptt) REVERT: F 221 TRP cc_start: 0.8656 (t-100) cc_final: 0.8377 (t-100) REVERT: F 231 ASN cc_start: 0.8632 (m110) cc_final: 0.8339 (p0) REVERT: F 261 GLU cc_start: 0.8276 (tp30) cc_final: 0.7958 (tp30) REVERT: F 290 ARG cc_start: 0.9003 (mtp180) cc_final: 0.8766 (ttt180) REVERT: F 310 MET cc_start: 0.8722 (tpp) cc_final: 0.8310 (tpp) REVERT: F 361 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8758 (mt) REVERT: F 400 SER cc_start: 0.8415 (t) cc_final: 0.8112 (m) outliers start: 105 outliers final: 73 residues processed: 570 average time/residue: 0.4425 time to fit residues: 379.7624 Evaluate side-chains 571 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 486 time to evaluate : 2.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 147 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 51 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 418 ILE 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 692 VAL Chi-restraints excluded: chain C residue 734 GLU Chi-restraints excluded: chain C residue 798 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 C residue 1122 LEU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 159 LYS Chi-restraints excluded: chain D residue 226 PHE Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 423 ASP 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 493 GLU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 713 ASP 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 859 LEU Chi-restraints excluded: chain D residue 871 TYR Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 959 VAL Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 992 GLU Chi-restraints excluded: chain D residue 994 VAL Chi-restraints excluded: chain D residue 1158 ILE 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 E residue 53 TYR Chi-restraints excluded: chain E residue 101 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 263 optimal weight: 8.9990 chunk 332 optimal weight: 10.0000 chunk 6 optimal weight: 0.0270 chunk 309 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 113 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 253 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 overall best weight: 1.3444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 HIS C 918 ASN D 369 ASN ** D 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 692 GLN ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 423 GLN ** F 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.121009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.084153 restraints weight = 75369.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.087253 restraints weight = 42478.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.089272 restraints weight = 29238.931| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.5010 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= 0.150 Angle : 0.697 16.182 38614 Z= 0.352 Chirality : 0.044 0.368 4390 Planarity : 0.005 0.080 4789 Dihedral : 14.726 157.778 4567 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.50 % Allowed : 21.69 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.15), residues: 3305 helix: 0.57 (0.15), residues: 1228 sheet: -0.60 (0.26), residues: 391 loop : -0.28 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP F 288 HIS 0.005 0.001 HIS A 61 PHE 0.044 0.002 PHE D 226 TYR 0.038 0.002 TYR D 248 ARG 0.014 0.001 ARG C 412 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 1154) hydrogen bonds : angle 4.76609 ( 3162) metal coordination : bond 0.00876 ( 8) metal coordination : angle 3.30055 ( 12) covalent geometry : bond 0.00338 (28252) covalent geometry : angle 0.69492 (38602) *********************** 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 607 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 509 time to evaluate : 2.794 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: A 95 MET cc_start: 0.7947 (mmm) cc_final: 0.7587 (mmm) REVERT: A 99 LYS cc_start: 0.8541 (tptt) cc_final: 0.8331 (tptt) REVERT: A 191 LYS cc_start: 0.8845 (ttpp) cc_final: 0.8311 (ptpp) REVERT: B 1 MET cc_start: 0.6717 (pmm) cc_final: 0.6487 (pmm) REVERT: B 123 MET cc_start: 0.7928 (tmm) cc_final: 0.7684 (tmm) REVERT: B 179 GLU cc_start: 0.7861 (mp0) cc_final: 0.7399 (mp0) REVERT: B 191 LYS cc_start: 0.8692 (ptmm) cc_final: 0.8083 (ptmm) REVERT: B 226 ASN cc_start: 0.8950 (t0) cc_final: 0.8642 (t0) REVERT: C 79 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8531 (mm-30) REVERT: C 107 LYS cc_start: 0.8814 (mtmt) cc_final: 0.8431 (ptpp) REVERT: C 304 ARG cc_start: 0.8965 (tpp-160) cc_final: 0.8758 (tpp-160) REVERT: C 374 GLU cc_start: 0.8204 (mp0) cc_final: 0.7965 (tp30) REVERT: C 523 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8756 (p) REVERT: C 530 HIS cc_start: 0.8598 (m-70) cc_final: 