Starting phenix.real_space_refine on Mon Jun 23 15:51:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r6r_18959/06_2025/8r6r_18959.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r6r_18959/06_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_18959/06_2025/8r6r_18959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r6r_18959/06_2025/8r6r_18959.map" model { file = "/net/cci-nas-00/data/ceres_data/8r6r_18959/06_2025/8r6r_18959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r6r_18959/06_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 16.22, per 1000 atoms: 0.59 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: 7.05 Conformation dependent library (CDL) restraints added in 3.4 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: 10.43 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: 13.51 Time building geometry restraints manager: 8.15 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: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.190 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 77.890 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.450 ------------------------------------------------------------------------------- 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 : 3.055 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: 0.4703 time to fit residues: 630.6304 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 : 3.241 ------------------------------------------------------------------------------- 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 = 52)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.085644 restraints weight = 74350.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.088659 restraints weight = 42215.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.090660 restraints weight = 29146.997| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 : 11.77 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 5.17784 ( 3162) metal coordination : bond 0.01610 ( 8) metal coordination : angle 3.75211 ( 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 : 3.255 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: 0.8320 (p90) cc_final: 0.8089 (p90) REVERT: A 81 LYS cc_start: 0.9010 (mmtp) cc_final: 0.8711 (mmmt) REVERT: A 99 LYS cc_start: 0.8534 (tptt) cc_final: 0.8214 (tptt) REVERT: A 125 ILE cc_start: 0.9379 (mt) cc_final: 0.9087 (mm) REVERT: A 191 LYS cc_start: 0.7847 (ptpp) cc_final: 0.7594 (ptpp) REVERT: B 17 ASN cc_start: 0.8889 (m-40) cc_final: 0.8632 (m-40) REVERT: B 43 LEU cc_start: 0.8947 (tt) cc_final: 0.8674 (tp) REVERT: B 123 MET cc_start: 0.7870 (tmm) cc_final: 0.7666 (tmm) REVERT: B 128 LEU cc_start: 0.8016 (tp) cc_final: 0.7611 (tp) REVERT: B 131 LYS cc_start: 0.9006 (mmmt) cc_final: 0.8748 (mmmt) REVERT: B 173 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8646 (pptt) REVERT: B 179 GLU cc_start: 0.7580 (mp0) cc_final: 0.7165 (mp0) REVERT: B 191 LYS cc_start: 0.8575 (ptmm) cc_final: 0.7947 (ptmm) REVERT: B 199 LYS cc_start: 0.8439 (mttt) cc_final: 0.8115 (mttp) REVERT: B 226 ASN cc_start: 0.8743 (t0) cc_final: 0.8533 (t0) REVERT: C 72 ASN cc_start: 0.8349 (p0) cc_final: 0.7930 (p0) REVERT: C 151 MET cc_start: 0.7389 (ttm) cc_final: 0.6705 (mtm) REVERT: C 163 GLU cc_start: 0.8383 (tt0) cc_final: 0.8111 (tt0) REVERT: C 304 ARG cc_start: 0.9003 (tpp-160) cc_final: 0.8553 (tpp80) REVERT: C 374 GLU cc_start: 0.8239 (mp0) cc_final: 0.7995 (tp30) REVERT: C 394 ARG cc_start: 0.8885 (ttm170) cc_final: 0.8549 (ptm160) REVERT: C 412 ARG cc_start: 0.8034 (tpp-160) cc_final: 0.7759 (tpm170) REVERT: C 481 GLU cc_start: 0.7904 (pm20) cc_final: 0.7457 (mp0) REVERT: C 548 ASP cc_start: 0.8134 (p0) cc_final: 0.7744 (p0) REVERT: C 664 ARG cc_start: 0.8341 (mtp-110) cc_final: 0.8124 (mtp-110) REVERT: C 704 MET cc_start: 0.8166 (tpp) cc_final: 0.7883 (mpp) REVERT: C 724 ASP cc_start: 0.7510 (t0) cc_final: 0.7111 (t0) REVERT: C 811 LEU cc_start: 0.9051 (mt) cc_final: 0.8832 (mt) REVERT: C 813 ARG cc_start: 0.8566 (mmm160) cc_final: 0.8228 (mtp180) REVERT: C 1110 GLU cc_start: 0.7900 (tp30) cc_final: 0.7400 (tp30) REVERT: D 27 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7417 (pp20) REVERT: D 43 LYS cc_start: 0.8354 (tppt) cc_final: 0.7785 (tppt) REVERT: D 86 LYS cc_start: 0.8929 (pttm) cc_final: 0.8435 (pttm) REVERT: D 134 TYR cc_start: 0.8186 (m-10) cc_final: 0.7038 (m-10) REVERT: D 158 GLU cc_start: 0.9301 (tp30) cc_final: 0.8972 (tm-30) REVERT: D 226 PHE cc_start: 0.6429 (m-80) cc_final: 0.6053 (m-80) REVERT: D 233 GLN cc_start: 0.7687 (tm-30) cc_final: 0.7454 (tm-30) REVERT: D 235 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7612 (mp) REVERT: D 247 ARG cc_start: 0.7126 (mtm110) cc_final: 0.6902 (mtm110) REVERT: D 312 MET cc_start: 0.8164 (ptp) cc_final: 0.7803 (ptp) REVERT: D 457 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8398 (mtt) REVERT: D 469 ILE cc_start: 0.9281 (mm) cc_final: 0.9067 (mm) REVERT: D 493 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6365 (pt0) REVERT: D 518 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7427 (mm-30) REVERT: D 552 GLN cc_start: 0.8763 (mt0) cc_final: 0.8384 (mp10) REVERT: D 634 LYS cc_start: 0.9055 (ttmt) cc_final: 0.8792 (tptt) REVERT: D 685 GLU cc_start: 0.7868 (tp30) cc_final: 0.7610 (tp30) REVERT: D 741 LYS cc_start: 0.9366 (pptt) cc_final: 0.8850 (mmmt) REVERT: D 742 GLN cc_start: 0.8383 (mp10) cc_final: 0.7767 (pm20) REVERT: D 841 GLU cc_start: 0.8305 (tt0) cc_final: 0.7978 (tm-30) REVERT: D 859 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8996 (mm) REVERT: D 864 LEU cc_start: 0.9062 (mt) cc_final: 0.8790 (pp) REVERT: D 941 HIS cc_start: 0.7266 (t-170) cc_final: 0.7002 (t-170) REVERT: D 980 ARG cc_start: 0.8154 (ptm160) cc_final: 0.7870 (ptm160) REVERT: D 1236 ASP cc_start: 0.8995 (t0) cc_final: 0.8692 (m-30) REVERT: E 65 TYR cc_start: 0.7921 (m-80) cc_final: 0.7717 (m-80) REVERT: E 87 LYS cc_start: 0.8316 (mmtp) cc_final: 0.8052 (mptt) REVERT: E 94 ARG cc_start: 0.8021 (ttt-90) cc_final: 0.7649 (ttt180) REVERT: E 95 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7983 (tm-30) REVERT: F 192 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8358 (pt0) REVERT: F 196 TYR cc_start: 0.8729 (t80) cc_final: 0.8350 (t80) REVERT: F 221 TRP cc_start: 0.8755 (t-100) cc_final: 0.8533 (t-100) REVERT: F 268 ARG cc_start: 0.8888 (tpp80) cc_final: 0.8302 (tpt-90) REVERT: F 310 MET cc_start: 0.8759 (tpp) cc_final: 0.8277 (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: 0.9244 (tt) REVERT: J 101 ARG cc_start: 0.8674 (mmm160) cc_final: 0.8437 (mmm160) outliers start: 75 outliers final: 42 residues processed: 639 average time/residue: 0.4580 time to fit residues: 440.0853 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 : 2.908 ------------------------------------------------------------------------------- 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: 10.0000 chunk 151 optimal weight: 5.9990 chunk 289 optimal weight: 9.9990 chunk 186 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 139 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3902 r_free = 0.3902 target = 0.121071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.084395 restraints weight = 74773.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.087402 restraints weight = 42447.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.089392 restraints weight = 29423.522| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 28260 Z= 0.220 Angle : 0.689 9.365 38614 Z= 0.360 Chirality : 0.045 0.236 4390 Planarity : 0.005 0.086 4789 Dihedral : 14.712 160.024 4567 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.14 % Allowed : 16.66 % Favored : 80.20 % 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: -0.23 (0.14), residues: 3305 helix: 0.42 (0.15), residues: 1227 sheet: -0.71 (0.25), residues: 411 loop : -0.32 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 288 HIS 0.017 0.002 HIS B 231 PHE 0.017 0.002 PHE D 226 TYR 0.039 0.002 TYR E 53 ARG 0.027 0.001 ARG D 69 Details of bonding type rmsd hydrogen bonds : bond 0.04458 ( 1154) hydrogen bonds : angle 5.00961 ( 3162) metal coordination : bond 0.01549 ( 8) metal coordination : angle 3.99285 ( 12) covalent geometry : bond 0.00483 (28252) covalent geometry : angle 0.68571 (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 646 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 558 time to evaluate : 2.862 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 123 MET cc_start: 0.8324 (tmm) cc_final: 0.7931 (ttp) REVERT: A 124 HIS cc_start: 0.8543 (t-90) cc_final: 0.8119 (t-90) REVERT: A 177 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7516 (ptmm) REVERT: B 95 MET cc_start: 0.3557 (mmm) cc_final: 0.2961 (tpt) REVERT: B 123 MET cc_start: 0.7945 (tmm) cc_final: 0.7721 (tmm) REVERT: B 128 LEU cc_start: 0.8130 (tp) cc_final: 0.7648 (tp) REVERT: B 173 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8580 (pptt) REVERT: B 179 GLU cc_start: 0.7701 (mp0) cc_final: 0.7302 (mp0) REVERT: