Starting phenix.real_space_refine on Fri Jul 3 12:38:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ibx_52815/07_2026/9ibx_52815.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ibx_52815/07_2026/9ibx_52815.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ibx_52815/07_2026/9ibx_52815.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ibx_52815/07_2026/9ibx_52815.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ibx_52815/07_2026/9ibx_52815.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ibx_52815/07_2026/9ibx_52815.map" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.007 sd= 0.955 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 41 5.49 5 S 81 5.16 5 C 8865 2.51 5 N 2488 2.21 5 O 2653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14129 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 956, 7628 Classifications: {'peptide': 956} Link IDs: {'PTRANS': 62, 'TRANS': 893} Chain breaks: 6 Chain: "B" Number of atoms: 2850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2850 Classifications: {'peptide': 353} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 335} Chain breaks: 3 Chain: "C" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2842 Classifications: {'peptide': 352} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 334} Chain breaks: 3 Chain: "P" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 375 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "T" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 405 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'DCP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 3.30, per 1000 atoms: 0.23 Number of scatterers: 14129 At special positions: 0 Unit cell: (95.22, 101.844, 144.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 81 16.00 P 41 15.00 O 2653 8.00 N 2488 7.00 C 8865 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: 1.20 Conformation dependent library (CDL) restraints added in 584.1 milliseconds 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3084 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 47.0% alpha, 13.7% beta 17 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 63 through 71 removed outlier: 3.956A pdb=" N GLN A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 93 removed outlier: 3.571A pdb=" N HIS A 93 " --> pdb=" O HIS A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 142 Proline residue: A 132 - end of helix removed outlier: 3.728A pdb=" N ALA A 136 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.717A pdb=" N LEU A 227 " --> pdb=" O PRO A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 260 through 265 removed outlier: 6.719A pdb=" N GLU A 263 " --> pdb=" O HIS A 260 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR A 265 " --> pdb=" O ARG A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 286 Processing helix chain 'A' and resid 288 through 299 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 337 through 346 Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 370 through 400 Proline residue: A 394 - end of helix Processing helix chain 'A' and resid 402 through 410 removed outlier: 4.100A pdb=" N LEU A 406 " --> pdb=" O HIS A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 414 Processing helix chain 'A' and resid 421 through 454 removed outlier: 3.670A pdb=" N LEU A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN A 454 " --> pdb=" O ASN A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 459 through 464 removed outlier: 3.638A pdb=" N LYS A 462 " --> pdb=" O GLU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 533 removed outlier: 3.921A pdb=" N LEU A 533 " --> pdb=" O ARG A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 540 removed outlier: 3.506A pdb=" N THR A 537 " --> pdb=" O ARG A 534 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP A 538 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 556 removed outlier: 3.695A pdb=" N LYS A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 584 Processing helix chain 'A' and resid 629 through 644 Processing helix chain 'A' and resid 748 through 755 Processing helix chain 'A' and resid 764 through 788 removed outlier: 5.216A pdb=" N PHE A 778 " --> pdb=" O LYS A 774 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N TRP A 779 " --> pdb=" O MET A 775 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LYS A 784 " --> pdb=" O ARG A 780 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ARG A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 805 Processing helix chain 'A' and resid 852 through 856 Processing helix chain 'A' and resid 871 through 886 Processing helix chain 'A' and resid 892 through 900 Processing helix chain 'A' and resid 908 through 918 Processing helix chain 'A' and resid 920 through 933 removed outlier: 4.099A pdb=" N ILE A 926 " --> pdb=" O GLU A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 948 Processing helix chain 'A' and resid 952 through 966 removed outlier: 3.536A pdb=" N VAL A 966 " --> pdb=" O GLN A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1045 Processing helix chain 'A' and resid 1058 through 1062 removed outlier: 3.837A pdb=" N GLU A1062 " --> pdb=" O ARG A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1102 removed outlier: 3.585A pdb=" N VAL A1078 " --> pdb=" O ARG A1074 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL A1079 " --> pdb=" O VAL A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1146 Processing helix chain 'A' and resid 1183 through 1188 Processing helix chain 'A' and resid 1197 through 1206 Processing helix chain 'B' and resid 68 through 76 Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 119 removed outlier: 3.616A pdb=" N GLU B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 191 removed outlier: 3.714A pdb=" N GLU B 191 " --> pdb=" O HIS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 193 No H-bonds generated for 'chain 'B' and resid 192 through 193' Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 247 through 266 removed outlier: 4.110A pdb=" N PHE B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 318 through 323 removed outlier: 3.973A pdb=" N LYS B 321 " --> pdb=" O ASN B 318 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS B 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 354 Processing helix chain 'B' and resid 391 through 408 Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 424 through 435 Processing helix chain 'B' and resid 446 through 451 Processing helix chain 'B' and resid 470 through 482 Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 87 through 92 Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 185 through 191 removed outlier: 3.554A pdb=" N ALA C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 193 No H-bonds generated for 'chain 'C' and resid 192 through 193' Processing helix chain 'C' and resid 194 through 198 removed outlier: 3.612A pdb=" N ASP C 198 " --> pdb=" O ASN C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 266 removed outlier: 4.216A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 391 through 409 removed outlier: 3.633A pdb=" N VAL C 398 " --> pdb=" O GLU C 394 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'C' and resid 424 through 435 Processing helix chain 'C' and resid 445 through 450 removed outlier: 3.792A pdb=" N GLU C 449 " --> pdb=" O GLU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 482 removed outlier: 3.530A pdb=" N ALA C 482 " --> pdb=" O TYR C 478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 169 removed outlier: 3.890A pdb=" N TRP A 203 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU A 178 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLN A 247 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU A 275 " --> pdb=" O GLN A 247 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL A 249 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 417 through 420 removed outlier: 4.804A pdb=" N TYR A 815 " --> pdb=" O LEU A 794 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 726 through 729 Processing sheet with id=AA4, first strand: chain 'A' and resid 1105 through 1109 removed outlier: 7.103A pdb=" N GLY A1105 " --> pdb=" O ARG A1120 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ARG A1120 " --> pdb=" O GLY A1105 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N PHE A1107 " --> pdb=" O LEU A1118 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N LEU A1118 " --> pdb=" O PHE A1107 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.343A pdb=" N PHE B 126 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N ILE B 211 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N VAL B 335 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU B 301 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS B 278 " --> pdb=" O GLY B 286 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA7, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AA8, first strand: chain 'B' and resid 413 through 415 removed outlier: 7.192A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ALA B 384 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL B 443 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASP B 386 " --> pdb=" O VAL B 443 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.331A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS C 297 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N PHE C 293 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU C 301 " --> pdb=" O LEU C 289 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 133 through 134 Processing sheet with id=AB2, first strand: chain 'C' and resid 324 through 326 removed outlier: 3.722A pdb=" N LYS C 329 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 413 through 415 removed outlier: 7.363A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) 623 hydrogen bonds defined for protein. 1758 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 2.79 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3907 1.33 - 1.45: 2714 1.45 - 1.57: 7738 1.57 - 1.69: 79 1.69 - 1.81: 128 Bond restraints: 14566 Sorted by residual: bond pdb=" O3B DCP A1301 " pdb=" PG DCP A1301 " ideal model delta sigma weight residual 1.746 1.609 0.137 2.00e-02 2.50e+03 4.72e+01 bond pdb=" C3' DC P 15 " pdb=" C2' DC P 15 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" O3A DCP A1301 " pdb=" PB DCP A1301 " ideal model delta sigma weight residual 1.672 1.608 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C3' DA T 27 " pdb=" C2' DA T 27 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.60e+00 bond pdb=" C3' DT P 25 " pdb=" C2' DT P 25 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.17e+00 ... (remaining 14561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 19705 2.41 - 4.82: 191 4.82 - 7.23: 5 7.23 - 9.65: 1 9.65 - 12.06: 1 Bond angle restraints: 19903 Sorted by residual: angle pdb=" N3 DT P 16 " pdb=" C4 DT P 16 " pdb=" O4 DT P 16 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT T 22 " pdb=" C4 DT T 22 " pdb=" O4 DT T 22 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT T 24 " pdb=" C4 DT T 24 " pdb=" O4 DT T 24 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT P 25 " pdb=" C4 DT P 25 " pdb=" O4 DT P 25 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT P 14 " pdb=" C4 DT P 14 " pdb=" O4 DT P 14 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.65e+01 ... (remaining 19898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 7736 16.43 - 32.87: 617 32.87 - 49.30: 172 49.30 - 65.74: 58 65.74 - 82.17: 3 Dihedral angle restraints: 8586 sinusoidal: 3804 harmonic: 4782 Sorted by residual: dihedral pdb=" CA VAL A 179 " pdb=" C VAL A 179 " pdb=" N PHE A 180 " pdb=" CA PHE A 180 " ideal model delta harmonic sigma weight residual 180.00 -161.46 -18.54 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA HIS B 77 " pdb=" C HIS B 77 " pdb=" N PHE B 78 " pdb=" CA PHE B 78 " ideal model delta harmonic sigma weight residual 180.00 163.82 16.18 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA HIS C 77 " pdb=" C HIS C 77 " pdb=" N PHE C 78 " pdb=" CA PHE C 78 " ideal model delta harmonic sigma weight residual 180.00 164.10 15.90 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 8583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1653 0.047 - 0.093: 355 0.093 - 0.140: 118 0.140 - 0.187: 1 0.187 - 0.234: 2 Chirality restraints: 2129 Sorted by residual: chirality pdb=" C1' DCP A1301 " pdb=" C2' DCP A1301 " pdb=" N1 DCP A1301 " pdb=" O4' DCP A1301 " both_signs ideal model delta sigma weight residual False 2.25 2.48 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA VAL C 240 " pdb=" N VAL C 240 " pdb=" C VAL C 240 " pdb=" CB VAL C 240 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.90e-01 chirality pdb=" CA VAL C 332 " pdb=" N VAL C 332 " pdb=" C VAL C 332 " pdb=" CB VAL C 332 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 2126 not shown) Planarity restraints: 2426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 766 " -0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO A 767 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 