0.8195 (m-70) REVERT: C 548 ASP cc_start: 0.8310 (p0) cc_final: 0.7793 (p0) REVERT: C 571 ASP cc_start: 0.8157 (m-30) cc_final: 0.7904 (m-30) REVERT: C 594 ASN cc_start: 0.9082 (OUTLIER) cc_final: 0.8790 (p0) REVERT: C 619 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.8109 (p) REVERT: C 715 MET cc_start: 0.8765 (ptm) cc_final: 0.8484 (ptm) REVERT: C 724 ASP cc_start: 0.7752 (t0) cc_final: 0.7385 (t0) REVERT: C 883 LYS cc_start: 0.8903 (pttm) cc_final: 0.8468 (ptmm) REVERT: C 921 GLN cc_start: 0.7824 (pt0) cc_final: 0.7580 (pt0) REVERT: C 1067 MET cc_start: 0.8669 (ttm) cc_final: 0.8323 (ttm) REVERT: C 1110 GLU cc_start: 0.8289 (tp30) cc_final: 0.7875 (tp30) REVERT: D 27 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7416 (pp20) REVERT: D 43 LYS cc_start: 0.8392 (tppt) cc_final: 0.7641 (tppt) REVERT: D 44 ASP cc_start: 0.7724 (t0) cc_final: 0.7151 (t0) REVERT: D 134 TYR cc_start: 0.8003 (m-10) cc_final: 0.7540 (m-10) REVERT: D 143 MET cc_start: 0.8291 (mtm) cc_final: 0.7753 (ptp) REVERT: D 158 GLU cc_start: 0.9345 (tp30) cc_final: 0.8991 (tm-30) REVERT: D 233 GLN cc_start: 0.7891 (tm-30) cc_final: 0.7478 (tm-30) REVERT: D 235 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7597 (mp) REVERT: D 247 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7047 (mtm180) REVERT: D 256 MET cc_start: 0.6588 (OUTLIER) cc_final: 0.6210 (ttm) REVERT: D 295 ARG cc_start: 0.8695 (ttm170) cc_final: 0.7937 (mtp-110) REVERT: D 346 ARG cc_start: 0.7824 (mmm-85) cc_final: 0.7403 (mmm-85) REVERT: D 356 ARG cc_start: 0.8655 (mmp80) cc_final: 0.8317 (mmp80) REVERT: D 383 ASP cc_start: 0.8898 (t0) cc_final: 0.8333 (p0) REVERT: D 404 ASP cc_start: 0.8625 (t0) cc_final: 0.8379 (t0) REVERT: D 423 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7965 (t70) REVERT: D 457 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8406 (tpp) REVERT: D 474 ARG cc_start: 0.7453 (tpt90) cc_final: 0.6915 (tpt170) REVERT: D 475 MET cc_start: 0.7593 (ptm) cc_final: 0.7206 (ptp) REVERT: D 493 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6283 (pt0) REVERT: D 518 GLU cc_start: 0.7516 (mm-30) cc_final: 0.6952 (mm-30) REVERT: D 541 MET cc_start: 0.8556 (tpp) cc_final: 0.8300 (mmm) REVERT: D 552 GLN cc_start: 0.8665 (mt0) cc_final: 0.8265 (mp10) REVERT: D 622 MET cc_start: 0.8860 (ptp) cc_final: 0.8548 (ptp) REVERT: D 634 LYS cc_start: 0.9074 (ttmt) cc_final: 0.8800 (tptt) REVERT: D 717 ASP cc_start: 0.8526 (m-30) cc_final: 0.8214 (m-30) REVERT: D 741 LYS cc_start: 0.9311 (pptt) cc_final: 0.8820 (mmmt) REVERT: D 742 GLN cc_start: 0.8470 (mp10) cc_final: 0.8018 (pm20) REVERT: D 841 GLU cc_start: 0.8285 (tt0) cc_final: 0.7832 (tm-30) REVERT: D 859 LEU cc_start: 0.9413 (mm) cc_final: 0.9200 (mm) REVERT: D 864 LEU cc_start: 0.9111 (pp) cc_final: 0.8397 (pp) REVERT: D 868 ASP cc_start: 0.7972 (t0) cc_final: 0.7505 (p0) REVERT: D 941 HIS cc_start: 0.7530 (t-170) cc_final: 0.7278 (t-170) REVERT: D 951 LEU cc_start: 0.8695 (mt) cc_final: 0.7911 (pp) REVERT: D 976 MET cc_start: 0.8464 (mpp) cc_final: 0.7722 (tpp) REVERT: D 1232 ARG cc_start: 0.8989 (mtm110) cc_final: 0.8573 (mtm110) REVERT: D 1236 ASP cc_start: 0.9030 (t0) cc_final: 0.8723 (m-30) REVERT: D 1254 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7643 (mm) REVERT: E 82 PRO cc_start: 0.9034 (Cg_endo) cc_final: 0.8829 (Cg_exo) REVERT: E 97 HIS cc_start: 0.8473 (t-90) cc_final: 0.8054 (t-170) REVERT: F 190 ARG cc_start: 0.8804 (mtm180) cc_final: 0.8526 (mtm-85) REVERT: F 192 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8084 (pt0) REVERT: F 196 TYR cc_start: 0.8692 (t80) cc_final: 0.8163 (t80) REVERT: F 201 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9104 (mt) REVERT: F 219 MET cc_start: 0.9092 (ptp) cc_final: 0.8881 (ptt) REVERT: F 221 TRP cc_start: 0.8642 (t-100) cc_final: 0.8355 (t-100) REVERT: F 261 GLU cc_start: 0.8166 (tp30) cc_final: 0.7843 (tp30) REVERT: F 268 ARG cc_start: 0.9038 (tpp80) cc_final: 0.8720 (tpp80) REVERT: F 310 MET cc_start: 0.8689 (tpp) cc_final: 0.8316 (tpp) REVERT: F 361 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8685 (mt) REVERT: F 462 ARG cc_start: 0.8018 (ptp-170) cc_final: 0.7695 (mtt90) outliers start: 98 outliers final: 66 residues processed: 562 average time/residue: 0.4382 time to fit residues: 374.8531 Evaluate side-chains 571 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 492 time to evaluate : 3.330 ------------------------------------------------------------------------------- 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 83 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 113 CYS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 226 THR 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 523 THR 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 806 THR 