B 191 LYS cc_start: 0.8502 (ptmm) cc_final: 0.7960 (ptmm) REVERT: B 199 LYS cc_start: 0.8291 (mttt) cc_final: 0.8050 (mttt) REVERT: B 226 ASN cc_start: 0.8784 (t0) cc_final: 0.8565 (t0) REVERT: C 107 LYS cc_start: 0.8778 (mtmt) cc_final: 0.8429 (ptpp) REVERT: C 304 ARG cc_start: 0.9021 (tpp-160) cc_final: 0.8519 (tpp80) REVERT: C 374 GLU cc_start: 0.8211 (mp0) cc_final: 0.7959 (tp30) REVERT: C 481 GLU cc_start: 0.7936 (pm20) cc_final: 0.7722 (pm20) REVERT: C 548 ASP cc_start: 0.8208 (p0) cc_final: 0.7737 (p0) REVERT: C 619 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8298 (p) REVERT: C 715 MET cc_start: 0.8904 (ptm) cc_final: 0.8638 (ptm) REVERT: C 724 ASP cc_start: 0.7707 (t0) cc_final: 0.7197 (t0) REVERT: C 774 ASP cc_start: 0.7768 (t0) cc_final: 0.7563 (t0) REVERT: C 811 LEU cc_start: 0.8962 (mt) cc_final: 0.8757 (mt) REVERT: C 950 LEU cc_start: 0.9207 (mt) cc_final: 0.8759 (mp) REVERT: C 1110 GLU cc_start: 0.7980 (tp30) cc_final: 0.7615 (tp30) REVERT: D 27 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7456 (pp20) REVERT: D 43 LYS cc_start: 0.8394 (tppt) cc_final: 0.7784 (tppt) REVERT: D 81 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7926 (tm-30) REVERT: D 84 ARG cc_start: 0.8531 (tpt170) cc_final: 0.8329 (tpt90) REVERT: D 90 GLU cc_start: 0.8356 (pt0) cc_final: 0.8134 (pt0) REVERT: D 134 TYR cc_start: 0.7938 (m-10) cc_final: 0.7458 (m-10) REVERT: D 143 MET cc_start: 0.8373 (mtm) cc_final: 0.7929 (ptp) REVERT: D 145 HIS cc_start: 0.7665 (p90) cc_final: 0.7445 (p90) REVERT: D 158 GLU cc_start: 0.9342 (tp30) cc_final: 0.8939 (tm-30) REVERT: D 233 GLN cc_start: 0.7817 (tm-30) cc_final: 0.7439 (tm-30) REVERT: D 235 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7599 (mp) REVERT: D 256 MET cc_start: 0.6019 (OUTLIER) cc_final: 0.5334 (ttm) REVERT: D 356 ARG cc_start: 0.8636 (mmp80) cc_final: 0.8371 (mmp80) REVERT: D 373 MET cc_start: 0.6950 (mtm) cc_final: 0.6630 (mtt) REVERT: D 457 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8431 (mtt) REVERT: D 518 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7446 (mm-30) REVERT: D 530 GLU cc_start: 0.8392 (tt0) cc_final: 0.8151 (tt0) REVERT: D 541 MET cc_start: 0.8522 (tpp) cc_final: 0.8181 (mmm) REVERT: D 552 GLN cc_start: 0.8709 (mt0) cc_final: 0.8297 (mp10) REVERT: D 634 LYS cc_start: 0.9107 (ttmt) cc_final: 0.8615 (mmmt) REVERT: D 717 ASP cc_start: 0.8587 (m-30) cc_final: 0.8309 (m-30) REVERT: D 741 LYS cc_start: 0.9357 (pptt) cc_final: 0.8818 (mmmt) REVERT: D 742 GLN cc_start: 0.8424 (mp10) cc_final: 0.7841 (pm20) REVERT: D 841 GLU cc_start: 0.8332 (tt0) cc_final: 0.7958 (tm-30) REVERT: D 859 LEU cc_start: 0.9341 (mm) cc_final: 0.9057 (mm) REVERT: D 980 ARG cc_start: 0.8100 (ptm160) cc_final: 0.7826 (ptm160) REVERT: D 1232 ARG cc_start: 0.8980 (mtm110) cc_final: 0.8543 (mtm110) REVERT: D 1236 ASP cc_start: 0.9007 (t0) cc_final: 0.8685 (m-30) REVERT: E 94 ARG cc_start: 0.8065 (ttt-90) cc_final: 0.7708 (ttt180) REVERT: E 97 HIS cc_start: 0.8681 (t-90) cc_final: 0.8129 (t-170) REVERT: F 192 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8236 (pt0) REVERT: F 196 TYR cc_start: 0.8723 (t80) cc_final: 0.8179 (t80) REVERT: F 219 MET cc_start: 0.9194 (ptp) cc_final: 0.8897 (ptp) REVERT: F 221 TRP cc_start: 0.8625 (t-100) cc_final: 0.8382 (t-100) REVERT: F 231 ASN cc_start: 0.8657 (m110) cc_final: 0.8436 (p0) REVERT: F 261 GLU cc_start: 0.8231 (tp30) cc_final: 0.7897 (tp30) REVERT: F 268 ARG cc_start: 0.8922 (tpp80) cc_final: 0.8618 (tpp80) REVERT: F 279 TYR cc_start: 0.7042 (m-80) cc_final: 0.6494 (m-80) REVERT: F 310 MET cc_start: 0.8745 (tpp) cc_final: 0.8304 (tpp) REVERT: F 391 PHE cc_start: 0.8841 (t80) cc_final: 0.8446 (t80) REVERT: F 393 LEU cc_start: 0.9560 (mt) cc_final: 0.9223 (tt) REVERT: J 101 ARG cc_start: 0.8675 (mmm160) cc_final: 0.8442 (mmm160) outliers start: 88 outliers final: 51 residues processed: 603 average time/residue: 0.4588 time to fit residues: 420.4756 Evaluate side-chains 584 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 526 time to evaluate : 3.562 ------------------------------------------------------------------------------- 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 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 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 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 524 LEU Chi-restraints excluded: chain D residue 560 LEU 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 737 VAL 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 115 optimal weight: 1.9990 chunk 219 optimal weight: 0.4980 chunk 212 optimal weight: 4.9990 chunk 304 optimal weight: 2.9990 chunk 276 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 134 optimal weight: 0.0570 chunk 113 optimal weight: 0.7980 chunk 76 optimal weight: 9.9990 overall best weight: 1.2702 ------------------------------------------------------------------------------- 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 609 GLN ** D 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 853 HIS D 881 GLN ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.122687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.085836 restraints weight = 75329.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.088919 restraints weight = 42971.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.090947 restraints weight = 29734.582| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28260 Z= 0.148 Angle : 0.663 13.889 38614 Z= 0.340 Chirality : 0.044 0.218 4390 Planarity : 0.005 0.081 4789 Dihedral : 14.691 159.924 4567 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.43 % Allowed : 18.55 % Favored : 79.02 % 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: -0.13 (0.14), residues: 3305 helix: 0.52 (0.15), residues: 1221 sheet: -0.62 (0.25), residues: 407 loop : -0.29 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 288 HIS 0.013 0.001 HIS D 941 PHE 0.044 0.002 PHE D 226 TYR 0.043 0.002 TYR D 248 ARG 0.012 0.001 ARG F 216 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 1154) hydrogen bonds : angle 4.84697 ( 3162) metal coordination : bond 0.00943 ( 8) metal coordination : angle 3.41034 ( 12) covalent geometry : bond 0.00325 (28252) covalent geometry : angle 0.66035 (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 611 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 543 time to evaluate : 2.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 LYS cc_start: 0.8820 (ttpp) cc_final: 0.8316 (ptpp) REVERT: B 1 MET cc_start: 0.6541 (pmm) cc_final: 0.6094 (pmm) REVERT: B 43 LEU cc_start: 0.8921 (tt) cc_final: 0.8523 (tp) REVERT: B 95 MET cc_start: 0.3495 (mmm) cc_final: 0.2945 (tpt) REVERT: B 123 MET cc_start: 0.7995 (tmm) cc_final: 0.7786 (tmm) REVERT: B 128 LEU cc_start: 0.8228 (tp) cc_final: 0.7687 (tp) REVERT: B 173 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8646 (pptt) REVERT: B 179 GLU cc_start: 0.7863 (mp0) cc_final: 0.7437 (mp0) REVERT: B 191 LYS cc_start: 0.8586 (ptmm) cc_final: 0.8092 (ptmm) REVERT: B 225 LEU cc_start: 0.9101 (mm) cc_final: 0.8674 (mp) REVERT: B 226 ASN cc_start: 0.8759 (t0) cc_final: 0.8457 (t0) REVERT: C 62 ARG cc_start: 0.9089 (mtt90) cc_final: 0.8599 (mtp85) REVERT: C 107 LYS cc_start: 0.8758 (mtmt) cc_final: 0.8393 (ptpp) REVERT: C 250 MET cc_start: 0.8860 (mmt) cc_final: 0.8551 (mmp) REVERT: C 304 ARG cc_start: 0.8977 (tpp-160) cc_final: 0.8747 (tpp-160) REVERT: C 374 GLU cc_start: 0.8189 (mp0) cc_final: 0.7939 (tp30) REVERT: C 594 ASN cc_start: 0.9071 (OUTLIER) cc_final: 0.8825 (p0) REVERT: C 613 GLU cc_start: 0.7665 (tp30) cc_final: 0.7450 (tp30) REVERT: C 619 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.7957 (p) REVERT: C 652 MET cc_start: 0.9014 (tpp) cc_final: 0.8782 (tpp) REVERT: C 703 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7422 (mp0) REVERT: C 715 MET cc_start: 0.8825 (ptm) cc_final: 0.8580 (ptm) REVERT: C 724 ASP cc_start: 0.7718 (t0) cc_final: 0.7046 (t0) REVERT: C 734 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7624 (mt-10) REVERT: C 774 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7485 (t0) REVERT: C 788 ARG cc_start: 0.7349 (mmp80) cc_final: 0.7041 (mmp80) REVERT: C 791 ASP cc_start: 0.8023 (m-30) cc_final: 0.7724 (p0) REVERT: C 950 LEU cc_start: 0.9224 (mt) cc_final: 0.8812 (mp) REVERT: C 1008 GLU cc_start: 0.8411 (mp0) cc_final: 0.8051 (mp0) REVERT: C 1110 GLU cc_start: 0.8136 (tp30) cc_final: 0.7714 (tp30) REVERT: D 27 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7365 (pp20) REVERT: D 43 LYS cc_start: 0.8420 (tppt) cc_final: 0.7724 (tppt) REVERT: D 58 TRP cc_start: 0.8132 (m100) cc_final: 0.7882 (m100) REVERT: D 81 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7826 (tm-30) REVERT: D 134 TYR cc_start: 0.7852 (m-10) cc_final: 0.7449 (m-10) REVERT: D 158 GLU cc_start: 0.9330 (tp30) cc_final: 0.8953 (tm-30) REVERT: D 247 ARG cc_start: 0.7378 (ptp-170) cc_final: 0.7105 (mtm180) REVERT: D 256 MET cc_start: 0.6095 (OUTLIER) cc_final: 0.5748 (ttm) REVERT: D 356 ARG cc_start: 0.8618 (mmp80) cc_final: 0.8321 (mmp80) REVERT: D 373 MET cc_start: 0.6733 (mtm) cc_final: 0.6473 (mtt) REVERT: D 423 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8171 (t70) REVERT: D 424 TYR cc_start: 0.8801 (m-80) cc_final: 0.8560 (m-80) REVERT: D 457 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8148 (mmm) REVERT: D 474 ARG cc_start: 0.7350 (tpt90) cc_final: 0.6753 (tpt90) REVERT: D 518 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7286 (mm-30) REVERT: D 541 MET cc_start: 0.8523 (tpp) cc_final: 0.8108 (mmm) REVERT: D 552 GLN cc_start: 0.8677 (mt0) cc_final: 0.8254 (mp10) REVERT: D 634 LYS cc_start: 0.9069 (ttmt) cc_final: 0.8718 (tppt) REVERT: D 717 ASP cc_start: 0.8539 (m-30) cc_final: 0.8268 (m-30) REVERT: D 741 LYS cc_start: 0.9319 (pptt) cc_final: 0.8802 (mmmt) REVERT: D 742 GLN cc_start: 0.8406 (mp10) cc_final: 0.7867 (pm20) REVERT: D 841 GLU cc_start: 0.8318 (tt0) cc_final: 0.7971 (tm-30) REVERT: D 868 ASP cc_start: 0.7982 (t0) cc_final: 0.7538 (p0) REVERT: D 941 HIS cc_start: 0.7457 (t-170) cc_final: 0.7234 (t-170) REVERT: D 1232 ARG cc_start: 0.8970 (mtm110) cc_final: 0.8501 (mtm110) REVERT: D 1236 ASP cc_start: 0.9023 (t0) cc_final: 0.8703 (m-30) REVERT: E 94 ARG cc_start: 0.8093 (ttt-90) cc_final: 0.7760 (ttt-90) REVERT: E 97 HIS cc_start: 0.8567 (t-90) cc_final: 0.8111 (t-170) REVERT: F 192 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8186 (pt0) REVERT: F 196 TYR cc_start: 0.8684 (t80) cc_final: 0.8208 (t80) REVERT: F 219 MET cc_start: 0.9163 (ptp) cc_final: 0.8913 (ptp) REVERT: F 221 TRP cc_start: 0.8586 (t-100) cc_final: 0.8317 (t-100) REVERT: F 231 ASN cc_start: 0.8613 (m110) cc_final: 0.8390 (p0) REVERT: F 261 GLU cc_start: 0.8192 (tp30) cc_final: 0.7914 (tp30) REVERT: F 268 ARG cc_start: 0.8979 (tpp80) cc_final: 0.8649 (tpp80) REVERT: F 279 TYR cc_start: 0.6974 (m-80) cc_final: 0.6462 (m-80) REVERT: F 310 MET cc_start: 0.8645 (tpp) cc_final: 0.8290 (tpp) REVERT: F 391 PHE cc_start: 0.8849 (t80) cc_final: 0.8449 (t80) REVERT: F 393 LEU cc_start: 0.9574 (mt) cc_final: 0.9239 (tt) REVERT: J 101 ARG cc_start: 0.8715 (mmm160) cc_final: 0.8484 (mmm160) outliers start: 68 outliers final: 44 residues processed: 577 average time/residue: 0.4597 time to fit residues: 400.8245 Evaluate side-chains 562 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 510 time to evaluate : 3.104 ------------------------------------------------------------------------------- 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 61 HIS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 594 ASN Chi-restraints excluded: chain C residue 619 THR Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 648 TYR Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 774 ASP Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain C residue 859 LEU Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 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 248 TYR Chi-restraints excluded: chain D residue 256 MET 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 676 LEU Chi-restraints excluded: chain D residue 713 ASP Chi-restraints excluded: chain D residue 732 MET Chi-restraints excluded: chain D residue 823 VAL 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 1216 LEU Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1247 ASN Chi-restraints excluded: chain D residue 1265 ILE 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: 0.0970 chunk 212 optimal weight: 0.9980 chunk 284 optimal weight: 7.9990 chunk 260 optimal weight: 20.0000 chunk 139 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 277 optimal weight: 9.9990 chunk 132 optimal weight: 0.0980 chunk 248 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 241 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 410 GLN ** D 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1132 GLN ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3932 r_free = 0.3932 target = 0.123058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.086680 restraints weight = 74348.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.089808 restraints weight = 42028.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.091879 restraints weight = 28885.544| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28260 Z= 0.131 Angle : 0.666 10.966 38614 Z= 0.338 Chirality : 0.043 0.288 4390 Planarity : 0.005 0.074 4789 Dihedral : 14.662 159.735 4567 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.75 % Allowed : 19.98 % Favored : 77.27 % 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: -0.09 (0.15), residues: 3305 helix: 0.56 (0.15), residues: 1220 sheet: -0.56 (0.26), residues: 397 loop : -0.29 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 288 HIS 0.008 0.001 HIS A 61 PHE 0.046 0.001 PHE D 226 TYR 0.041 0.002 TYR D 248 ARG 0.013 0.001 ARG D 334 Details of bonding type rmsd hydrogen bonds : bond 0.03823 ( 1154) hydrogen bonds : angle 4.74977 ( 3162) metal coordination : bond 0.00625 ( 8) metal coordination : angle 3.11487 ( 12) covalent geometry : bond 0.00289 (28252) covalent geometry : angle 0.66387 (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 620 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 543 time to evaluate : 3.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.8579 (tptp) cc_final: 0.7690 (tptt) REVERT: A 123 MET cc_start: 0.8260 (tmm) cc_final: 0.7826 (ttp) REVERT: A 191 LYS cc_start: 0.8831 (ttpp) cc_final: 0.8349 (ptpp) REVERT: B 1 MET cc_start: 0.6517 (pmm) cc_final: 0.6313 (pmm) REVERT: B 43 LEU cc_start: 0.8944 (tt) cc_final: 0.8516 (tp) REVERT: B 95 MET cc_start: 0.3243 (mmm) cc_final: 0.2804 (tpt) REVERT: B 98 ARG cc_start: 0.7900 (tpt170) cc_final: 0.7649 (tpm170) REVERT: B 123 MET cc_start: 0.8033 (tmm) cc_final: 0.7713 (tmm) REVERT: B 128 LEU cc_start: 0.8241 (tp) cc_final: 0.7705 (tp) REVERT: B 173 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8643 (pptt) REVERT: B 179 GLU cc_start: 0.7908 (mp0) cc_final: 0.7441 (mp0) REVERT: B 191 LYS cc_start: 0.8635 (ptmm) cc_final: 0.8106 (ptmm) REVERT: B 225 LEU cc_start: 0.9079 (mm) cc_final: 0.8667 (mp) REVERT: B 226 ASN cc_start: 0.8798 (t0) cc_final: 0.8491 (t0) REVERT: C 62 ARG cc_start: 0.9096 (mtt90) cc_final: 0.8587 (mtp85) REVERT: C 107 LYS cc_start: 0.8775 (mtmt) cc_final: 0.8400 (ptpp) REVERT: C 346 MET cc_start: 0.7907 (tmm) cc_final: 0.7354 (tpt) REVERT: C 374 GLU cc_start: 0.8199 (mp0) cc_final: 0.7934 (tp30) REVERT: C 530 HIS cc_start: 0.8497 (m-70) cc_final: 0.8063 (m-70) REVERT: C 548 ASP cc_start: 0.8249 (p0) cc_final: 0.7733 (p0) REVERT: C 571 ASP cc_start: 0.8151 (m-30) cc_final: 0.7797 (m-30) REVERT: C 594 ASN cc_start: 0.9086 (OUTLIER) cc_final: 0.8654 (p0) REVERT: C 602 MET cc_start: 0.8705 (mtm) cc_final: 0.8489 (mtm) REVERT: C 619 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8142 (p) REVERT: C 703 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7287 (mp0) REVERT: C 715 MET cc_start: 0.8803 (ptm) cc_final: 0.8542 (ptm) REVERT: C 724 ASP cc_start: 0.7524 (t0) cc_final: 0.7070 (t0) REVERT: C 734 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7825 (mp0) REVERT: C 774 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7404 (t0) REVERT: C 791 ASP cc_start: 0.7980 (m-30) cc_final: 0.7753 (p0) REVERT: C 813 ARG cc_start: 0.8600 (mmm160) cc_final: 0.8244 (mtp180) REVERT: C 867 LYS cc_start: 0.8903 (mtpp) cc_final: 0.8625 (tttp) REVERT: C 915 ARG cc_start: 0.7911 (tmm-80) cc_final: 0.7662 (tmm-80) REVERT: C 1008 GLU cc_start: 0.8442 (mp0) cc_final: 0.8085 (mp0) REVERT: C 1110 GLU cc_start: 0.8114 (tp30) cc_final: 0.7743 (tp30) REVERT: D 27 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7214 (pp20) REVERT: D 43 LYS cc_start: 0.8432 (tppt) cc_final: 0.7708 (tppt) REVERT: D 134 TYR cc_start: 0.7958 (m-10) cc_final: 0.7506 (m-10) REVERT: D 143 MET cc_start: 0.8284 (mtm) cc_final: 0.7764 (ptp) REVERT: D 158 GLU cc_start: 0.9309 (tp30) cc_final: 0.8957 (tm-30) REVERT: D 233 GLN cc_start: 0.7877 (tm-30) cc_final: 0.7467 (tm-30) REVERT: D 235 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7644 (mp) REVERT: D 247 ARG cc_start: 0.7441 (ptp-170) cc_final: 0.7033 (mtm180) REVERT: D 256 MET cc_start: 0.6423 (OUTLIER) cc_final: 0.5625 (ttm) REVERT: D 334 ARG cc_start: 0.7864 (mmm160) cc_final: 0.7521 (tpt90) REVERT: D 356 ARG cc_start: 0.8621 (mmp80) cc_final: 0.8320 (mmp80) REVERT: D 373 MET cc_start: 0.6629 (mtm) cc_final: 0.6405 (mtt) REVERT: D 383 ASP cc_start: 0.8880 (t0) cc_final: 0.8315 (p0) REVERT: D 423 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8101 (t70) REVERT: D 424 TYR cc_start: 0.8737 (m-80) cc_final: 0.8456 (m-80) REVERT: D 457 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8382 (tpp) REVERT: D 474 ARG cc_start: 0.7363 (tpt90) cc_final: 0.6830 (tpt170) REVERT: D 541 MET cc_start: 0.8544 (tpp) cc_final: 0.8160 (mmm) REVERT: D 552 GLN cc_start: 0.8680 (mt0) cc_final: 0.8281 (mp10) REVERT: D 634 LYS cc_start: 0.9060 (ttmt) cc_final: 0.8720 (tppt) REVERT: D 717 ASP cc_start: 0.8538 (m-30) cc_final: 0.8264 (m-30) REVERT: D 741 LYS cc_start: 0.9307 (pptt) cc_final: 0.8804 (mmmt) REVERT: D 742 GLN cc_start: 0.8378 (mp10) cc_final: 0.7870 (pm20) REVERT: D 841 GLU cc_start: 0.8267 (tt0) cc_final: 0.7939 (tm-30) REVERT: D 868 ASP cc_start: 0.7964 (t0) cc_final: 0.7496 (p0) REVERT: D 941 HIS cc_start: 0.7436 (t-170) cc_final: 0.7184 (t-170) REVERT: D 1132 GLN cc_start: 0.9364 (OUTLIER) cc_final: 0.8958 (mp10) REVERT: E 94 ARG cc_start: 0.8154 (ttt-90) cc_final: 0.7822 (ttt180) REVERT: E 97 HIS cc_start: 0.8519 (t-90) cc_final: 0.8073 (t-170) REVERT: F 159 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7642 (mt) REVERT: F 192 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8101 (pt0) REVERT: F 196 TYR cc_start: 0.8658 (t80) cc_final: 0.8131 (t80) REVERT: F 219 MET cc_start: 0.9105 (ptp) cc_final: 0.8850 (ptt) REVERT: F 221 TRP cc_start: 0.8610 (t-100) cc_final: 0.8331 (t-100) REVERT: F 261 GLU cc_start: 0.8167 (tp30) cc_final: 0.7844 (tp30) REVERT: F 268 ARG cc_start: 0.8980 (tpp80) cc_final: 0.8705 (tpp80) REVERT: F 310 MET cc_start: 0.8624 (tpp) cc_final: 0.8201 (tpp) REVERT: F 356 ARG cc_start: 0.8178 (mmp80) cc_final: 0.7893 (ptm-80) REVERT: F 391 PHE cc_start: 0.8869 (t80) cc_final: 0.8414 (t80) outliers start: 77 outliers final: 45 residues processed: 585 average time/residue: 0.6275 time to fit residues: 570.8156 Evaluate side-chains 563 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 507 time to evaluate : 3.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR 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 106 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 594 ASN Chi-restraints excluded: chain C residue 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 774 ASP Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1043 ILE Chi-restraints excluded: chain C residue 1080 LEU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 159 LYS 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 244 LEU Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 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 613 SER Chi-restraints excluded: chain D residue 713 ASP 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 963 SER Chi-restraints excluded: chain D residue 1132 GLN Chi-restraints excluded: chain D residue 1169 ILE Chi-restraints excluded: chain D residue 1216 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 159 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: 7.9990 chunk 262 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 214 optimal weight: 10.0000 chunk 321 optimal weight: 8.9990 chunk 280 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 160 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 64 optimal weight: 0.4980 overall best weight: 2.3584 ------------------------------------------------------------------------------- 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** D1132 GLN ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 ASN ** 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 = 0.3901 r_free = 0.3901 target = 0.120784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.083573 restraints weight = 76642.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.086624 restraints weight = 43289.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.088671 restraints weight = 29966.317| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 28260 Z= 0.197 Angle : 0.685 11.580 38614 Z= 0.353 Chirality : 0.043 0.205 4390 Planarity : 0.005 0.076 4789 Dihedral : 14.712 158.899 4567 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.14 % Allowed : 20.69 % Favored : 76.17 % 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: -0.13 (0.15), residues: 3305 helix: 0.50 (0.15), residues: 1223 sheet: -0.62 (0.26), residues: 395 loop : -0.28 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 23 HIS 0.008 0.001 HIS A 61 PHE 0.045 0.002 PHE D 226 TYR 0.039 0.002 TYR E 53 ARG 0.021 0.001 ARG D 56 Details of bonding type rmsd hydrogen bonds : bond 0.04021 ( 1154) hydrogen bonds : angle 4.85056 ( 3162) metal coordination : bond 0.01482 ( 8) metal coordination : angle 3.41490 ( 12) covalent geometry : bond 0.00436 (28252) covalent geometry : angle 0.68279 (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 595 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 507 time to evaluate : 2.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8323 (tmm) cc_final: 0.8115 (tmm) REVERT: A 191 LYS cc_start: 0.8880 (ttpp) cc_final: 0.8313 (ptpp) REVERT: B 1 MET cc_start: 0.6702 (pmm) cc_final: 0.6473 (pmm) REVERT: B 98 ARG cc_start: 0.7834 (tpt170) cc_final: 0.7356 (tpp-160) REVERT: B 173 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8627 (pptt) REVERT: B 179 GLU cc_start: 0.7932 (mp0) cc_final: 0.7465 (mp0) REVERT: B 191 LYS cc_start: 0.8678 (ptmm) cc_final: 0.8146 (ptmm) REVERT: B 226 ASN cc_start: 0.8883 (t0) cc_final: 0.8564 (t0) REVERT: C 62 ARG cc_start: 0.9133 (mtt90) cc_final: 0.8654 (mtp85) REVERT: C 79 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8577 (mm-30) REVERT: C 107 LYS cc_start: 0.8809 (mtmt) cc_final: 0.8417 (ptpp) REVERT: C 172 ARG cc_start: 0.7970 (mmt90) cc_final: 0.7739 (mmt90) REVERT: C 374 GLU cc_start: 0.8225 (mp0) cc_final: 0.7986 (tp30) REVERT: C 529 ARG cc_start: 0.8435 (tpt90) cc_final: 0.8175 (tpt90) REVERT: C 530 HIS cc_start: 0.8528 (m-70) cc_final: 0.8056 (m-70) REVERT: C 594 ASN cc_start: 0.9074 (OUTLIER) cc_final: 0.8641 (p0) REVERT: C 602 MET cc_start: 0.8775 (mtm) cc_final: 0.8570 (mtm) REVERT: C 619 THR cc_start: 0.8659 (OUTLIER) cc_final: 0.8149 (p) REVERT: C 715 MET cc_start: 0.8833 (ptm) cc_final: 0.8530 (ptm) REVERT: C 724 ASP cc_start: 0.7591 (t0) cc_final: 0.7130 (t0) REVERT: C 774 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7515 (t0) REVERT: C 788 ARG cc_start: 0.7340 (mmp80) cc_final: 0.7024 (mmp80) REVERT: C 791 ASP cc_start: 0.8017 (m-30) cc_final: 0.7814 (p0) REVERT: C 813 ARG cc_start: 0.8622 (mmm160) cc_final: 0.8391 (mtp180) REVERT: C 915 ARG cc_start: 0.7925 (tmm-80) cc_final: 0.7600 (tmm-80) REVERT: C 1008 GLU cc_start: 0.8421 (mp0) cc_final: 0.8074 (mp0) REVERT: C 1110 GLU cc_start: 0.8272 (tp30) cc_final: 0.7870 (tp30) REVERT: D 27 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7486 (pp20) REVERT: D 43 LYS cc_start: 0.8429 (tppt) cc_final: 0.7681 (tppt) REVERT: D 44 ASP cc_start: 0.7746 (t0) cc_final: 0.7129 (t0) REVERT: D 134 TYR cc_start: 0.7980 (m-10) cc_final: 0.7515 (m-10) REVERT: D 143 MET cc_start: 0.8346 (mtm) cc_final: 0.7825 (ptp) REVERT: D 158 GLU cc_start: 0.9341 (tp30) cc_final: 0.8989 (tm-30) REVERT: D 233 GLN cc_start: 0.7873 (tm-30) cc_final: 0.7429 (tm-30) REVERT: D 235 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7609 (mp) REVERT: D 247 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.7058 (mtm180) REVERT: D 256 MET cc_start: 0.6490 (OUTLIER) cc_final: 0.6128 (ttm) REVERT: D 356 ARG cc_start: 0.8654 (mmp80) cc_final: 0.8356 (mmp80) REVERT: D 383 ASP cc_start: 0.8957 (t0) cc_final: 0.8359 (p0) REVERT: D 423 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.8120 (t70) REVERT: D 457 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8434 (tpp) REVERT: D 474 ARG cc_start: 0.7449 (tpt90) cc_final: 0.6913 (tpt170) REVERT: D 475 MET cc_start: 0.7520 (ptm) cc_final: 0.7150 (ptp) REVERT: D 518 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7049 (mm-30) REVERT: D 541 MET cc_start: 0.8485 (tpp) cc_final: 0.8198 (mmm) REVERT: D 552 GLN cc_start: 0.8699 (mt0) cc_final: 0.8307 (mp10) REVERT: D 634 LYS cc_start: 0.9107 (ttmt) cc_final: 0.8837 (tptt) REVERT: D 717 ASP cc_start: 0.8569 (m-30) cc_final: 0.8317 (m-30) REVERT: D 741 LYS cc_start: 0.9311 (pptt) cc_final: 0.8822 (mmmt) REVERT: D 742 GLN cc_start: 0.8467 (mp10) cc_final: 0.7998 (pm20) REVERT: D 841 GLU cc_start: 0.8321 (tt0) cc_final: 0.8100 (tm-30) REVERT: D 868 ASP cc_start: 0.7988 (t0) cc_final: 0.7519 (p0) REVERT: D 911 ARG cc_start: 0.8314 (mtp180) cc_final: 0.7949 (ttm170) REVERT: D 941 HIS cc_start: 0.7543 (t-170) cc_final: 0.7286 (t-170) REVERT: D 976 MET cc_start: 0.8403 (mpp) cc_final: 0.7963 (mpp) REVERT: D 1132 GLN cc_start: 0.9473 (OUTLIER) cc_final: 0.9061 (mp10) REVERT: D 1254 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7723 (mm) REVERT: E 94 ARG cc_start: 0.8188 (ttt-90) cc_final: 0.7925 (ttt-90) REVERT: E 97 HIS cc_start: 0.8524 (t-90) cc_final: 0.8094 (t-170) REVERT: F 192 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8133 (pt0) REVERT: F 196 TYR cc_start: 0.8704 (t80) cc_final: 0.8170 (t80) REVERT: F 219 MET cc_start: 0.9100 (ptp) cc_final: 0.8880 (ptt) REVERT: F 221 TRP cc_start: 0.8659 (t-100) cc_final: 0.8382 (t-100) REVERT: F 231 ASN cc_start: 0.8616 (m110) cc_final: 0.8331 (p0) REVERT: F 261 GLU cc_start: 0.8201 (tp30) cc_final: 0.7888 (tp30) REVERT: F 268 ARG cc_start: 0.9015 (tpp80) cc_final: 0.8705 (tpp80) REVERT: F 299 ASP cc_start: 0.9042 (t70) cc_final: 0.8835 (t0) REVERT: F 310 MET cc_start: 0.8700 (tpp) cc_final: 0.8413 (tpp) outliers start: 88 outliers final: 63 residues processed: 555 average time/residue: 0.4367 time to fit residues: 367.4190 Evaluate side-chains 563 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 488 time to evaluate : 3.016 ------------------------------------------------------------------------------- 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 225 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 51 VAL 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 B residue 173 LYS Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 594 ASN Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 619 THR Chi-restraints excluded: chain C residue 648 TYR Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 774 ASP 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 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 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 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 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 822 LEU Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 959 VAL Chi-restraints excluded: chain D residue 1131 VAL Chi-restraints excluded: chain D residue 1132 GLN 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 1230 THR Chi-restraints excluded: chain D residue 1254 ILE Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 270 VAL 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: 0.6980 chunk 332 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 309 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 253 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 256 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** D 692 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.122345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.085139 restraints weight = 75356.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.088271 restraints weight = 42531.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.090354 restraints weight = 29293.680| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28260 Z= 0.133 Angle : 0.696 15.973 38614 Z= 0.349 Chirality : 0.044 0.399 4390 Planarity : 0.005 0.067 4789 Dihedral : 14.691 158.504 4567 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.21 % Allowed : 22.01 % Favored : 74.78 % 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: -0.13 (0.15), residues: 3305 helix: 0.49 (0.15), residues: 1228 sheet: -0.66 (0.25), residues: 417 loop : -0.25 (0.16), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP D 23 HIS 0.005 0.001 HIS A 61 PHE 0.045 0.002 PHE D 226 TYR 0.039 0.002 TYR D 248 ARG 0.016 0.001 ARG D 67 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 1154) hydrogen bonds : angle 4.74366 ( 3162) metal coordination : bond 0.00690 ( 8) metal coordination : angle 3.20948 ( 12) covalent geometry : bond 0.00298 (28252) covalent geometry : angle 0.69383 (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 606 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 516 time to evaluate : 2.863 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: A 99 LYS cc_start: 0.8599 (tptt) cc_final: 0.8155 (tptt) REVERT: A 191 LYS cc_start: 0.8932 (ttpp) cc_final: 0.8406 (pttm) REVERT: B 1 MET cc_start: 0.6691 (pmm) cc_final: 0.6465 (pmm) REVERT: B 179 GLU cc_start: 0.7900 (mp0) cc_final: 0.7417 (mp0) REVERT: B 191 LYS cc_start: 0.8702 (ptmm) cc_final: 0.8094 (ptmm) REVERT: B 226 ASN cc_start: 0.8863 (t0) cc_final: 0.8583 (t0) REVERT: C 62 ARG cc_start: 0.9103 (mtt90) cc_final: 0.8588 (ptp-110) REVERT: C 79 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8539 (mm-30) REVERT: C 107 LYS cc_start: 0.8789 (mtmt) cc_final: 0.8396 (ptpp) REVERT: C 172 ARG cc_start: 0.7926 (mmt90) cc_final: 0.7719 (mmt90) REVERT: C 346 MET cc_start: 0.7703 (tmm) cc_final: 0.7362 (tpt) REVERT: C 374 GLU cc_start: 0.8210 (mp0) cc_final: 0.7953 (tp30) REVERT: C 523 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8590 (p) REVERT: C 529 ARG cc_start: 0.8510 (tpt90) cc_final: 0.8295 (tpt90) REVERT: C 530 HIS cc_start: 0.8518 (m-70) cc_final: 0.8073 (m-70) REVERT: C 548 ASP cc_start: 0.8284 (p0) cc_final: 0.7773 (p0) REVERT: C 571 ASP cc_start: 0.8090 (m-30) cc_final: 0.7795 (m-30) REVERT: C 594 ASN cc_start: 0.9099 (OUTLIER) cc_final: 0.8604 (p0) REVERT: C 602 MET cc_start: 0.8720 (mtm) cc_final: 0.8484 (mtm) REVERT: C 619 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8133 (p) REVERT: C 715 MET cc_start: 0.8761 (ptm) cc_final: 0.8490 (ptm) REVERT: C 724 ASP cc_start: 0.7619 (t0) cc_final: 0.7115 (t0) REVERT: C 734 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7806 (mp0) REVERT: C 788 ARG cc_start: 0.7274 (mmp80) cc_final: 0.7052 (mmp80) REVERT: C 813 ARG cc_start: 0.8630 (mmm160) cc_final: 0.8428 (mtp180) REVERT: C 867 LYS cc_start: 0.8919 (mtpp) cc_final: 0.8668 (tttp) REVERT: C 895 MET cc_start: 0.8811 (mmp) cc_final: 0.8590 (mmp) REVERT: C 915 ARG cc_start: 0.7915 (tmm-80) cc_final: 0.7707 (tmm-80) REVERT: C 1008 GLU cc_start: 0.8446 (mp0) cc_final: 0.8076 (mp0) REVERT: C 1110 GLU cc_start: 0.8260 (tp30) cc_final: 0.7841 (tp30) REVERT: D 23 TRP cc_start: 0.8256 (m-10) cc_final: 0.7182 (m-10) REVERT: D 27 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7411 (pp20) REVERT: D 43 LYS cc_start: 0.8431 (tppt) cc_final: 0.7656 (tppt) REVERT: D 44 ASP cc_start: 0.7666 (t0) cc_final: 0.7069 (t0) REVERT: D 134 TYR cc_start: 0.7983 (m-10) cc_final: 0.7521 (m-10) REVERT: D 143 MET cc_start: 0.8305 (mtm) cc_final: 0.7757 (ptp) REVERT: D 158 GLU cc_start: 0.9342 (tp30) cc_final: 0.8988 (tm-30) REVERT: D 234 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7837 (tt) REVERT: D 235 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7753 (mp) REVERT: D 247 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.7039 (mtm180) REVERT: D 256 MET cc_start: 0.6594 (OUTLIER) cc_final: 0.6239 (ttm) REVERT: D 295 ARG cc_start: 0.8790 (ttm170) cc_final: 0.8379 (ttm110) REVERT: D 356 ARG cc_start: 0.8641 (mmp80) cc_final: 0.8315 (mmp80) REVERT: D 383 ASP cc_start: 0.8914 (t0) cc_final: 0.8340 (p0) REVERT: D 404 ASP cc_start: 0.8882 (t0) cc_final: 0.8406 (t0) REVERT: D 423 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8079 (t70) REVERT: D 457 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8367 (tpp) REVERT: D 474 ARG cc_start: 0.7432 (tpt90) cc_final: 0.6886 (tpt170) REVERT: D 475 MET cc_start: 0.7520 (ptm) cc_final: 0.7140 (ptp) REVERT: D 493 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.6292 (pt0) REVERT: D 518 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7111 (mm-30) REVERT: D 541 MET cc_start: 0.8564 (tpp) cc_final: 0.8288 (mmm) REVERT: D 552 GLN cc_start: 0.8673 (mt0) cc_final: 0.8271 (mp10) REVERT: D 634 LYS cc_start: 0.9070 (ttmt) cc_final: 0.8647 (mmmt) REVERT: D 741 LYS cc_start: 0.9298 (pptt) cc_final: 0.8815 (mmmt) REVERT: D 742 GLN cc_start: 0.8425 (mp10) cc_final: 0.7964 (pm20) REVERT: D 841 GLU cc_start: 0.8331 (tt0) cc_final: 0.7997 (tm-30) REVERT: D 864 LEU cc_start: 0.9226 (pp) cc_final: 0.8517 (pt) REVERT: D 868 ASP cc_start: 0.7978 (t0) cc_final: 0.7486 (p0) REVERT: D 941 HIS cc_start: 0.7507 (t-170) cc_final: 0.7257 (t-170) REVERT: D 951 LEU cc_start: 0.8728 (mt) cc_final: 0.7967 (pp) REVERT: D 976 MET cc_start: 0.8392 (mpp) cc_final: 0.7948 (mpp) REVERT: D 1132 GLN cc_start: 0.9412 (OUTLIER) cc_final: 0.9009 (mp10) REVERT: D 1254 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7708 (mm) REVERT: E 82 PRO cc_start: 0.9000 (Cg_endo) cc_final: 0.8776 (Cg_exo) REVERT: E 97 HIS cc_start: 0.8483 (t-90) cc_final: 0.8043 (t-170) REVERT: F 192 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8049 (pt0) REVERT: F 196 TYR cc_start: 0.8672 (t80) cc_final: 0.8133 (t80) REVERT: F 201 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9097 (mt) REVERT: F 219 MET cc_start: 0.9086 (ptp) cc_final: 0.8821 (ptp) REVERT: F 221 TRP cc_start: 0.8642 (t-100) cc_final: 0.8364 (t-100) REVERT: F 261 GLU cc_start: 0.8184 (tp30) cc_final: 0.7848 (tp30) REVERT: F 268 ARG cc_start: 0.9014 (tpp80) cc_final: 0.8694 (tpp80) REVERT: F 310 MET cc_start: 0.8692 (tpp) cc_final: 0.8325 (tpp) outliers start: 90 outliers final: 57 residues processed: 566 average time/residue: 0.4362 time to fit residues: 373.7378 Evaluate side-chains 569 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 498 time to evaluate : 3.116 ------------------------------------------------------------------------------- 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 177 LYS Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 113 CYS 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 619 THR Chi-restraints excluded: chain C residue 648 TYR Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 798 THR Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain C residue 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 82 VAL 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 234 LEU 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 457 MET Chi-restraints excluded: chain D residue 493 GLU Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 613 SER 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 1132 GLN 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 D residue 1254 ILE 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 384 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 63 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 138 optimal weight: 0.0670 chunk 30 optimal weight: 0.0770 chunk 87 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 197 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 333 optimal weight: 7.9990 chunk 166 optimal weight: 5.9990 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 918 ASN D 369 ASN D1132 GLN ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.122216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.085191 restraints weight = 75690.