767 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 767 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 375 " 0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO B 376 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 376 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 376 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 55 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO A 56 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 56 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 56 " -0.024 5.00e-02 4.00e+02 ... (remaining 2423 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 164 2.65 - 3.21: 12284 3.21 - 3.77: 22157 3.77 - 4.34: 31682 4.34 - 4.90: 52006 Nonbonded interactions: 118293 Sorted by model distance: nonbonded pdb="CA CA A1300 " pdb=" O2G DCP A1301 " model vdw 2.084 3.250 nonbonded pdb=" NH2 ARG A 258 " pdb=" O SER A 415 " model vdw 2.218 3.120 nonbonded pdb=" OE1 GLU A 873 " pdb=" OH TYR A 933 " model vdw 2.245 3.040 nonbonded pdb=" O HIS A 783 " pdb=" OG SER A 787 " model vdw 2.259 3.040 nonbonded pdb=" NH2 ARG B 369 " pdb=" O ARG B 458 " model vdw 2.263 3.120 ... (remaining 118288 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 'B' and (resid 67 through 137 or resid 178 through 218 or resid 230 throu \ gh 482)) selection = (chain 'C' and (resid 67 through 137 or resid 178 through 482)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.660 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.610 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 14566 Z= 0.264 Angle : 0.586 12.057 19903 Z= 0.363 Chirality : 0.042 0.234 2129 Planarity : 0.004 0.049 2426 Dihedral : 13.627 82.172 5502 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.55 % Allowed : 5.82 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.21), residues: 1631 helix: 0.89 (0.20), residues: 683 sheet: -0.34 (0.34), residues: 230 loop : 0.01 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 259 TYR 0.011 0.001 TYR A1086 PHE 0.016 0.001 PHE B 403 TRP 0.010 0.001 TRP A 295 HIS 0.005 0.001 HIS A 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.26 (14566) covalent geometry : angle 0.58586 / 0.36 (19903) hydrogen bonds : bond 0.16921 / 11.43 ( 667) hydrogen bonds : angle 6.85222 / 4.74 ( 1846) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 209 time to evaluate : 0.496 Fit side-chains REVERT: A 54 LEU cc_start: 0.7428 (mt) cc_final: 0.7192 (mm) REVERT: A 95 LEU cc_start: 0.8977 (mt) cc_final: 0.8654 (mp) REVERT: A 112 ARG cc_start: 0.6805 (ttt-90) cc_final: 0.6520 (mpp-170) REVERT: A 296 MET cc_start: 0.6312 (mmm) cc_final: 0.5927 (mmt) REVERT: A 353 LYS cc_start: 0.8743 (ptpt) cc_final: 0.8358 (pptt) REVERT: A 365 ARG cc_start: 0.7063 (tpp-160) cc_final: 0.6625 (tpt170) REVERT: A 409 MET cc_start: 0.7243 (mtt) cc_final: 0.6832 (mtm) REVERT: A 577 MET cc_start: 0.8476 (mtt) cc_final: 0.8130 (mmm) REVERT: A 639 LYS cc_start: 0.7794 (ttmt) cc_final: 0.7453 (tmmt) REVERT: A 736 ASN cc_start: 0.7855 (m110) cc_final: 0.7397 (t0) REVERT: A 810 ASP cc_start: 0.7613 (t70) cc_final: 0.7182 (t0) REVERT: A 896 TRP cc_start: 0.8073 (t60) cc_final: 0.7838 (t60) REVERT: A 1099 GLU cc_start: 0.6664 (tt0) cc_final: 0.6329 (pt0) REVERT: A 1114 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7065 (mp0) REVERT: A 1203 GLU cc_start: 0.6635 (tt0) cc_final: 0.6374 (pt0) REVERT: B 253 ASP cc_start: 0.8040 (t70) cc_final: 0.7701 (t0) REVERT: B 285 LYS cc_start: 0.8378 (tttt) cc_final: 0.8125 (mmmm) REVERT: C 236 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7615 (mt-10) REVERT: C 257 ARG cc_start: 0.6134 (tpm170) cc_final: 0.5675 (ttp80) REVERT: C 285 LYS cc_start: 0.8073 (mtpt) cc_final: 0.7862 (ptmt) REVERT: C 396 ARG cc_start: 0.5948 (mtt180) cc_final: 0.5536 (mtp-110) REVERT: C 419 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6599 (mm-30) REVERT: C 422 GLN cc_start: 0.7414 (mm-40) cc_final: 0.6725 (mm-40) REVERT: C 427 GLN cc_start: 0.7730 (mt0) cc_final: 0.7286 (mt0) REVERT: C 465 MET cc_start: 0.7090 (mmm) cc_final: 0.6739 (mmt) outliers start: 8 outliers final: 5 residues processed: 215 average time/residue: 0.6470 time to fit residues: 151.9493 Evaluate side-chains 142 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 306 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 GLN A1112 HIS B 309 HIS B 404 ASN C 318 ASN C 323 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.155348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.118670 restraints weight = 18603.429| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.85 r_work: 0.3585 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14566 Z= 0.193 Angle : 0.591 8.949 19903 Z= 0.310 Chirality : 0.042 0.148 2129 Planarity : 0.005 0.062 2426 Dihedral : 13.548 63.039 2247 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.29 % Allowed : 10.66 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.21), residues: 1631 helix: 0.99 (0.20), residues: 689 sheet: 0.01 (0.32), residues: 257 loop : 0.02 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 638 TYR 0.012 0.002 TYR C 291 PHE 0.018 0.002 PHE B 403 TRP 0.016 0.001 TRP A 295 HIS 0.005 0.001 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (14566) covalent geometry : angle 0.59099 / 0.31 (19903) hydrogen bonds : bond 0.04824 / 3.35 ( 667) hydrogen bonds : angle 5.06790 / 3.54 ( 1846) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 146 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8922 (mt) cc_final: 0.8640 (mp) REVERT: A 103 LEU cc_start: 0.8316 (tp) cc_final: 0.8004 (mp) REVERT: A 112 ARG cc_start: 0.6736 (ttt-90) cc_final: 0.6429 (mpp-170) REVERT: A 292 ARG cc_start: 0.5326 (ttm170) cc_final: 0.4908 (ttm170) REVERT: A 296 MET cc_start: 0.6204 (mmm) cc_final: 0.5881 (mmt) REVERT: A 353 LYS cc_start: 0.8687 (ptpt) cc_final: 0.8257 (pptt) REVERT: A 365 ARG cc_start: 0.7079 (tpp-160) cc_final: 0.6548 (tpt170) REVERT: A 375 MET cc_start: 0.6197 (mmt) cc_final: 0.5809 (mmt) REVERT: A 409 MET cc_start: 0.6987 (mtt) cc_final: 0.6602 (mtm) REVERT: A 441 MET cc_start: 0.7529 (tpt) cc_final: 0.7277 (ttp) REVERT: A 577 MET cc_start: 0.8320 (mtt) cc_final: 0.7953 (mmm) REVERT: A 639 LYS cc_start: 0.7642 (ttmt) cc_final: 0.7294 (tmmt) REVERT: A 736 ASN cc_start: 0.7820 (m110) cc_final: 0.7237 (t0) REVERT: A 801 ARG cc_start: 0.6939 (mmt-90) cc_final: 0.6698 (mpt90) REVERT: A 810 ASP cc_start: 0.7614 (t70) cc_final: 0.7369 (t0) REVERT: A 896 TRP cc_start: 0.8199 (t60) cc_final: 0.7844 (t60) REVERT: A 1099 GLU cc_start: 