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 C residue 1122 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 136 ILE Chi-restraints excluded: chain D residue 159 LYS Chi-restraints excluded: chain D residue 226 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 423 ASP 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 493 GLU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 713 ASP 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 871 TYR Chi-restraints excluded: chain D residue 914 HIS Chi-restraints excluded: chain D residue 959 VAL Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 1158 ILE 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 1254 ILE Chi-restraints excluded: chain D residue 1265 ILE Chi-restraints excluded: chain E residue 53 TYR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 201 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 63 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 138 optimal weight: 0.6980 chunk 30 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 68 optimal weight: 20.0000 chunk 197 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 333 optimal weight: 7.9990 chunk 166 optimal weight: 1.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 HIS C 918 ASN D 416 ASN ** D 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 454 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 = 0.3890 r_free = 0.3890 target = 0.119870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.083343 restraints weight = 76093.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.086385 restraints weight = 43653.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.088345 restraints weight = 30242.747| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28260 Z= 0.194 Angle : 0.720 12.161 38614 Z= 0.367 Chirality : 0.044 0.326 4390 Planarity : 0.005 0.080 4789 Dihedral : 14.779 157.631 4567 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.53 % Allowed : 22.90 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.15), residues: 3305 helix: 0.47 (0.15), residues: 1231 sheet: -0.61 (0.25), residues: 401 loop : -0.25 (0.16), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP D 23 HIS 0.006 0.001 HIS C 911 PHE 0.043 0.002 PHE D 226 TYR 0.037 0.002 TYR D 248 ARG 0.018 0.001 ARG D 334 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 1154) hydrogen bonds : angle 4.89093 ( 3162) metal coordination : bond 0.01241 ( 8) metal coordination : angle 3.38826 ( 12) covalent geometry : bond 0.00431 (28252) covalent geometry : angle 0.71805 (38602) *********************** 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 608 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 509 time to evaluate : 2.823 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: A 1 MET cc_start: 0.6513 (tmm) cc_final: 0.6218 (tmm) REVERT: A 95 MET cc_start: 0.7917 (mmm) cc_final: 0.7603 (mmm) REVERT: A 99 LYS cc_start: 0.8578 (tptt) cc_final: 0.8239 (tptp) REVERT: A 191 LYS cc_start: 0.8887 (ttpp) cc_final: 0.8350 (ptpp) REVERT: B 1 MET cc_start: 0.6747 (pmm) cc_final: 0.6199 (pmm) REVERT: B 123 MET cc_start: 0.7936 (tmm) cc_final: 0.7661 (tmm) REVERT: B 134 LEU cc_start: 0.9027 (tp) cc_final: 0.8260 (pp) REVERT: B 179 GLU cc_start: 0.7834 (mp0) cc_final: 0.7396 (mp0) REVERT: B 191 LYS cc_start: 0.8717 (ptmm) cc_final: 0.7907 (ptmm) REVERT: B 226 ASN cc_start: 0.8984 (t0) cc_final: 0.8702 (t0) REVERT: C 79 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8562 (mm-30) REVERT: C 107 LYS cc_start: 0.8806 (mtmt) cc_final: 0.8424 (ptpp) REVERT: C 113 CYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8211 (m) REVERT: C 304 ARG cc_start: 0.8977 (tpp-160) cc_final: 0.8760 (tpp-160) REVERT: C 374 GLU cc_start: 0.8216 (mp0) cc_final: 0.7983 (tp30) REVERT: C 478 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8160 (tp30) REVERT: C 523 THR cc_start: 0.8867 (OUTLIER) cc_final: 0.8617 (p) REVERT: C 526 GLU cc_start: 0.8640 (mp0) cc_final: 0.8381 (pt0) REVERT: C 548 ASP cc_start: 0.8279 (p0) cc_final: 0.7880 (p0) REVERT: C 594 ASN cc_start: 0.9089 (OUTLIER) cc_final: 0.8789 (p0) REVERT: C 619 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8161 (p) REVERT: C 664 ARG cc_start: 0.8254 (mtp-110) cc_final: 0.8025 (mtp-110) REVERT: C 715 MET cc_start: 0.8783 (ptm) cc_final: 0.8479 (ptm) REVERT: C 724 ASP cc_start: 0.7721 (t0) cc_final: 0.7342 (t0) REVERT: C 883 LYS cc_start: 0.8938 (pttm) cc_final: 0.8472 (ptmm) REVERT: C 1110 GLU cc_start: 0.8351 (tp30) cc_final: 0.7931 (tp30) REVERT: D 27 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7433 (pp20) REVERT: D 37 ARG cc_start: 0.8982 (ttp80) cc_final: 0.8609 (mtp-110) REVERT: D 43 LYS cc_start: 0.8358 (tppt) cc_final: 0.7660 (tppt) REVERT: D 44 ASP cc_start: 0.7808 (t0) cc_final: 0.7323 (t0) REVERT: D 56 ARG cc_start: 0.7796 (mmp80) cc_final: 0.7424 (mmm160) REVERT: D 120 LEU cc_start: 0.9259 (mm) cc_final: 0.9027 (tp) REVERT: D 134 TYR cc_start: 0.8017 (m-10) cc_final: 0.7576 (m-10) REVERT: D 143 MET cc_start: 0.8314 (mtm) cc_final: 0.7773 (ptp) REVERT: D 158 GLU cc_start: 0.9335 (tp30) cc_final: 0.9051 (tm-30) REVERT: D 233 GLN cc_start: 0.7883 (tm-30) cc_final: 0.7490 (tm-30) REVERT: D 235 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7735 (mp) REVERT: D 247 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7153 (mtm180) REVERT: D 256 MET cc_start: 0.6765 (OUTLIER) cc_final: 0.6274 (ttm) REVERT: D 295 ARG cc_start: 0.8722 (ttm170) cc_final: 0.7974 (mtp-110) REVERT: D 334 ARG cc_start: 0.7629 (mmm160) cc_final: 0.7389 (mmm160) REVERT: D 356 ARG cc_start: 0.8657 (mmp80) cc_final: 0.8318 (mmp80) REVERT: D 383 ASP cc_start: 0.8897 (t0) cc_final: 0.8331 (p0) REVERT: D 423 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7978 (t70) REVERT: D 457 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8429 (tpp) REVERT: D 474 ARG cc_start: 0.7487 (tpt90) cc_final: 0.6929 (tpt170) REVERT: D 475 MET cc_start: 0.7674 (ptm) cc_final: 0.7262 (ptp) REVERT: D 518 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7042 (mm-30) REVERT: D 541 MET cc_start: 0.8527 (tpp) cc_final: 0.8276 (mmm) REVERT: D 552 GLN cc_start: 0.8674 (mt0) cc_final: 0.8305 (mp10) REVERT: D 622 MET cc_start: 0.8860 (ptp) cc_final: 0.8631 (ptp) REVERT: D 634 LYS cc_start: 0.9086 (ttmt) cc_final: 0.8806 (tptt) REVERT: D 741 LYS cc_start: 0.9327 (pptt) cc_final: 0.8847 (mmmt) REVERT: D 742 GLN cc_start: 0.8491 (mp10) cc_final: 0.8003 (pm20) REVERT: D 747 ARG cc_start: 0.9289 (mmm160) cc_final: 0.8957 (mmp80) REVERT: D 841 GLU cc_start: 0.8260 (tt0) cc_final: 0.7854 (tm-30) REVERT: D 859 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9194 (mm) REVERT: D 864 LEU cc_start: 0.9126 (pp) cc_final: 0.8463 (pp) REVERT: D 868 ASP cc_start: 0.7963 (t0) cc_final: 0.7491 (p0) REVERT: D 941 HIS cc_start: 0.7565 (t-170) cc_final: 0.7285 (t-170) REVERT: D 976 MET cc_start: 0.8459 (mpp) cc_final: 0.7722 (tpp) REVERT: D 992 GLU cc_start: 0.8051 (tp30) cc_final: 0.7779 (mp0) REVERT: D 1232 ARG cc_start: 0.8969 (mtm110) cc_final: 0.8560 (mtm110) REVERT: D 1236 ASP cc_start: 0.9023 (t0) cc_final: 0.8722 (m-30) REVERT: D 1254 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7674 (mm) REVERT: E 56 LYS cc_start: 0.8928 (ttmm) cc_final: 0.8586 (ttpp) REVERT: E 97 HIS cc_start: 0.8425 (t-90) cc_final: 0.7981 (t-170) REVERT: F 190 ARG cc_start: 0.8779 (mtm180) cc_final: 0.8506 (mtm-85) REVERT: F 192 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8105 (pt0) REVERT: F 196 TYR cc_start: 0.8693 (t80) cc_final: 0.8156 (t80) REVERT: F 219 MET cc_start: 0.9082 (ptp) cc_final: 0.8871 (ptt) REVERT: F 221 TRP cc_start: 0.8671 (t-100) cc_final: 0.8405 (t-100) REVERT: F 268 ARG cc_start: 0.9031 (tpp80) cc_final: 0.8612 (tpp80) REVERT: F 310 MET cc_start: 0.8696 (tpp) cc_final: 0.8407 (tpp) REVERT: F 361 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8700 (mt) REVERT: F 400 SER cc_start: 0.8378 (t) cc_final: 0.8092 (m) REVERT: F 462 ARG cc_start: 0.7992 (ptp-170) cc_final: 0.7667 (mtt90) outliers start: 99 outliers final: 63 residues processed: 567 average time/residue: 0.4556 time to fit residues: 391.7819 Evaluate side-chains 568 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 492 time to evaluate : 2.869 ------------------------------------------------------------------------------- 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 83 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 113 CYS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 226 THR 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 523 THR 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 C residue 1122 LEU Chi-restraints excluded: chain D residue 27 GLU 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 235 ILE Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 423 ASP 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 565 ILE Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 713 ASP 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 859 LEU Chi-restraints excluded: chain D residue 871 TYR Chi-restraints excluded: chain D residue 959 VAL Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 994 VAL Chi-restraints excluded: chain D residue 1158 ILE 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 1247 ASN Chi-restraints excluded: chain D residue 1254 ILE Chi-restraints excluded: chain D residue 1265 ILE Chi-restraints excluded: chain E residue 53 TYR 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 272 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 152 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 315 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 255 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 134 optimal weight: 1.9990 chunk 184 optimal weight: 9.9990 chunk 223 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 918 ASN C1057 GLN ** D 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 423 GLN ** F 454 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 = 0.3908 r_free = 0.3908 target = 0.121031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.084264 restraints weight = 75932.