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.088291 restraints weight = 42549.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.090402 restraints weight = 29305.225| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28260 Z= 0.138 Angle : 0.712 12.368 38614 Z= 0.357 Chirality : 0.043 0.252 4390 Planarity : 0.005 0.075 4789 Dihedral : 14.692 158.227 4567 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.21 % Allowed : 22.48 % Favored : 74.31 % 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: -0.17 (0.15), residues: 3305 helix: 0.42 (0.15), residues: 1232 sheet: -0.67 (0.24), residues: 433 loop : -0.24 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 23 HIS 0.005 0.001 HIS A 61 PHE 0.043 0.002 PHE D 226 TYR 0.038 0.002 TYR D 248 ARG 0.017 0.001 ARG D 334 Details of bonding type rmsd hydrogen bonds : bond 0.03765 ( 1154) hydrogen bonds : angle 4.79823 ( 3162) metal coordination : bond 0.00704 ( 8) metal coordination : angle 3.05697 ( 12) covalent geometry : bond 0.00312 (28252) covalent geometry : angle 0.70994 (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 594 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 504 time to evaluate : 3.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6843 (tmm) cc_final: 0.6370 (tmm) REVERT: A 62 GLU cc_start: 0.8184 (pm20) cc_final: 0.7950 (pm20) REVERT: A 99 LYS cc_start: 0.8595 (tptt) cc_final: 0.8196 (tptt) REVERT: B 1 MET cc_start: 0.6738 (pmm) cc_final: 0.6527 (pmm) REVERT: B 179 GLU cc_start: 0.7907 (mp0) cc_final: 0.7437 (mp0) REVERT: B 191 LYS cc_start: 0.8715 (ptmm) cc_final: 0.7905 (ptmm) REVERT: C 79 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8528 (mm-30) REVERT: C 107 LYS cc_start: 0.8792 (mtmt) cc_final: 0.8338 (ptpp) REVERT: C 113 CYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8213 (m) REVERT: C 172 ARG cc_start: 0.7927 (mmt90) cc_final: 0.7693 (mmt90) REVERT: C 346 MET cc_start: 0.7678 (tmm) cc_final: 0.7455 (tpt) REVERT: C 374 GLU cc_start: 0.8218 (mp0) cc_final: 0.7969 (tp30) REVERT: C 530 HIS cc_start: 0.8554 (m-70) cc_final: 0.8139 (m-70) REVERT: C 548 ASP cc_start: 0.8292 (p0) cc_final: 0.7831 (p0) REVERT: C 571 ASP cc_start: 0.8198 (m-30) cc_final: 0.7863 (m-30) REVERT: C 594 ASN cc_start: 0.9077 (OUTLIER) cc_final: 0.8622 (p0) REVERT: C 602 MET cc_start: 0.8701 (mtm) cc_final: 0.8455 (mtm) REVERT: C 613 GLU cc_start: 0.7701 (tp30) cc_final: 0.7483 (tp30) REVERT: C 619 THR cc_start: 0.8568 (OUTLIER) cc_final: 0.8007 (p) REVERT: C 664 ARG cc_start: 0.8309 (mtp-110) cc_final: 0.8055 (mtp-110) REVERT: C 715 MET cc_start: 0.8753 (ptm) cc_final: 0.8485 (ptm) REVERT: C 724 ASP cc_start: 0.7711 (t0) cc_final: 0.7415 (t0) REVERT: C 867 LYS cc_start: 0.8902 (mtpp) cc_final: 0.8632 (tttp) REVERT: C 915 ARG cc_start: 0.7905 (tmm-80) cc_final: 0.7699 (tmm-80) REVERT: C 918 ASN cc_start: 0.9267 (OUTLIER) cc_final: 0.8292 (p0) REVERT: C 921 GLN cc_start: 0.7874 (pt0) cc_final: 0.7447 (pt0) REVERT: C 1008 GLU cc_start: 0.8433 (mp0) cc_final: 0.8073 (mp0) REVERT: C 1110 GLU cc_start: 0.8240 (tp30) cc_final: 0.7861 (tp30) REVERT: D 27 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7390 (pp20) REVERT: D 44 ASP cc_start: 0.7696 (t0) cc_final: 0.7094 (t0) REVERT: D 86 LYS cc_start: 0.8839 (pttm) cc_final: 0.8617 (pttm) REVERT: D 113 ARG cc_start: 0.8350 (mpt180) cc_final: 0.8130 (mmp80) REVERT: D 134 TYR cc_start: 0.7998 (m-10) cc_final: 0.7555 (m-10) REVERT: D 143 MET cc_start: 0.8267 (mtm) cc_final: 0.7709 (ptp) REVERT: D 158 GLU cc_start: 0.9348 (tp30) cc_final: 0.8992 (tm-30) REVERT: D 233 GLN cc_start: 0.7817 (tm-30) cc_final: 0.7394 (tm-30) REVERT: D 235 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7624 (mp) REVERT: D 247 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7092 (mtm180) REVERT: D 256 MET cc_start: 0.6731 (OUTLIER) cc_final: 0.6258 (ttm) REVERT: D 295 ARG cc_start: 0.8818 (ttm170) cc_final: 0.7990 (mtp-110) REVERT: D 350 ARG cc_start: 0.8033 (mtt180) cc_final: 0.7401 (mtp85) REVERT: D 356 ARG cc_start: 0.8646 (mmp80) cc_final: 0.8311 (mmp80) REVERT: D 383 ASP cc_start: 0.8894 (t0) cc_final: 0.8276 (p0) REVERT: D 400 LYS cc_start: 0.8492 (tttp) cc_final: 0.7878 (tttp) REVERT: D 404 ASP cc_start: 0.8626 (t0) cc_final: 0.8393 (t0) REVERT: D 423 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.8057 (t70) REVERT: D 457 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8372 (tpp) REVERT: D 474 ARG cc_start: 0.7444 (tpt90) cc_final: 0.6647 (tpt90) REVERT: D 475 MET cc_start: 0.7545 (ptm) cc_final: 0.6850 (ptp) REVERT: D 518 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7062 (mm-30) REVERT: D 541 MET cc_start: 0.8549 (tpp) cc_final: 0.8272 (mmm) REVERT: D 552 GLN cc_start: 0.8675 (mt0) cc_final: 0.8292 (mp10) REVERT: D 576 MET cc_start: 0.8200 (mpp) cc_final: 0.7989 (mpp) REVERT: D 622 MET cc_start: 0.8832 (ptp) cc_final: 0.8621 (ptp) REVERT: D 634 LYS cc_start: 0.9086 (ttmt) cc_final: 0.8662 (mmmt) REVERT: D 717 ASP cc_start: 0.8506 (m-30) cc_final: 0.8260 (m-30) REVERT: D 741 LYS cc_start: 0.9297 (pptt) cc_final: 0.8813 (mmmt) REVERT: D 742 GLN cc_start: 0.8456 (mp10) cc_final: 0.8016 (pm20) REVERT: D 841 GLU cc_start: 0.8307 (tt0) cc_final: 0.7908 (tm-30) REVERT: D 868 ASP cc_start: 0.7963 (t0) cc_final: 0.7478 (p0) REVERT: D 941 HIS cc_start: 0.7532 (t-170) cc_final: 0.7281 (t-170) REVERT: D 951 LEU cc_start: 0.8750 (mt) cc_final: 0.7981 (pp) REVERT: D 1132 GLN cc_start: 0.9443 (OUTLIER) cc_final: 0.9072 (mp10) REVERT: D 1165 ARG cc_start: 0.7769 (mtm-85) cc_final: 0.7458 (ttm-80) REVERT: D 1254 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7721 (mm) REVERT: E 97 HIS cc_start: 0.8344 (t-90) cc_final: 0.7861 (t-170) REVERT: F 192 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8077 (pt0) REVERT: F 196 TYR cc_start: 0.8689 (t80) cc_final: 0.8144 (t80) REVERT: F 201 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9100 (mt) REVERT: F 219 MET cc_start: 0.9073 (ptp) cc_final: 0.8797 (ptp) REVERT: F 221 TRP cc_start: 0.8657 (t-100) cc_final: 0.8404 (t-100) REVERT: F 256 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7488 (pt) REVERT: F 261 GLU cc_start: 0.8208 (tp30) cc_final: 0.7864 (tp30) REVERT: F 268 ARG cc_start: 0.9010 (tpp80) cc_final: 0.8678 (tpp80) REVERT: F 310 MET cc_start: 0.8697 (tpp) cc_final: 0.8323 (tpp) REVERT: J 101 ARG cc_start: 0.8584 (mmm160) cc_final: 0.8268 (mmm160) outliers start: 90 outliers final: 60 residues processed: 554 average time/residue: 0.4379 time to fit residues: 370.9815 Evaluate side-chains 555 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 481 time to evaluate : 3.283 ------------------------------------------------------------------------------- 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 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 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 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 1064 CYS 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 82 VAL 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 234 LEU 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 327 MET 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 529 CYS Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 613 SER 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 959 VAL Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 1132 GLN Chi-restraints excluded: chain D residue 1158 ILE Chi-restraints excluded: chain D residue 1216 LEU Chi-restraints excluded: chain D residue 1247 ASN Chi-restraints excluded: chain D residue 1254 ILE Chi-restraints excluded: chain E residue 53 TYR Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 256 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: 20.0000 chunk 81 optimal weight: 0.9990 chunk 152 optimal weight: 0.8980 chunk 98 optimal weight: 8.9990 chunk 315 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 255 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 184 optimal weight: 9.9990 chunk 223 optimal weight: 5.