0.6671 (tt0) cc_final: 0.6446 (pt0) REVERT: A 1114 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7081 (mp0) REVERT: A 1203 GLU cc_start: 0.6647 (tt0) cc_final: 0.6326 (pt0) REVERT: B 253 ASP cc_start: 0.7820 (t70) cc_final: 0.7476 (t0) REVERT: B 313 HIS cc_start: 0.6686 (t-170) cc_final: 0.6312 (m-70) REVERT: C 236 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7648 (mt-10) REVERT: C 257 ARG cc_start: 0.6077 (tpm170) cc_final: 0.5639 (ttp80) REVERT: C 285 LYS cc_start: 0.7948 (mtpt) cc_final: 0.7731 (ptmt) REVERT: C 309 HIS cc_start: 0.7493 (m90) cc_final: 0.7008 (m90) REVERT: C 396 ARG cc_start: 0.5674 (mtt180) cc_final: 0.5326 (mtp-110) REVERT: C 419 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6471 (mm-30) REVERT: C 421 MET cc_start: 0.7584 (ppp) cc_final: 0.6566 (ptp) outliers start: 33 outliers final: 11 residues processed: 169 average time/residue: 0.6799 time to fit residues: 125.2599 Evaluate side-chains 142 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 938 SER Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 466 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 158 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 5 optimal weight: 0.1980 chunk 93 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 114 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 GLN A1076 ASN B 309 HIS C 318 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.157789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.121289 restraints weight = 18658.868| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.87 r_work: 0.3618 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14566 Z= 0.117 Angle : 0.502 7.085 19903 Z= 0.267 Chirality : 0.039 0.145 2129 Planarity : 0.004 0.045 2426 Dihedral : 13.424 62.516 2241 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.87 % Allowed : 11.84 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.21), residues: 1631 helix: 1.23 (0.20), residues: 691 sheet: 0.22 (0.32), residues: 256 loop : 0.22 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 292 TYR 0.010 0.001 TYR C 291 PHE 0.017 0.001 PHE B 403 TRP 0.012 0.001 TRP A 295 HIS 0.005 0.001 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (14566) covalent geometry : angle 0.50183 / 0.27 (19903) hydrogen bonds : bond 0.03909 / 2.71 ( 667) hydrogen bonds : angle 4.70713 / 3.29 ( 1846) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.556 Fit side-chains REVERT: A 95 LEU cc_start: 0.8922 (mt) cc_final: 0.8584 (mp) REVERT: A 103 LEU cc_start: 0.8284 (tp) cc_final: 0.8014 (OUTLIER) REVERT: A 112 ARG cc_start: 0.6744 (ttt-90) cc_final: 0.6461 (mpp-170) REVERT: A 296 MET cc_start: 0.6240 (mmm) cc_final: 0.5930 (mmt) REVERT: A 353 LYS cc_start: 0.8712 (ptpt) cc_final: 0.8238 (pptt) REVERT: A 365 ARG cc_start: 0.7098 (tpp-160) cc_final: 0.6554 (tpm170) REVERT: A 375 MET cc_start: 0.6277 (mmt) cc_final: 0.5831 (mmt) REVERT: A 409 MET cc_start: 0.6978 (mtt) cc_final: 0.6623 (mtm) REVERT: A 441 MET cc_start: 0.7517 (tpt) cc_final: 0.7298 (ttp) REVERT: A 447 ASP cc_start: 0.7383 (m-30) cc_final: 0.7037 (m-30) REVERT: A 451 ASP cc_start: 0.7508 (m-30) cc_final: 0.7237 (m-30) REVERT: A 556 LYS cc_start: 0.7543 (mtmt) cc_final: 0.6706 (mmtt) REVERT: A 577 MET cc_start: 0.8339 (mtt) cc_final: 0.8019 (mmm) REVERT: A 639 LYS cc_start: 0.7668 (ttmt) cc_final: 0.7336 (tmmt) REVERT: A 736 ASN cc_start: 0.7742 (m110) cc_final: 0.7149 (t0) REVERT: A 801 ARG cc_start: 0.6976 (mmt-90) cc_final: 0.6713 (mpt90) REVERT: A 810 ASP cc_start: 0.7624 (t70) cc_final: 0.7386 (t0) REVERT: A 863 VAL cc_start: 0.7187 (OUTLIER) cc_final: 0.6974 (m) REVERT: A 896 TRP cc_start: 0.8215 (t60) cc_final: 0.7834 (t60) REVERT: A 1099 GLU cc_start: 0.6640 (tt0) cc_final: 0.6421 (pt0) REVERT: A 1114 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7217 (mp0) REVERT: B 280 ASP cc_start: 0.6242 (t0) cc_final: 0.5534 (t0) REVERT: B 281 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7100 (pm20) REVERT: B 313 HIS cc_start: 0.6636 (t-170) cc_final: 0.6315 (m-70) REVERT: C 236 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7624 (mt-10) REVERT: C 257 ARG cc_start: 0.5845 (tpm170) cc_final: 0.5374 (ttp80) REVERT: C 285 LYS cc_start: 0.7985 (mtpt) cc_final: 0.7770 (ptmm) REVERT: C 309 HIS cc_start: 0.7441 (m90) cc_final: 0.7066 (m90) REVERT: C 394 GLU cc_start: 0.6307 (mt-10) cc_final: 0.5530 (tp30) REVERT: C 396 ARG cc_start: 0.5571 (mtt180) cc_final: 0.5228 (mtp-110) REVERT: C 419 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6491 (mm-30) REVERT: C 421 MET cc_start: 0.7536 (ppp) cc_final: 0.7087 (ppp) outliers start: 27 outliers final: 13 residues processed: 166 average time/residue: 0.6553 time to fit residues: 118.8457 Evaluate side-chains 143 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 938 SER Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 466 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 158 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 chunk 4 optimal weight: 0.0770 chunk 138 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 GLN A 789 GLN ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1076 ASN B 309 HIS C 318 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.157529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.121033 restraints weight = 18583.639| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.87 r_work: 0.3613 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14566 Z= 0.127 Angle : 0.496 8.023 19903 Z= 0.262 Chirality : 0.039 0.147 2129 Planarity : 0.004 0.048 2426 Dihedral : 13.358 61.516 2241 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.63 % Allowed : 12.81 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.21), residues: 1631 helix: 1.33 (0.20), residues: 692 sheet: 0.39 (0.32), residues: 256 loop : 0.31 (0.25), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 631 TYR 0.011 0.001 TYR C 291 PHE 0.015 0.001 PHE B 403 TRP 0.011 0.001 TRP A 295 HIS 0.004 0.001 HIS A 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (14566) covalent geometry : angle 0.49586 / 0.26 (19903) hydrogen bonds : bond 0.03714 / 2.59 ( 667) hydrogen bonds : angle 4.51806 / 3.15 ( 1846) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 0.611 Fit side-chains REVERT: A 54 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7398 (mm) REVERT: A 95 LEU cc_start: 0.8951 (mt) cc_final: 0.8651 (mp) REVERT: A 98 GLN cc_start: 0.8681 (tp-100) cc_final: 0.8479 (tp-100) REVERT: A 103 LEU cc_start: 0.8333 (tp) cc_final: 0.8061 (mp) REVERT: A 112 ARG cc_start: 