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.087271 restraints weight = 43812.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.089268 restraints weight = 30558.378| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28260 Z= 0.148 Angle : 0.744 14.952 38614 Z= 0.373 Chirality : 0.044 0.384 4390 Planarity : 0.005 0.093 4789 Dihedral : 14.776 157.636 4567 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.03 % Allowed : 23.65 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.15), residues: 3305 helix: 0.47 (0.15), residues: 1228 sheet: -0.55 (0.26), residues: 391 loop : -0.26 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP F 288 HIS 0.007 0.001 HIS C 530 PHE 0.044 0.002 PHE D 226 TYR 0.037 0.002 TYR D 248 ARG 0.020 0.001 ARG J 101 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 1154) hydrogen bonds : angle 4.84344 ( 3162) metal coordination : bond 0.00827 ( 8) metal coordination : angle 3.17410 ( 12) covalent geometry : bond 0.00335 (28252) covalent geometry : angle 0.74193 (38602) *********************** 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 596 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 511 time to evaluate : 2.807 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: A 1 MET cc_start: 0.6852 (tmm) cc_final: 0.6424 (tmm) REVERT: A 99 LYS cc_start: 0.8556 (tptt) cc_final: 0.8299 (tptt) REVERT: A 191 LYS cc_start: 0.8883 (ttpp) cc_final: 0.8343 (ptpp) REVERT: B 1 MET cc_start: 0.6399 (pmm) cc_final: 0.6179 (pmm) REVERT: B 81 LYS cc_start: 0.7858 (mtmm) cc_final: 0.7354 (mtmm) REVERT: B 123 MET cc_start: 0.7908 (tmm) cc_final: 0.7618 (tmm) REVERT: B 179 GLU cc_start: 0.7869 (mp0) cc_final: 0.7427 (mp0) REVERT: B 191 LYS cc_start: 0.8722 (ptmm) cc_final: 0.7945 (ptmm) REVERT: B 226 ASN cc_start: 0.8993 (t0) cc_final: 0.8732 (t0) REVERT: C 79 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8523 (mm-30) REVERT: C 107 LYS cc_start: 0.8831 (mtmt) cc_final: 0.8348 (ptpp) REVERT: C 113 CYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8180 (m) REVERT: C 374 GLU cc_start: 0.8213 (mp0) cc_final: 0.7970 (tp30) REVERT: C 478 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8177 (tp30) REVERT: C 523 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8671 (p) REVERT: C 526 GLU cc_start: 0.8567 (mp0) cc_final: 0.8366 (pt0) REVERT: C 548 ASP cc_start: 0.8359 (p0) cc_final: 0.7873 (p0) REVERT: C 571 ASP cc_start: 0.8123 (m-30) cc_final: 0.7821 (m-30) REVERT: C 594 ASN cc_start: 0.9097 (OUTLIER) cc_final: 0.8810 (p0) REVERT: C 619 THR cc_start: 0.8679 (OUTLIER) cc_final: 0.8139 (p) REVERT: C 664 ARG cc_start: 0.8336 (mtp-110) cc_final: 0.8101 (mtp-110) REVERT: C 715 MET cc_start: 0.8762 (ptm) cc_final: 0.8487 (ptm) REVERT: C 724 ASP cc_start: 0.7691 (t0) cc_final: 0.7318 (t0) REVERT: C 734 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7395 (mt-10) REVERT: C 883 LYS cc_start: 0.8944 (pttm) cc_final: 0.8440 (ptmm) REVERT: C 918 ASN cc_start: 0.9031 (OUTLIER) cc_final: 0.8609 (p0) REVERT: C 1110 GLU cc_start: 0.8328 (tp30) cc_final: 0.7926 (tp30) REVERT: D 27 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7520 (pp20) REVERT: D 37 ARG cc_start: 0.8965 (ttp80) cc_final: 0.8502 (mtp-110) REVERT: D 44 ASP cc_start: 0.7730 (t0) cc_final: 0.7195 (t0) REVERT: D 120 LEU cc_start: 0.9269 (mm) cc_final: 0.9019 (tp) REVERT: D 134 TYR cc_start: 0.8017 (m-10) cc_final: 0.7559 (m-10) REVERT: D 143 MET cc_start: 0.8265 (mtm) cc_final: 0.7726 (ptp) REVERT: D 158 GLU cc_start: 0.9377 (tp30) cc_final: 0.9084 (tm-30) REVERT: D 233 GLN cc_start: 0.7882 (tm-30) cc_final: 0.7449 (tm-30) REVERT: D 235 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7590 (mp) REVERT: D 247 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.7144 (mtm180) REVERT: D 256 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.6206 (ttm) REVERT: D 295 ARG cc_start: 0.8710 (ttm170) cc_final: 0.7915 (mtp-110) REVERT: D 335 PHE cc_start: 0.8127 (m-10) cc_final: 0.7043 (m-10) REVERT: D 356 ARG cc_start: 0.8645 (mmp80) cc_final: 0.8322 (mmp80) REVERT: D 383 ASP cc_start: 0.8820 (t0) cc_final: 0.8300 (p0) REVERT: D 423 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7929 (t70) REVERT: D 453 LYS cc_start: 0.8957 (tttp) cc_final: 0.8600 (tppt) REVERT: D 457 