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 ** C1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 ASN D 410 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.122377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.085779 restraints weight = 75418.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.088848 restraints weight = 43221.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.090862 restraints weight = 29977.508| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 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 : 0.003 0.053 28260 Z= 0.138 Angle : 0.725 14.031 38614 Z= 0.362 Chirality : 0.044 0.317 4390 Planarity : 0.005 0.066 4789 Dihedral : 14.703 158.097 4567 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.85 % Allowed : 23.12 % Favored : 74.03 % 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: -0.21 (0.15), residues: 3305 helix: 0.37 (0.15), residues: 1231 sheet: -0.66 (0.24), residues: 433 loop : -0.24 (0.16), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP D 23 HIS 0.004 0.001 HIS F 454 PHE 0.044 0.002 PHE D 226 TYR 0.037 0.002 TYR D 248 ARG 0.015 0.001 ARG C 412 Details of bonding type rmsd hydrogen bonds : bond 0.03786 ( 1154) hydrogen bonds : angle 4.81781 ( 3162) metal coordination : bond 0.00694 ( 8) metal coordination : angle 3.10576 ( 12) covalent geometry : bond 0.00309 (28252) covalent geometry : angle 0.72310 (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 573 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 493 time to evaluate : 2.854 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: A 1 MET cc_start: 0.6917 (tmm) cc_final: 0.6672 (tmm) REVERT: A 62 GLU cc_start: 0.8195 (pm20) cc_final: 0.7984 (pm20) REVERT: A 99 LYS cc_start: 0.8606 (tptt) cc_final: 0.8404 (tptt) REVERT: A 191 LYS cc_start: 0.8894 (ttpp) cc_final: 0.8320 (ptpp) REVERT: B 179 GLU cc_start: 0.7892 (mp0) cc_final: 0.7442 (mp0) REVERT: B 191 LYS cc_start: 0.8727 (ptmm) cc_final: 0.8134 (ptmm) REVERT: C 62 ARG cc_start: 0.9087 (mtt90) cc_final: 0.8576 (ptp-110) REVERT: C 79 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8503 (mm-30) REVERT: C 107 LYS cc_start: 0.8774 (mtmt) cc_final: 0.8408 (ptpp) REVERT: C 113 CYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8190 (m) REVERT: C 172 ARG cc_start: 0.7887 (mmt90) cc_final: 0.7681 (mmt90) REVERT: C 374 GLU cc_start: 0.8201 (mp0) cc_final: 0.7954 (tp30) REVERT: C 548 ASP cc_start: 0.8332 (p0) cc_final: 0.7813 (p0) REVERT: C 571 ASP cc_start: 0.8067 (m-30) cc_final: 0.7751 (m-30) REVERT: C 594 ASN cc_start: 0.9083 (OUTLIER) cc_final: 0.8610 (p0) REVERT: C 602 MET cc_start: 0.8711 (mtm) cc_final: 0.8446 (mtm) REVERT: C 613 GLU cc_start: 0.7694 (tp30) cc_final: 0.7433 (tp30) REVERT: C 619 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8058 (p) REVERT: C 664 ARG cc_start: 0.8276 (mtp-110) cc_final: 0.8036 (mtp-110) REVERT: C 715 MET cc_start: 0.8683 (ptm) cc_final: 0.8432 (ptm) REVERT: C 724 ASP cc_start: 0.7722 (t0) cc_final: 0.7329 (t0) REVERT: C 734 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7764 (mp0) REVERT: C 867 LYS cc_start: 0.8902 (mtpp) cc_final: 0.8624 (tttp) REVERT: C 918 ASN cc_start: 0.9141 (OUTLIER) cc_final: 0.8214 (p0) REVERT: C 921 GLN cc_start: 0.7915 (pt0) cc_final: 0.7475 (pt0) REVERT: C 1008 GLU cc_start: 0.8436 (mp0) cc_final: 0.8074 (mp0) REVERT: C 1110 GLU cc_start: 0.8285 (tp30) cc_final: 0.7912 (tp30) REVERT: D 21 ARG cc_start: 0.8609 (mpt180) cc_final: 0.8058 (mmt180) REVERT: D 27 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7379 (pp20) REVERT: D 44 ASP cc_start: 0.7659 (t0) cc_final: 0.7134 (t0) REVERT: D 86 LYS cc_start: 0.8934 (pttm) cc_final: 0.8533 (pttm) REVERT: D 134 TYR cc_start: 0.7997 (m-10) cc_final: 0.7510 (m-10) REVERT: D 143 MET cc_start: 0.8246 (mtm) cc_final: 0.7688 (ptp) REVERT: D 158 GLU cc_start: 0.9331 (tp30) cc_final: 0.9030 (tm-30) REVERT: D 233 GLN cc_start: 0.7828 (tm-30) cc_final: 0.7398 (tm-30) REVERT: D 234 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7761 (tt) REVERT: D 235 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7605 (mp) REVERT: D 247 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7107 (mtm180) REVERT: D 256 MET cc_start: 0.6797 (OUTLIER) cc_final: 0.6204 (ttm) REVERT: D 295 ARG cc_start: 0.8817 (ttm170) cc_final: 0.7969 (mtp-110) REVERT: D 356 ARG cc_start: 0.8610 (mmp80) cc_final: 0.8296 (mmp80) REVERT: D 383 ASP cc_start: 0.8873 (t0) cc_final: 0.8267 (p0) REVERT: D 400 LYS cc_start: 0.8422 (tttp) cc_final: 0.7849 (tttp) REVERT: D 423 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.8076 (t70) REVERT: D 457 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8354 (tpp) REVERT: D 474 ARG cc_start: 0.7406 (tpt90) cc_final: 0.6791 (tpt90) REVERT: D 475 MET cc_start: 0.7582 (ptm) cc_final: 0.6447 (ptp) REVERT: D 518 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7029 (mm-30) REVERT: D 541 MET cc_start: 0.8546 (tpp) cc_final: 0.8278 (mmm) REVERT: D 552 GLN cc_start: 0.8644 (mt0) cc_final: 0.8266 (mp10) REVERT: D 576 MET cc_start: 0.8171 (mpp) cc_final: 0.7941 (mpp) REVERT: D 634 LYS cc_start: 0.9087 (ttmt) cc_final: 0.8662 (mmmt) REVERT: D 741 LYS cc_start: 0.9312 (pptt) cc_final: 0.8818 (mmmt) REVERT: D 742 GLN cc_start: 0.8438 (mp10) cc_final: 0.8005 (pm20) REVERT: D 819 MET cc_start: 0.7122 (tpt) cc_final: 0.6870 (tpt) REVERT: D 841 GLU cc_start: 0.8255 (tt0) cc_final: 0.7821 (tm-30) REVERT: D 864 LEU cc_start: 0.9273 (pp) cc_final: 0.8499 (pt) REVERT: D 868 ASP cc_start: 0.7926 (t0) cc_final: 0.7454 (p0) REVERT: D 941 HIS cc_start: 0.7510 (t-170) cc_final: 0.7276 (t-170) REVERT: D 951 LEU cc_start: 0.8769 (mt) cc_final: 0.7988 (pp) REVERT: D 976 MET cc_start: 0.8311 (mpp) cc_final: 0.7974 (mpp) REVERT: D 1132 GLN cc_start: 0.9412 (OUTLIER) cc_final: 0.9089 (mp10) REVERT: D 1165 ARG cc_start: 0.7698 (mtm-85) cc_final: 0.7490 (ttm-80) REVERT: D 1254 ILE cc_start: 0.7954 (mm) cc_final: 0.7740 (mm) REVERT: E 97 HIS cc_start: 0.8321 (t-90) cc_final: 0.7824 (t-170) REVERT: F 190 ARG cc_start: 0.8763 (mtm180) cc_final: 0.8495 (mtm-85) REVERT: F 192 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8039 (pt0) REVERT: F 196 TYR cc_start: 0.8687 (t80) cc_final: 0.8467 (t80) REVERT: F 201 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9080 (mt) REVERT: F 219 MET cc_start: 0.9048 (ptp) cc_final: 0.8768 (ptp) REVERT: F 221 TRP cc_start: 0.8669 (t-100) cc_final: 0.8417 (t-100) REVERT: F 256 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8397 (pt) REVERT: F 261 GLU cc_start: 0.8228 (tp30) cc_final: 0.7881 (tp30) REVERT: F 268 ARG cc_start: 0.9010 (tpp80) cc_final: 0.8581 (tpp80) REVERT: F 297 MET cc_start: 0.8351 (ppp) cc_final: 0.8100 (ppp) REVERT: F 310 MET cc_start: 0.8663 (tpp) cc_final: 0.8270 (tpp) REVERT: F 400 SER cc_start: 0.8341 (t) cc_final: 0.8050 (m) REVERT: J 101 ARG cc_start: 0.8614 (mmm160) cc_final: 0.8292 (mmm160) outliers start: 80 outliers final: 57 residues processed: 537 average time/residue: 0.4330 time to fit residues: 353.2028 Evaluate side-chains 549 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 478 time to evaluate : 2.956 ------------------------------------------------------------------------------- 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 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 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 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 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 82 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 226 PHE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 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 327 MET 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 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 871 TYR Chi-restraints excluded: chain D residue 959 VAL Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 1132 GLN Chi-restraints excluded: chain D residue 1158 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 201 LEU Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 354 TYR 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: 0.9990 chunk 17 optimal weight: 0.8980 chunk 231 optimal weight: 6.9990 chunk 181 optimal weight: 0.8980 chunk 96 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 298 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 313 optimal weight: 0.9990 chunk 279 optimal weight: 0.1980 chunk 269 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** C1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** 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 = 0.3932 r_free = 0.3932 target = 0.122670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.086366 restraints weight = 75093.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.089384 restraints weight = 42944.