0.6748 (ttt-90) cc_final: 0.6462 (mpp-170) REVERT: A 353 LYS cc_start: 0.8727 (ptpt) cc_final: 0.8273 (pptt) REVERT: A 365 ARG cc_start: 0.7112 (tpp-160) cc_final: 0.6532 (tpm170) REVERT: A 375 MET cc_start: 0.6377 (mmt) cc_final: 0.5899 (mmt) REVERT: A 409 MET cc_start: 0.6997 (mtt) cc_final: 0.6631 (mtm) REVERT: A 441 MET cc_start: 0.7556 (tpt) cc_final: 0.7339 (ttp) REVERT: A 447 ASP cc_start: 0.7366 (m-30) cc_final: 0.6984 (m-30) REVERT: A 451 ASP cc_start: 0.7529 (m-30) cc_final: 0.7203 (m-30) REVERT: A 556 LYS cc_start: 0.7564 (mtmt) cc_final: 0.6751 (mmtt) REVERT: A 577 MET cc_start: 0.8343 (mtt) cc_final: 0.8001 (mmm) REVERT: A 639 LYS cc_start: 0.7671 (ttmt) cc_final: 0.7344 (tmmt) REVERT: A 736 ASN cc_start: 0.7747 (m110) cc_final: 0.7129 (t0) REVERT: A 810 ASP cc_start: 0.7564 (t0) cc_final: 0.7355 (t0) REVERT: A 896 TRP cc_start: 0.8118 (t60) cc_final: 0.7824 (t60) REVERT: A 941 GLU cc_start: 0.5801 (OUTLIER) cc_final: 0.5420 (pp20) REVERT: A 1099 GLU cc_start: 0.6630 (tt0) cc_final: 0.6419 (pt0) REVERT: A 1114 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7253 (mp0) REVERT: A 1141 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6234 (tpt) REVERT: B 281 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7391 (pm20) REVERT: B 313 HIS cc_start: 0.6545 (t-170) cc_final: 0.6191 (m-70) REVERT: C 236 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7641 (mt-10) REVERT: C 257 ARG cc_start: 0.6089 (tpm170) cc_final: 0.5657 (ttp80) REVERT: C 285 LYS cc_start: 0.7949 (mtpt) cc_final: 0.7740 (ptmm) REVERT: C 309 HIS cc_start: 0.7442 (m90) cc_final: 0.7043 (m90) REVERT: C 394 GLU cc_start: 0.6264 (mt-10) cc_final: 0.5562 (tp30) REVERT: C 396 ARG cc_start: 0.5628 (mtt180) cc_final: 0.5272 (mtp-110) REVERT: C 409 ASN cc_start: 0.7097 (m110) cc_final: 0.6772 (m110) REVERT: C 419 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6487 (mm-30) REVERT: C 421 MET cc_start: 0.7526 (ppp) cc_final: 0.7084 (ppp) outliers start: 38 outliers final: 16 residues processed: 161 average time/residue: 0.6460 time to fit residues: 113.6887 Evaluate side-chains 145 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 941 GLU Chi-restraints excluded: chain A residue 1141 MET Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 466 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 93 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1076 ASN B 309 HIS C 318 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.156370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.119843 restraints weight = 18729.505| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.87 r_work: 0.3600 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14566 Z= 0.165 Angle : 0.520 8.754 19903 Z= 0.273 Chirality : 0.040 0.150 2129 Planarity : 0.004 0.049 2426 Dihedral : 13.378 60.736 2241 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.19 % Allowed : 13.50 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.21), residues: 1631 helix: 1.29 (0.20), residues: 692 sheet: 0.46 (0.32), residues: 256 loop : 0.29 (0.25), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 631 TYR 0.012 0.001 TYR C 291 PHE 0.014 0.001 PHE B 403 TRP 0.011 0.001 TRP A 295 HIS 0.006 0.001 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (14566) covalent geometry : angle 0.51990 / 0.27 (19903) hydrogen bonds : bond 0.03880 / 2.71 ( 667) hydrogen bonds : angle 4.51066 / 3.15 ( 1846) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 131 time to evaluate : 0.576 Fit side-chains REVERT: A 95 LEU cc_start: 0.8980 (mt) cc_final: 0.8615 (mp) REVERT: A 103 LEU cc_start: 0.8356 (tp) cc_final: 0.8085 (mp) REVERT: A 112 ARG cc_start: 0.6767 (ttt-90) cc_final: 0.6465 (mpp-170) REVERT: A 353 LYS cc_start: 0.8726 (ptpt) cc_final: 0.8290 (pptt) REVERT: A 365 ARG cc_start: 0.7121 (tpp-160) cc_final: 0.6584 (tpm170) REVERT: A 409 MET cc_start: 0.7038 (mtt) cc_final: 0.6635 (mtm) REVERT: A 441 MET cc_start: 0.7536 (tpt) cc_final: 0.7290 (ttp) REVERT: A 447 ASP cc_start: 0.7368 (m-30) cc_final: 0.7015 (m-30) REVERT: A 451 ASP cc_start: 0.7537 (m-30) cc_final: 0.7226 (m-30) REVERT: A 556 LYS cc_start: 0.7561 (mtmt) cc_final: 0.6759 (mmtt) REVERT: A 577 MET cc_start: 0.8347 (mtt) cc_final: 0.7965 (mmm) REVERT: A 639 LYS cc_start: 0.7673 (ttmt) cc_final: 0.7346 (tmmt) REVERT: A 736 ASN cc_start: 0.7778 (m110) cc_final: 0.7189 (t0) REVERT: A 801 ARG cc_start: 0.7494 (pmm-80) cc_final: 0.7025 (mpt90) REVERT: A 810 ASP cc_start: 0.7489 (t0) cc_final: 0.7273 (t0) REVERT: A 896 TRP cc_start: 0.8141 (t60) cc_final: 0.7877 (t60) REVERT: A 945 MET cc_start: 0.2238 (OUTLIER) cc_final: 0.1993 (mtt) REVERT: A 1099 GLU cc_start: 0.6644 (tt0) cc_final: 0.6428 (pt0) REVERT: A 1114 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7313 (mp0) REVERT: A 1141 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.6264 (tpt) REVERT: B 313 HIS cc_start: 0.6558 (t-170) cc_final: 0.6180 (m-70) REVERT: B 421 MET cc_start: 0.7216 (tpt) cc_final: 0.6997 (tmt) REVERT: C 129 ASP cc_start: 0.7724 (t70) cc_final: 0.7506 (t0) REVERT: C 236 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7676 (mt-10) REVERT: C 257 ARG cc_start: 0.6129 (tpm170) cc_final: 0.5657 (ttp80) REVERT: C 285 LYS cc_start: 0.8029 (mtpt) cc_final: 0.7824 (ptmm) REVERT: C 309 HIS cc_start: 0.7482 (m90) cc_final: 0.7112 (m90) REVERT: C 394 GLU cc_start: 0.6194 (mt-10) cc_final: 0.5514 (tp30) REVERT: C 396 ARG cc_start: 0.5640 (mtt180) cc_final: 0.5281 (mtp-110) REVERT: C 419 GLU cc_start: 0.6899 (mm-30) cc_final: 0.6484 (mm-30) REVERT: C 421 MET cc_start: 0.7556 (ppp) cc_final: 0.7113 (ppp) REVERT: C 445 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6633 (mt-10) outliers start: 46 outliers final: 23 residues processed: 166 average time/residue: 0.6258 time to fit residues: 113.5603 Evaluate side-chains 153 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 945 MET Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1141 MET Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 466 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 11 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS C 318 ASN C 409 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.155999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.119489 restraints weight = 18555.617| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.86 r_work: 0.3593 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14566 Z= 0.171 Angle : 0.537 11.618 19903 Z= 0.281 Chirality : 0.041 0.150 2129 Planarity : 0.004 0.049 2426 Dihedral : 13.416 60.258 2241 