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8451 (tpp) REVERT: D 474 ARG cc_start: 0.7482 (tpt90) cc_final: 0.6831 (tpt90) REVERT: D 475 MET cc_start: 0.7654 (ptm) cc_final: 0.6774 (ptp) REVERT: D 493 GLU cc_start: 0.7588 (pt0) cc_final: 0.7262 (pm20) REVERT: D 518 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7027 (mm-30) REVERT: D 541 MET cc_start: 0.8576 (tpp) cc_final: 0.8309 (mmm) REVERT: D 552 GLN cc_start: 0.8656 (mt0) cc_final: 0.8259 (mp10) REVERT: D 622 MET cc_start: 0.8823 (ptp) cc_final: 0.8544 (ptp) REVERT: D 634 LYS cc_start: 0.9069 (ttmt) cc_final: 0.8636 (tptt) REVERT: D 741 LYS cc_start: 0.9314 (pptt) cc_final: 0.8900 (mmtm) REVERT: D 742 GLN cc_start: 0.8478 (mp10) cc_final: 0.7975 (pm20) REVERT: D 747 ARG cc_start: 0.9310 (mmm160) cc_final: 0.8989 (mmp80) REVERT: D 841 GLU cc_start: 0.8262 (tt0) cc_final: 0.7829 (tm-30) REVERT: D 859 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9190 (mm) REVERT: D 864 LEU cc_start: 0.9099 (pp) cc_final: 0.8381 (pp) REVERT: D 868 ASP cc_start: 0.7968 (t0) cc_final: 0.7515 (p0) REVERT: D 941 HIS cc_start: 0.7561 (t-170) cc_final: 0.7328 (t-170) REVERT: D 951 LEU cc_start: 0.8718 (mt) cc_final: 0.7957 (pp) REVERT: D 976 MET cc_start: 0.8466 (mpp) cc_final: 0.7712 (tpp) REVERT: D 1232 ARG cc_start: 0.9005 (mtm110) cc_final: 0.8588 (mtm110) REVERT: D 1236 ASP cc_start: 0.9060 (t0) cc_final: 0.8736 (m-30) REVERT: D 1254 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7689 (mm) REVERT: E 87 LYS cc_start: 0.7642 (ptpt) cc_final: 0.7399 (ptpt) REVERT: E 97 HIS cc_start: 0.8376 (t-90) cc_final: 0.7882 (t-170) REVERT: F 190 ARG cc_start: 0.8805 (mtm180) cc_final: 0.8523 (mtm-85) REVERT: F 192 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8078 (pt0) REVERT: F 196 TYR cc_start: 0.8706 (t80) cc_final: 0.8167 (t80) REVERT: F 219 MET cc_start: 0.9096 (ptp) cc_final: 0.8878 (ptt) REVERT: F 221 TRP cc_start: 0.8677 (t-100) cc_final: 0.8409 (t-100) REVERT: F 268 ARG cc_start: 0.9016 (tpp80) cc_final: 0.8521 (ttm-80) REVERT: F 297 MET cc_start: 0.8479 (ppp) cc_final: 0.8256 (ppp) REVERT: F 310 MET cc_start: 0.8698 (tpp) cc_final: 0.8435 (tpp) REVERT: F 361 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8615 (mt) REVERT: F 462 ARG cc_start: 0.7975 (ptp-170) cc_final: 0.7642 (mtt90) outliers start: 85 outliers final: 64 residues processed: 558 average time/residue: 0.4361 time to fit residues: 369.5380 Evaluate side-chains 560 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 482 time to evaluate : 3.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 76 ILE 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 65 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 113 CYS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 226 THR 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 523 THR 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 754 LYS 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 C residue 1122 LEU Chi-restraints excluded: chain D residue 27 GLU 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 235 ILE Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 423 ASP 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 613 SER Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 713 ASP 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 859 LEU Chi-restraints excluded: chain D residue 871 TYR Chi-restraints excluded: chain D residue 959 VAL Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 1158 ILE 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 1247 ASN Chi-restraints excluded: chain D residue 1254 ILE Chi-restraints excluded: chain D residue 1265 ILE Chi-restraints excluded: chain E residue 53 TYR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 112 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 231 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 313 optimal weight: 0.9980 chunk 279 optimal weight: 0.9990 chunk 269 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 GLN ** F 454 HIS ** 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 = 0.3912 r_free = 0.3912 target = 0.121423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.084805 restraints weight = 75323.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.087862 restraints weight = 43109.