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.091404 restraints weight = 29816.100| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.5369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 28260 Z= 0.138 Angle : 0.748 15.500 38614 Z= 0.373 Chirality : 0.044 0.398 4390 Planarity : 0.005 0.081 4789 Dihedral : 14.714 158.245 4567 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.50 % Allowed : 23.83 % Favored : 73.67 % 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: -0.18 (0.15), residues: 3305 helix: 0.34 (0.15), residues: 1231 sheet: -0.50 (0.25), residues: 412 loop : -0.25 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP D 23 HIS 0.006 0.001 HIS D 505 PHE 0.044 0.002 PHE D 226 TYR 0.037 0.002 TYR D 248 ARG 0.012 0.001 ARG D 218 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 1154) hydrogen bonds : angle 4.85705 ( 3162) metal coordination : bond 0.00590 ( 8) metal coordination : angle 3.03704 ( 12) covalent geometry : bond 0.00311 (28252) covalent geometry : angle 0.74606 (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 571 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 501 time to evaluate : 3.635 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: A 61 HIS cc_start: 0.8258 (p90) cc_final: 0.7771 (p90) REVERT: A 99 LYS cc_start: 0.8601 (tptt) cc_final: 0.8393 (tptt) REVERT: A 161 ARG cc_start: 0.8475 (mpt180) cc_final: 0.8131 (mpt180) REVERT: A 191 LYS cc_start: 0.8915 (ttpp) cc_final: 0.8340 (ptpp) REVERT: A 205 ARG cc_start: 0.8794 (ttt-90) cc_final: 0.8356 (tpt-90) REVERT: B 179 GLU cc_start: 0.7913 (mp0) cc_final: 0.7465 (mp0) REVERT: B 191 LYS cc_start: 0.8724 (ptmm) cc_final: 0.7952 (ptmm) REVERT: C 79 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8494 (mm-30) REVERT: C 107 LYS cc_start: 0.8763 (mtmt) cc_final: 0.8376 (ptpp) REVERT: C 113 CYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8168 (m) REVERT: C 172 ARG cc_start: 0.7883 (mmt90) cc_final: 0.7663 (mmt90) REVERT: C 374 GLU cc_start: 0.8205 (mp0) cc_final: 0.7953 (tp30) REVERT: C 548 ASP cc_start: 0.8310 (p0) cc_final: 0.7819 (p0) REVERT: C 594 ASN cc_start: 0.9079 (OUTLIER) cc_final: 0.8649 (p0) REVERT: C 602 MET cc_start: 0.8702 (mtm) cc_final: 0.8439 (mtm) REVERT: C 613 GLU cc_start: 0.7680 (tp30) cc_final: 0.7358 (tp30) REVERT: C 619 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8091 (p) REVERT: C 664 ARG cc_start: 0.8279 (mtp-110) cc_final: 0.8046 (mtp-110) REVERT: C 715 MET cc_start: 0.8653 (ptm) cc_final: 0.8405 (ptm) REVERT: C 734 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7764 (mp0) REVERT: C 867 LYS cc_start: 0.8902 (mtpp) cc_final: 0.8637 (tttp) REVERT: C 1008 GLU cc_start: 0.8442 (mp0) cc_final: 0.8077 (mp0) REVERT: C 1110 GLU cc_start: 0.8275 (tp30) cc_final: 0.7912 (tp30) REVERT: D 27 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7529 (pp20) REVERT: D 44 ASP cc_start: 0.7593 (t0) cc_final: 0.7228 (t0) REVERT: D 58 TRP cc_start: 0.7796 (m100) cc_final: 0.7528 (m100) REVERT: D 86 LYS cc_start: 0.8947 (pttm) cc_final: 0.8552 (pttm) REVERT: D 116 TYR cc_start: 0.8149 (m-10) cc_final: 0.7872 (m-10) REVERT: D 124 ASP cc_start: 0.8307 (m-30) cc_final: 0.7888 (p0) REVERT: D 134 TYR cc_start: 0.8016 (m-10) cc_final: 0.7514 (m-10) REVERT: D 143 MET cc_start: 0.8237 (mtm) cc_final: 0.7685 (ptp) REVERT: D 158 GLU cc_start: 0.9358 (tp30) cc_final: 0.9057 (tm-30) REVERT: D 233 GLN cc_start: 0.7796 (tm-30) cc_final: 0.7359 (tm-30) REVERT: D 234 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7746 (tt) REVERT: D 235 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7568 (mp) REVERT: D 247 ARG cc_start: 0.7569 (ptp-170) cc_final: 0.7144 (mtm180) REVERT: D 256 MET cc_start: 0.6821 (OUTLIER) cc_final: 0.6241 (ttm) REVERT: D 295 ARG cc_start: 0.8824 (ttm170) cc_final: 0.7885 (mtp-110) REVERT: D 356 ARG cc_start: 0.8608 (mmp80) cc_final: 0.8262 (mmp80) REVERT: D 383 ASP cc_start: 0.8867 (t0) cc_final: 0.8215 (p0) REVERT: D 453 LYS cc_start: 0.8929 (tttp) cc_final: 0.8529 (tppt) REVERT: D 457 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8371 (tpp) REVERT: D 474 ARG cc_start: 0.7421 (tpt90) cc_final: 0.6805 (tpt90) REVERT: D 475 MET cc_start: 0.7551 (ptm) cc_final: 0.6407 (ptp) REVERT: D 518 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7045 (mm-30) REVERT: D 541 MET cc_start: 0.8601 (tpp) cc_final: 0.8279 (mmm) REVERT: D 552 GLN cc_start: 0.8636 (mt0) cc_final: 0.8229 (mp10) REVERT: D 558 LEU cc_start: 0.9259 (mm) cc_final: 0.8924 (mp) REVERT: D 576 MET cc_start: 0.8154 (mpp) cc_final: 0.7948 (mpp) REVERT: D 622 MET cc_start: 0.8757 (ptp) cc_final: 0.8415 (ptp) REVERT: D 634 LYS cc_start: 0.9091 (ttmt) cc_final: 0.8757 (tppt) REVERT: D 741 LYS cc_start: 0.9317 (pptt) cc_final: 0.8819 (mmmt) REVERT: D 742 GLN cc_start: 0.8441 (mp10) cc_final: 0.7950 (pm20) REVERT: D 747 ARG cc_start: 0.9306 (mmm160) cc_final: 0.8982 (mmp80) REVERT: D 819 MET cc_start: 0.6926 (tpt) cc_final: 0.6636 (tpt) REVERT: D 841 GLU cc_start: 0.8228 (tt0) cc_final: 0.7798 (tm-30) REVERT: D 864 LEU cc_start: 0.9272 (pp) cc_final: 0.8565 (pt) REVERT: D 868 ASP cc_start: 0.7902 (t0) cc_final: 0.7433 (p0) REVERT: D 941 HIS cc_start: 0.7520 (t-170) cc_final: 0.7208 (t-170) REVERT: D 951 LEU cc_start: 0.8745 (mt) cc_final: 0.7951 (pp) REVERT: D 976 MET cc_start: 0.8279 (mpp) cc_final: 0.7934 (mpp) REVERT: D 1165 ARG cc_start: 0.7681 (mtm-85) cc_final: 0.7337 (ttm-80) REVERT: D 1254 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7728 (mm) REVERT: E 97 HIS cc_start: 0.8242 (t-90) cc_final: 0.7780 (t-170) REVERT: F 190 ARG cc_start: 0.8756 (mtm180) cc_final: 0.8482 (mtm-85) REVERT: F 192 GLU cc_start: 0.8684 (mt-10) cc_final: 0.7993 (pt0) REVERT: F 196 TYR cc_start: 0.8667 (t80) cc_final: 0.8455 (t80) REVERT: F 219 MET cc_start: 0.9040 (ptp) cc_final: 0.8742 (ptp) REVERT: F 221 TRP cc_start: 0.8660 (t-100) cc_final: 0.8416 (t-100) REVERT: F 231 ASN cc_start: 0.8575 (m110) cc_final: 0.8207 (p0) REVERT: F 256 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8326 (pt) REVERT: F 268 ARG cc_start: 0.8995 (tpp80) cc_final: 0.8705 (mmm-85) REVERT: F 297 MET cc_start: 0.8322 (ppp) cc_final: 0.8111 (ppp) REVERT: F 310 MET cc_start: 0.8659 (tpp) cc_final: 0.8340 (tpp) REVERT: F 315 ASN cc_start: 0.8956 (p0) cc_final: 0.8704 (p0) REVERT: F 400 SER cc_start: 0.8358 (t) cc_final: 0.8077 (m) REVERT: J 101 ARG cc_start: 0.8623 (mmm160) cc_final: 0.8297 (mmm160) outliers start: 70 outliers final: 56 residues processed: 538 average time/residue: 0.4632 time to fit residues: 380.3427 Evaluate side-chains 555 residues out of total 2803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 489 time to evaluate : 2.835 ------------------------------------------------------------------------------- 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 65 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 90 PHE 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 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 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 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 36 TYR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 136 ILE 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 260 SER Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 732 MET Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 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 1247 ASN Chi-restraints excluded: chain D residue 1254 ILE Chi-restraints excluded: chain E residue 53 TYR Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 308 VAL 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: 2.9990 chunk 129 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 300 optimal weight: 9.9990 chunk 314 optimal weight: 9.9990 chunk 307 optimal weight: 4.9990 chunk 234 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1057 GLN ** D 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 ASN ** 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 = 0.3891 r_free = 0.3891 target = 0.119727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.083041 restraints weight = 76458.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.085953 restraints weight = 44353.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.087909 restraints weight = 31108.922| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 28260 Z= 0.222 Angle : 0.777 14.134 38614 Z= 0.391 Chirality : 0.046 0.408 4390 Planarity : 0.005 0.077 4789 Dihedral : 14.803 158.037 4567 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.82 % Allowed : 23.97 % Favored : 73.21 % 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 (0.15), residues: 3305 helix: 0.29 (0.15), residues: 1238 sheet: -0.50 (0.26), residues: 388 loop : -0.26 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP D 23 HIS 0.005 0.001 HIS C 530 PHE 0.045 0.002 PHE D 226 TYR 0.036 0.002 TYR D 248 ARG 0.016 0.001 ARG C 412 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 1154) hydrogen bonds : angle 5.01592 ( 3162) metal coordination : bond 0.01406 ( 8) metal coordination : angle 3.45227 ( 12) covalent geometry : bond 0.00490 (28252) covalent geometry : angle 0.77440 (38602) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12285.06 seconds wall clock time: 216 minutes 45.01 seconds (13005.01 seconds total)