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.91 % Allowed : 14.27 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.21), residues: 1631 helix: 1.31 (0.20), residues: 687 sheet: 0.48 (0.32), residues: 256 loop : 0.25 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 631 TYR 0.012 0.001 TYR C 291 PHE 0.015 0.001 PHE B 403 TRP 0.012 0.001 TRP A 96 HIS 0.006 0.001 HIS A 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (14566) covalent geometry : angle 0.53739 / 0.28 (19903) hydrogen bonds : bond 0.03889 / 2.71 ( 667) hydrogen bonds : angle 4.48253 / 3.12 ( 1846) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8955 (mt) cc_final: 0.8280 (mp) REVERT: A 103 LEU cc_start: 0.8370 (tp) cc_final: 0.8091 (mp) REVERT: A 112 ARG cc_start: 0.6761 (ttt-90) cc_final: 0.6452 (mpp-170) REVERT: A 292 ARG cc_start: 0.5113 (ttm170) cc_final: 0.4617 (ttm170) REVERT: A 353 LYS cc_start: 0.8693 (ptpt) cc_final: 0.8239 (pptt) REVERT: A 365 ARG cc_start: 0.7123 (tpp-160) cc_final: 0.6582 (tpm170) REVERT: A 409 MET cc_start: 0.7035 (mtt) cc_final: 0.6626 (mtm) REVERT: A 441 MET cc_start: 0.7538 (tpt) cc_final: 0.7283 (ttp) REVERT: A 447 ASP cc_start: 0.7348 (m-30) cc_final: 0.7004 (m-30) REVERT: A 451 ASP cc_start: 0.7597 (m-30) cc_final: 0.7309 (m-30) REVERT: A 556 LYS cc_start: 0.7533 (mtmt) cc_final: 0.6731 (mmtt) REVERT: A 577 MET cc_start: 0.8370 (mtt) cc_final: 0.7992 (mmm) REVERT: A 639 LYS cc_start: 0.7675 (ttmt) cc_final: 0.7342 (tmmt) REVERT: A 736 ASN cc_start: 0.7768 (m110) cc_final: 0.7224 (t0) REVERT: A 801 ARG cc_start: 0.7483 (pmm-80) cc_final: 0.7068 (mpt90) REVERT: A 810 ASP cc_start: 0.7440 (t0) cc_final: 0.7202 (t0) REVERT: A 896 TRP cc_start: 0.8148 (t60) cc_final: 0.7700 (t60) REVERT: A 1099 GLU cc_start: 0.6659 (tt0) cc_final: 0.6447 (pt0) REVERT: A 1114 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7277 (mp0) REVERT: A 1141 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6263 (tpt) REVERT: B 253 ASP cc_start: 0.7851 (t70) cc_final: 0.7513 (t0) REVERT: B 313 HIS cc_start: 0.6539 (t-170) cc_final: 0.6176 (m-70) REVERT: C 129 ASP cc_start: 0.7642 (t70) cc_final: 0.7411 (t0) REVERT: C 236 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7676 (mt-10) REVERT: C 257 ARG cc_start: 0.6134 (tpm170) cc_final: 0.5658 (ttp80) REVERT: C 285 LYS cc_start: 0.8015 (mtpt) cc_final: 0.7794 (ptmm) REVERT: C 309 HIS cc_start: 0.7398 (m90) cc_final: 0.7065 (m90) REVERT: C 394 GLU cc_start: 0.6200 (mt-10) cc_final: 0.5535 (tp30) REVERT: C 396 ARG cc_start: 0.5641 (mtt180) cc_final: 0.5280 (mtp-110) REVERT: C 409 ASN cc_start: 0.7011 (m-40) cc_final: 0.6678 (m110) REVERT: C 419 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6521 (mm-30) REVERT: C 421 MET cc_start: 0.7564 (ppp) cc_final: 0.7123 (ppp) REVERT: C 445 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.6619 (mt-10) outliers start: 42 outliers final: 24 residues processed: 164 average time/residue: 0.6288 time to fit residues: 112.7194 Evaluate side-chains 157 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1141 MET Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 466 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 162 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 164 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 HIS ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1076 ASN B 309 HIS B 404 ASN C 318 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.157662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.121209 restraints weight = 18546.346| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.87 r_work: 0.3616 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14566 Z= 0.120 Angle : 0.504 12.829 19903 Z= 0.264 Chirality : 0.039 0.145 2129 Planarity : 0.004 0.050 2426 Dihedral : 13.372 59.858 2241 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.22 % Allowed : 15.24 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.21), residues: 1631 helix: 1.45 (0.20), residues: 685 sheet: 0.57 (0.32), residues: 256 loop : 0.32 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 631 TYR 0.011 0.001 TYR C 291 PHE 0.016 0.001 PHE B 403 TRP 0.011 0.001 TRP A 295 HIS 0.006 0.001 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (14566) covalent geometry : angle 0.50396 / 0.26 (19903) hydrogen bonds : bond 0.03504 / 2.44 ( 667) hydrogen bonds : angle 4.37910 / 3.05 ( 1846) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8769 (mt) cc_final: 0.7685 (mp) REVERT: A 98 GLN cc_start: 0.8821 (mt0) cc_final: 0.8162 (mp10) REVERT: A 103 LEU cc_start: 0.8349 (tp) cc_final: 0.8083 (mp) REVERT: A 112 ARG cc_start: 0.6773 (ttt-90) cc_final: 0.6486 (mpp-170) REVERT: A 292 ARG cc_start: 0.5136 (ttm170) cc_final: 0.4661 (ttm170) REVERT: A 353 LYS cc_start: 0.8716 (ptpt) cc_final: 0.8244 (pptt) REVERT: A 365 ARG cc_start: 0.7114 (tpp-160) cc_final: 0.6526 (tpm170) REVERT: A 409 MET cc_start: 0.6994 (mtt) cc_final: 0.6617 (mtm) REVERT: A 441 MET cc_start: 0.7568 (tpt) cc_final: 0.7332 (ttp) REVERT: A 446 MET cc_start: 0.7764 (mtp) cc_final: 0.7509 (mtm) REVERT: A 447 ASP cc_start: 0.7386 (m-30) cc_final: 0.7018 (m-30) REVERT: A 451 ASP cc_start: 0.7485 (m-30) cc_final: 0.7197 (m-30) REVERT: A 556 LYS cc_start: 0.7528 (mtmt) cc_final: 0.6710 (mmtt) REVERT: A 577 MET cc_start: 0.8333 (mtt) cc_final: 0.7967 (mmm) REVERT: A 639 LYS cc_start: 0.7655 (ttmt) cc_final: 0.7337 (tmmt) REVERT: A 736 ASN cc_start: 0.7702 (m110) cc_final: 0.7087 (t0) REVERT: A 801 ARG cc_start: 0.7424 (pmm-80) cc_final: 0.7011 (mpt90) REVERT: A 896 TRP cc_start: 0.8058 (t60) cc_final: 0.7595 (t60) REVERT: A 1099 GLU cc_start: 0.6629 (tt0) cc_final: 0.6412 (pt0) REVERT: A 1114 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7270 (mp0) REVERT: A 1141 MET cc_start: 0.7193 (OUTLIER) cc_final: 0.6330 (tpt) REVERT: B 313 HIS cc_start: 0.6506 (t-170) cc_final: 0.6166 (m-70) REVERT: B 421 MET cc_start: 0.7185 (tmt) cc_final: 0.6934 (tmt) REVERT: C 129 ASP cc_start: 0.7607 (t70) cc_final: 0.7393 (t0) REVERT: C 236 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7677 (mt-10) REVERT: C 257 ARG cc_start: 0.5970 (tpm170) cc_final: 0.5506 (ttp80) REVERT: C 309 HIS cc_start: 0.7358 (m90) cc_final: 0.7018 (m90) REVERT: C 346 MET cc_start: 0.5954 (OUTLIER) cc_final: 0.5673 (mtp) REVERT: C 394 GLU cc_start: 0.6193 (mt-10) cc_final: 0.5574 (tp30) REVERT: C 396 ARG cc_start: 0.5652 (mtt180) cc_final: 0.5290 (mtp-110) REVERT: C 409 ASN cc_start: 0.7138 (m-40) cc_final: 0.6918 (m110) REVERT: C 419 GLU cc_start: 0.6887 (mm-30) cc_final: 0.6462 (mm-30) REVERT: C 421 MET cc_start: 0.7558 (ppp) cc_final: 0.7174 (ppp) REVERT: C 462 MET cc_start: 0.5747 (tpp) cc_final: 0.5535 (mmt) outliers start: 32 outliers final: 14 residues processed: 158 average time/residue: 0.6404 time to fit residues: 110.6625 Evaluate side-chains 143 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 1141 MET Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 466 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 23 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 HIS A 370 ASN ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN C 318 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.158007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.121530 restraints weight = 18500.742| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.86 r_work: 0.3619 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14566 Z= 0.119 Angle : 0.496 13.375 19903 Z= 0.261 Chirality : 0.039 0.146 2129 Planarity : 0.004 0.050 2426 Dihedral : 13.303 59.680 2240 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.01 % Allowed : 15.79 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.21), residues: 1631 helix: 1.52 (0.20), residues: 685 sheet: 0.61 (0.32), residues: 256 loop : 0.33 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 631 TYR 0.011 0.001 TYR C 291 PHE 0.014 0.001 PHE B 403 TRP 0.010 0.001 TRP B 241 HIS 0.004 0.001 HIS A 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (14566) covalent geometry : angle 0.49594 / 0.26 (19903) hydrogen bonds : bond 0.03430 / 2.38 ( 667) hydrogen bonds : angle 4.31556 / 3.01 ( 1846) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8758 (mt) cc_final: 0.7819 (mp) REVERT: A 98 GLN cc_start: 0.8863 (mt0) cc_final: 0.8229 (mp10) REVERT: A 103 LEU cc_start: 0.8342 (tp) cc_final: 0.8078 (mp) REVERT: A 112 ARG cc_start: 0.6792 (ttt-90) cc_final: 0.6502 (mpp-170) REVERT: A 292 ARG cc_start: 0.5106 (ttm170) cc_final: 0.4687 (ttm170) REVERT: A 353 LYS cc_start: 0.8711 (ptpt) cc_final: 0.8227 (pptt) REVERT: A 365 ARG cc_start: 0.7104 (tpp-160) cc_final: 0.6521 (tpm170) REVERT: A 409 MET cc_start: 0.6985 (mtt) cc_final: 0.6604 (mtm) REVERT: A 441 MET cc_start: 0.7556 (tpt) cc_final: 0.7321 (ttp) REVERT: A 446 MET cc_start: 0.7795 (mtp) cc_final: 0.7537 (mtm) REVERT: A 447 ASP cc_start: 0.7377 (m-30) cc_final: 0.7017 (m-30) REVERT: A 451 ASP cc_start: 0.7452 (m-30) cc_final: 0.7149 (m-30) REVERT: A 556 LYS cc_start: 0.7554 (mtmt) cc_final: 0.6730 (mmtt) REVERT: A 577 MET cc_start: 0.8319 (mtt) cc_final: 0.7948 (mmm) REVERT: A 639 LYS cc_start: 0.7702 (ttmt) cc_final: 0.7370 (tmmt) REVERT: A 736 ASN cc_start: 0.7688 (m110) cc_final: 0.7080 (t0) REVERT: A 801 ARG cc_start: 0.7387 (pmm-80) cc_final: 0.6990 (mpt90) REVERT: A 896 TRP cc_start: 0.8042 (t60) cc_final: 0.7712 (t60) REVERT: A 1099 GLU cc_start: 0.6626 (tt0) cc_final: 0.6406 (pt0) REVERT: A 1114 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7267 (mp0) REVERT: A 1141 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6323 (tpt) REVERT: B 313 HIS cc_start: 0.6505 (t-170) cc_final: 0.6169 (m-70) REVERT: B 421 MET cc_start: 0.7212 (tmt) cc_final: 0.6934 (tmt) REVERT: C 236 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7637 (mt-10) REVERT: C 257 ARG cc_start: 0.5955 (tpm170) cc_final: 0.5496 (ttp80) REVERT: C 309 HIS cc_start: 0.7311 (m90) cc_final: 0.6956 (m90) REVERT: C 346 MET cc_start: 0.5978 (OUTLIER) cc_final: 0.5712 (mtp) REVERT: C 394 GLU cc_start: 0.6236 (mt-10) cc_final: 0.5624 (tp30) REVERT: C 396 ARG cc_start: 0.5655 (mtt180) cc_final: 0.5292 (mtp-110) REVERT: C 409 ASN cc_start: 0.7142 (m-40) cc_final: 0.6914 (m-40) REVERT: C 419 GLU cc_start: 0.6890 (mm-30) cc_final: 0.6465 (mm-30) REVERT: C 421 MET cc_start: 0.7559 (ppp) cc_final: 0.7135 (ppp) outliers start: 29 outliers final: 16 residues processed: 154 average time/residue: 0.6608 time to fit residues: 110.9045 Evaluate side-chains 148 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1141 MET Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 466 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 18 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 HIS ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1076 ASN B 85 GLN B 400 GLN C 318 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.155416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.118796 restraints weight = 18597.371| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.86 r_work: 0.3583 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14566 Z= 0.212 Angle : 0.572 13.805 19903 Z= 0.297 Chirality : 0.042 0.152 2129 Planarity : 0.005 0.055 2426 Dihedral : 13.376 59.993 2240 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.56 % Allowed : 15.65 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.21), residues: 1631 helix: 1.22 (0.20), residues: 693 sheet: 0.56 (0.32), residues: 250 loop : 0.18 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 631 TYR 0.013 0.002 TYR C 291 PHE 0.016 0.002 PHE A 728 TRP 0.010 0.001 TRP A 295 HIS 0.008 0.001 HIS A 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.21 (14566) covalent geometry : angle 0.57177 / 0.30 (19903) hydrogen bonds : bond 0.04074 / 2.83 ( 667) hydrogen bonds : angle 4.44064 / 3.09 ( 1846) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8770 (mt) cc_final: 0.7800 (mp) REVERT: A 98 GLN cc_start: 0.8883 (mt0) cc_final: 0.8276 (mp10) REVERT: A 103 LEU cc_start: 0.8326 (tp) cc_final: 0.8064 (mp) REVERT: A 112 ARG cc_start: 0.6763 (ttt-90) cc_final: 0.6442 (mpp-170) REVERT: A 292 ARG cc_start: 0.5094 (ttm170) cc_final: 0.4480 (ttm170) REVERT: A 296 MET cc_start: 0.5729 (OUTLIER) cc_final: 0.5415 (mpp) REVERT: A 353 LYS cc_start: 0.8691 (ptpt) cc_final: 0.8217 (pptt) REVERT: A 365 ARG cc_start: 0.7052 (tpp-160) cc_final: 0.6532 (tpt170) REVERT: A 441 MET cc_start: 0.7503 (tpt) cc_final: 0.7215 (ttp) REVERT: A 446 MET cc_start: 0.7672 (mtp) cc_final: 0.7452 (mtm) REVERT: A 447 ASP cc_start: 0.7269 (m-30) cc_final: 0.6898 (m-30) REVERT: A 451 ASP cc_start: 0.7385 (m-30) cc_final: 0.7099 (m-30) REVERT: A 577 MET cc_start: 0.8312 (mtt) cc_final: 0.7909 (mmm) REVERT: A 639 LYS cc_start: 0.7653 (ttmt) cc_final: 0.7342 (tmmt) REVERT: A 736 ASN cc_start: 0.7737 (m110) cc_final: 0.7145 (t0) REVERT: A 801 ARG cc_start: 0.7391 (pmm-80) cc_final: 0.6989 (mpt90) REVERT: A 888 MET cc_start: 0.6635 (mtm) cc_final: 0.6363 (ttm) REVERT: A 896 TRP cc_start: 0.8061 (t60) cc_final: 0.7684 (t60) REVERT: A 1032 GLU cc_start: 0.6077 (pm20) cc_final: 0.5566 (pm20) REVERT: A 1099 GLU