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.089841 restraints weight = 29881.728| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 28260 Z= 0.143 Angle : 0.767 15.004 38614 Z= 0.384 Chirality : 0.045 0.402 4390 Planarity : 0.005 0.083 4789 Dihedral : 14.798 157.804 4567 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.93 % Allowed : 24.01 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.15), residues: 3305 helix: 0.41 (0.15), residues: 1232 sheet: -0.52 (0.26), residues: 390 loop : -0.25 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP F 288 HIS 0.009 0.001 HIS C 530 PHE 0.044 0.002 PHE D 226 TYR 0.037 0.002 TYR D 248 ARG 0.016 0.001 ARG D 334 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 1154) hydrogen bonds : angle 4.86507 ( 3162) metal coordination : bond 0.00684 ( 8) metal coordination : angle 3.02934 ( 12) covalent geometry : bond 0.00325 (28252) covalent geometry : angle 0.76494 (38602) ********************** 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 589 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 507 time to evaluate : 3.211 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: A 99 LYS cc_start: 0.8540 (tptt) cc_final: 0.8156 (tptp) REVERT: A 191 LYS cc_start: 0.8867 (ttpp) cc_final: 0.8374 (ptpp) REVERT: B 1 MET cc_start: 0.6381 (pmm) cc_final: 0.6165 (pmm) REVERT: B 81 LYS cc_start: 0.7833 (mtmm) cc_final: 0.7438 (mtmm) REVERT: B 123 MET cc_start: 0.7895 (tmm) cc_final: 0.7601 (tmm) REVERT: B 179 GLU cc_start: 0.7858 (mp0) cc_final: 0.7391 (mp0) REVERT: B 191 LYS cc_start: 0.8716 (ptmm) cc_final: 0.7979 (ptmm) REVERT: B 226 ASN cc_start: 0.9005 (t0) cc_final: 0.8731 (t0) REVERT: C 79 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8520 (mm-30) REVERT: C 107 LYS cc_start: 0.8823 (mtmt) cc_final: 0.8339 (ptpp) REVERT: C 113 CYS cc_start: 0.8459 (t) cc_final: 0.8195 (m) REVERT: C 145 MET cc_start: 0.8507 (tpp) cc_final: 0.8274 (tpp) REVERT: C 304 ARG cc_start: 0.8616 (tpp-160) cc_final: 0.8185 (tpp80) REVERT: C 374 GLU cc_start: 0.8210 (mp0) cc_final: 0.7966 (tp30) REVERT: C 412 ARG cc_start: 0.8189 (tpp-160) cc_final: 0.7821 (tpm170) REVERT: C 478 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8200 (tp30) REVERT: C 523 THR cc_start: 0.8872 (OUTLIER) cc_final: 0.8660 (p) REVERT: C 526 GLU cc_start: 0.8576 (mp0) cc_final: 0.8256 (pt0) REVERT: C 548 ASP cc_start: 0.8368 (p0) cc_final: 0.7884 (p0) REVERT: C 571 ASP cc_start: 0.8169 (m-30) cc_final: 0.7918 (m-30) REVERT: C 594 ASN cc_start: 0.9087 (OUTLIER) cc_final: 0.8810 (p0) REVERT: C 613 GLU cc_start: 0.7748 (tp30) cc_final: 0.7493 (tp30) REVERT: C 619 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8067 (p) REVERT: C 664 ARG cc_start: 0.8391 (mtp-110) cc_final: 0.8147 (mtp-110) REVERT: C 715 MET cc_start: 0.8731 (ptm) cc_final: 0.8455 (ptm) REVERT: C 724 ASP cc_start: 0.7731 (t0) cc_final: 0.7357 (t0) REVERT: C 734 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7461 (mt-10) REVERT: C 883 LYS cc_start: 0.8891 (pttm) cc_final: 0.8332 (ptmm) REVERT: C 890 LEU cc_start: 0.8691 (mt) cc_final: 0.8480 (tp) REVERT: C 1008 GLU cc_start: 0.8410 (mp0) cc_final: 0.8102 (mp0) REVERT: C 1110 GLU cc_start: 0.8316 (tp30) cc_final: 0.7906 (tp30) REVERT: D 27 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7585 (pp20) REVERT: D 44 ASP cc_start: 0.7695 (t0) cc_final: 0.7248 (t0) REVERT: D 116 TYR cc_start: 0.8185 (m-10) cc_final: 0.7646 (m-10) REVERT: D 134 TYR cc_start: 0.8034 (m-10) cc_final: 0.7560 (m-10) REVERT: D 143 MET cc_start: 0.8262 (mtm) cc_final: 0.7713 (ptp) REVERT: D 158 GLU cc_start: 0.9352 (tp30) cc_final: 0.9055 (tm-30) REVERT: D 223 TRP cc_start: 0.8488 (t-100) cc_final: 0.8126 (t-100) REVERT: D 233 GLN cc_start: 0.7842 (tm-30) cc_final: 0.7421 (tm-30) REVERT: D 235 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7562 (mp) REVERT: D 247 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.6955 (mtm180) REVERT: D 248 TYR cc_start: 0.8849 (OUTLIER) cc_final: 0.7987 (p90) REVERT: D 256 MET cc_start: 0.6858 (OUTLIER) cc_final: 0.6258 (ttm) REVERT: D 295 ARG cc_start: 0.8699 (ttm170) cc_final: 0.7904 (mtp-110) REVERT: D 335 PHE cc_start: 0.7920 (m-10) cc_final: 0.7709 (m-10) REVERT: D 356 ARG cc_start: 0.8655 (mmp80) cc_final: 0.8306 (mmp80) REVERT: D 383 ASP cc_start: 0.8871 (t0) cc_final: 0.8322 (p0) REVERT: D 423 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7920 (t70) REVERT: D 453 LYS cc_start: 0.8930 (tttp) cc_final: 0.8535 (tppt) REVERT: D 457 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8436 (tpp) REVERT: D 474 ARG cc_start: 0.7489 (tpt90) cc_final: 0.6822 (tpt90) REVERT: D 475 MET cc_start: 0.7659 (ptm) cc_final: 0.6775 (ptp) REVERT: D 518 GLU cc_start: 0.7495 (mm-30) cc_final: 0.6991 (mm-30) REVERT: D 541 MET cc_start: 0.8593 (tpp) cc_final: 0.8289 (mmm) REVERT: D 552 GLN cc_start: 0.8670 (mt0) cc_final: 0.8234 (mp10) REVERT: D 622 MET cc_start: 0.8817 (ptp) cc_final: 0.8539 (ptp) REVERT: D 634 LYS cc_start: 0.8930 (ttmt) cc_final: 0.8657 (tptt) REVERT: D 741 LYS cc_start: 0.9319 (pptt) cc_final: 0.8809 (mmmt) REVERT: D 742 GLN cc_start: 0.8457 (mp10) cc_final: 0.8023 (pm20) REVERT: D 841 GLU cc_start: 0.8277 (tt0) cc_final: 0.7815 (tm-30) REVERT: D 859 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9195 (mm) REVERT: D 864 LEU cc_start: 0.9107 (pp) cc_final: 0.8385 (pp) REVERT: D 868 ASP cc_start: 0.7972 (t0) cc_final: 0.7484 (p0) REVERT: D 941 HIS cc_start: 0.7556 (t-170) cc_final: 0.7247 (t-170) REVERT: D 951 LEU cc_start: 0.8757 (mt) cc_final: 0.7965 (pp) REVERT: D 976 MET cc_start: 0.8454 (mpp) cc_final: 0.7710 (tpp) REVERT: D 982 MET cc_start: 0.8422 (tpp) cc_final: 0.8105 (tpp) REVERT: D 1165 ARG cc_start: 0.7754 (mtm-85) cc_final: 0.7447 (ttm-80) REVERT: D 1232 ARG cc_start: 0.9030 (mtm110) cc_final: 0.8604 (mtm110) REVERT: D 1236 ASP cc_start: 0.9066 (t0) cc_final: 0.8739 (m-30) REVERT: D 1254 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7674 (mm) REVERT: E 97 HIS cc_start: 0.8318 (t-90) cc_final: 0.7856 (t-170) REVERT: F 190 ARG cc_start: 0.8791 (mtm180) cc_final: 0.8514 (mtm-85) REVERT: F 192 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8078 (pt0) REVERT: F 196 TYR cc_start: 0.8690 (t80) cc_final: 0.7749 (t80) REVERT: F 219 MET cc_start: 0.9081 (ptp) cc_final: 0.8812 (ptp) REVERT: F 221 TRP cc_start: 0.8686 (t-100) cc_final: 0.8434 (t-100) REVERT: F 268 ARG cc_start: 0.9013 (tpp80) cc_final: 0.8573 (ttm-80) REVERT: F 297 MET cc_start: 0.8453 (ppp) cc_final: 0.8224 (ppp) REVERT: F 310 MET cc_start: 0.8718 (tpp) cc_final: 0.7883 (tpp) REVERT: F 462 ARG cc_start: 0.7963 (ptp-170) cc_final: 0.7622 (mtt90) REVERT: J 94 LEU cc_start: 0.8880 (mp) cc_final: 0.8526 (pp) REVERT: J 98 LEU cc_start: 0.8809 (mt) cc_final: 0.8403 (mt) outliers start: 82 outliers final: 63 residues processed: 547 average time/residue: 0.4332 time to fit residues: 361.1024 Evaluate side-chains 567 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 492 time to evaluate : 2.980 ------------------------------------------------------------------------------- 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 131 LYS Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 226 THR 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 523 THR 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 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 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 C residue 1122 LEU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 92 MET 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 235 ILE Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 423 ASP 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 619 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 859 LEU Chi-restraints excluded: chain D residue 871 TYR Chi-restraints excluded: chain D residue 959 VAL Chi-restraints excluded: chain D residue 963 SER 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 D residue 1254 ILE Chi-restraints excluded: chain D residue 1265 ILE Chi-restraints excluded: chain E residue 53 TYR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 212 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 205 optimal weight: 3.9990 chunk 179 optimal weight: 7.9990 chunk 64 optimal weight: 0.0040 chunk 59 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 300 optimal weight: 6.9990 chunk 314 optimal weight: 8.9990 chunk 307 optimal weight: 0.9990 chunk 234 optimal weight: 0.0870 overall best weight: 0.5972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 742 HIS ** C 918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1132 GLN ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 454 HIS ** 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 = 0.3923 r_free = 0.3923 target = 0.122191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.085532 restraints weight = 75619.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.088668 restraints weight = 42353.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.090747 restraints weight = 29089.992| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.5622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28260 Z= 0.137 Angle : 0.764 14.945 38614 Z= 0.378 Chirality : 0.045 0.402 4390 Planarity : 0.005 0.107 4789 Dihedral : 14.793 158.278 4567 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.78 % Allowed : 24.19 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.15), residues: 3305 helix: 0.43 (0.15), residues: 1231 sheet: -0.47 (0.26), residues: 395 loop : -0.25 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP F 288 HIS 0.005 0.001 HIS D 505 PHE 0.044 0.002 PHE D 226 TYR 0.037 0.002 TYR D 248 ARG 0.025 0.001 ARG J 101 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 1154) hydrogen bonds : angle 4.85465 ( 3162) metal coordination : bond 0.00502 ( 8) metal coordination : angle 2.81200 ( 12) covalent geometry : bond 0.00308 (28252) covalent geometry : angle 0.76239 (38602) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11370.14 seconds wall clock time: 198 minutes 6.70 seconds (11886.70 seconds total)