cc_start: 0.6645 (tt0) cc_final: 0.6412 (pt0) REVERT: A 1114 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7283 (mp0) REVERT: A 1141 MET cc_start: 0.7008 (OUTLIER) cc_final: 0.6170 (tpt) REVERT: B 253 ASP cc_start: 0.7827 (t70) cc_final: 0.7482 (t0) REVERT: B 313 HIS cc_start: 0.6491 (t-170) cc_final: 0.6122 (m-70) REVERT: C 129 ASP cc_start: 0.7628 (t70) cc_final: 0.7392 (t0) REVERT: C 236 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7594 (mt-10) REVERT: C 257 ARG cc_start: 0.6101 (tpm170) cc_final: 0.5642 (ttp80) REVERT: C 309 HIS cc_start: 0.7276 (m90) cc_final: 0.6915 (m90) REVERT: C 394 GLU cc_start: 0.6166 (mt-10) cc_final: 0.5520 (tp30) REVERT: C 396 ARG cc_start: 0.5567 (mtt180) cc_final: 0.5204 (mtp-110) REVERT: C 409 ASN cc_start: 0.7066 (m-40) cc_final: 0.6737 (m-40) REVERT: C 419 GLU cc_start: 0.6892 (mm-30) cc_final: 0.6520 (mm-30) REVERT: C 421 MET cc_start: 0.7561 (ppp) cc_final: 0.7195 (ppp) REVERT: C 445 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6599 (mt-10) outliers start: 37 outliers final: 22 residues processed: 159 average time/residue: 0.6392 time to fit residues: 110.8020 Evaluate side-chains 153 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1141 MET Chi-restraints excluded: chain A residue 1171 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 466 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 132 optimal weight: 8.9990 chunk 164 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 HIS ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1076 ASN B 85 GLN B 309 HIS B 400 GLN C 318 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.156273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.119669 restraints weight = 18570.131| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.86 r_work: 0.3595 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14566 Z= 0.167 Angle : 0.545 14.214 19903 Z= 0.284 Chirality : 0.041 0.149 2129 Planarity : 0.004 0.056 2426 Dihedral : 13.400 59.998 2240 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.01 % Allowed : 16.34 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.21), residues: 1631 helix: 1.30 (0.20), residues: 686 sheet: 0.53 (0.32), residues: 256 loop : 0.21 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 631 TYR 0.013 0.001 TYR C 291 PHE 0.019 0.001 PHE A 947 TRP 0.011 0.001 TRP A 295 HIS 0.006 0.001 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (14566) covalent geometry : angle 0.54490 / 0.28 (19903) hydrogen bonds : bond 0.03806 / 2.64 ( 667) hydrogen bonds : angle 4.41611 / 3.07 ( 1846) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8790 (mt) cc_final: 0.8009 (mp) REVERT: A 98 GLN cc_start: 0.8891 (mt0) cc_final: 0.8340 (mp10) REVERT: A 103 LEU cc_start: 0.8333 (tp) cc_final: 0.8080 (mp) REVERT: A 112 ARG cc_start: 0.6779 (ttt-90) cc_final: 0.6472 (mpp-170) REVERT: A 292 ARG cc_start: 0.5153 (ttm170) cc_final: 0.4544 (ttm170) REVERT: A 296 MET cc_start: 0.5760 (OUTLIER) cc_final: 0.5434 (mpp) REVERT: A 353 LYS cc_start: 0.8724 (ptpt) cc_final: 0.8274 (pptt) REVERT: A 365 ARG cc_start: 0.7096 (tpp-160) cc_final: 0.6582 (tpt170) REVERT: A 441 MET cc_start: 0.7567 (tpt) cc_final: 0.7278 (ttp) REVERT: A 446 MET cc_start: 0.7765 (mtp) cc_final: 0.7544 (mtm) REVERT: A 447 ASP cc_start: 0.7359 (m-30) cc_final: 0.6996 (m-30) REVERT: A 451 ASP cc_start: 0.7514 (m-30) cc_final: 0.7219 (m-30) REVERT: A 556 LYS cc_start: 0.7492 (mtmt) cc_final: 0.6720 (mmtt) REVERT: A 577 MET cc_start: 0.8351 (mtt) cc_final: 0.7980 (mmm) REVERT: A 639 LYS cc_start: 0.7676 (ttmt) cc_final: 0.7366 (tmmt) REVERT: A 736 ASN cc_start: 0.7740 (m110) cc_final: 0.7125 (t0) REVERT: A 801 ARG cc_start: 0.7386 (pmm-80) cc_final: 0.7006 (mpt90) REVERT: A 888 MET cc_start: 0.6726 (mtm) cc_final: 0.6474 (ttm) REVERT: A 1032 GLU cc_start: 0.5985 (pm20) cc_final: 0.5440 (pm20) REVERT: A 1099 GLU cc_start: 0.6648 (tt0) cc_final: 0.6428 (pt0) REVERT: A 1114 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7303 (mp0) REVERT: A 1141 MET cc_start: 0.7099 (OUTLIER) cc_final: 0.6263 (tpt) REVERT: B 253 ASP cc_start: 0.7849 (t70) cc_final: 0.7493 (t0) REVERT: B 313 HIS cc_start: 0.6519 (t-170) cc_final: 0.6173 (m-70) REVERT: C 129 ASP cc_start: 0.7627 (t70) cc_final: 0.7410 (t0) REVERT: C 236 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7665 (mt-10) REVERT: C 257 ARG cc_start: 0.6097 (tpm170) cc_final: 0.5648 (ttp80) REVERT: C 309 HIS cc_start: 0.7283 (m90) cc_final: 0.6951 (m90) REVERT: C 346 MET cc_start: 0.5981 (ttm) cc_final: 0.5779 (mtp) REVERT: C 394 GLU cc_start: 0.6206 (mt-10) cc_final: 0.5566 (tp30) REVERT: C 396 ARG cc_start: 0.5663 (mtt180) cc_final: 0.5292 (mtp-110) REVERT: C 409 ASN cc_start: 0.7130 (m-40) cc_final: 0.6903 (m110) REVERT: C 419 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6546 (mm-30) REVERT: C 421 MET cc_start: 0.7564 (ppp) cc_final: 0.7197 (ppp) outliers start: 29 outliers final: 21 residues processed: 153 average time/residue: 0.6199 time to fit residues: 103.4813 Evaluate side-chains 151 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1141 MET Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 466 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 27 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 0.6980 chunk 126 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 139 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN B 400 GLN C 318 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.155405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.118680 restraints weight = 18580.206| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.86 r_work: 0.3577 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14566 Z= 0.198 Angle : 0.564 14.198 19903 Z= 0.294 Chirality : 0.042 0.152 2129 Planarity : 0.005 0.055 2426 Dihedral : 13.440 59.855 2240 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.94 % Allowed : 16.34 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.21), residues: 1631 helix: 1.15 (0.20), residues: 693 sheet: 0.53 (0.32), residues: 250 loop : 0.15 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 631 TYR 0.013 0.002 TYR C 291 PHE 0.023 0.002 PHE A 947 TRP 0.015 0.001 TRP A 896 HIS 0.007 0.001 HIS A 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (14566) covalent geometry : angle 0.56374 / 0.29 (19903) hydrogen bonds : bond 0.04030 / 2.80 ( 667) hydrogen bonds : angle 4.46505 / 3.11 ( 1846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4920.87 seconds wall clock time: 84 minutes 48.46 seconds (5088.46 seconds total)