Starting phenix.real_space_refine on Thu Sep 18 04:57:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ibx_52815/09_2025/9ibx_52815.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ibx_52815/09_2025/9ibx_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_52815/09_2025/9ibx_52815.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ibx_52815/09_2025/9ibx_52815.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ibx_52815/09_2025/9ibx_52815.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ibx_52815/09_2025/9ibx_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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, 29 Unusual residues: {' CA': 1, 'DCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.67, per 1000 atoms: 0.26 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: 1.44 Conformation dependent library (CDL) restraints added in 651.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.95 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: 2.88 Time building geometry restraints manager: 1.86 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=" C6 DCP A1301 " pdb=" N1 DCP A1301 " ideal model delta sigma weight residual 1.375 1.333 0.042 1.20e-02 6.94e+03 1.20e+01 bond pdb=" C4 DCP A1301 " pdb=" C5 DCP A1301 " ideal model delta sigma weight residual 1.426 1.386 0.040 1.20e-02 6.94e+03 1.10e+01 bond pdb=" O1A DCP A1301 " pdb=" PA DCP A1301 " ideal model delta sigma weight residual 1.477 1.508 -0.031 1.00e-02 1.00e+04 9.59e+00 bond pdb=" O1B DCP A1301 " pdb=" PB DCP A1301 " ideal model delta sigma weight residual 1.477 1.509 -0.032 1.10e-02 8.26e+03 8.57e+00 bond pdb=" C5 DCP A1301 " pdb=" C6 DCP A1301 " ideal model delta sigma weight residual 1.345 1.386 -0.041 1.80e-02 3.09e+03 5.20e+00 ... (remaining 14561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.68: 19865 3.68 - 7.36: 35 7.36 - 11.04: 1 11.04 - 14.72: 0 14.72 - 18.40: 2 Bond angle restraints: 19903 Sorted by residual: angle pdb=" PB DCP A1301 " pdb=" O3B DCP A1301 " pdb=" PG DCP A1301 " ideal model delta sigma weight residual 139.87 121.47 18.40 1.00e+00 1.00e+00 3.39e+02 angle pdb=" PA DCP A1301 " pdb=" O3A DCP A1301 " pdb=" PB DCP A1301 " ideal model delta sigma weight residual 136.83 120.15 16.68 1.00e+00 1.00e+00 2.78e+02 angle pdb=" O1G DCP A1301 " pdb=" PG DCP A1301 " pdb=" O3B DCP A1301 " ideal model delta sigma weight residual 110.47 103.52 6.95 1.64e+00 3.70e-01 1.78e+01 angle pdb=" N GLY C 307 " pdb=" CA GLY C 307 " pdb=" C GLY C 307 " ideal model delta sigma weight residual 113.18 122.59 -9.41 2.37e+00 1.78e-01 1.58e+01 angle pdb=" C2' DCP A1301 " pdb=" C1' DCP A1301 " pdb=" N1 DCP A1301 " ideal model delta sigma weight residual 113.92 109.18 4.74 1.28e+00 6.12e-01 1.38e+01 ... (remaining 19898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 7722 16.43 - 32.87: 621 32.87 - 49.30: 175 49.30 - 65.74: 58 65.74 - 82.17: 3 Dihedral angle restraints: 8579 sinusoidal: 3797 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 8576 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1523 0.038 - 0.075: 445 0.075 - 0.113: 129 0.113 - 0.151: 31 0.151 - 0.189: 1 Chirality restraints: 2129 Sorted by residual: 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=" C3' DCP A1301 " pdb=" C2' DCP A1301 " pdb=" C4' DCP A1301 " pdb=" O3' DCP A1301 " both_signs ideal model delta sigma weight residual False -2.68 -2.53 -0.15 2.00e-01 2.50e+01 5.33e-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 2.510 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: 2.340 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: 0.210 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.610 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 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 0.055 14566 Z= 0.197 Angle : 0.589 18.399 19903 Z= 0.363 Chirality : 0.041 0.189 2129 Planarity : 0.004 0.049 2426 Dihedral : 13.658 82.172 5495 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 aren 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 covalent geometry : bond 0.00388 (14566) covalent geometry : angle 0.58863 (19903) hydrogen bonds : bond 0.16921 ( 667) hydrogen bonds : angle 6.85222 ( 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 : 0.566 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: 0.7092 time to fit residues: 166.0077 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 : 0.504 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.155405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.118754 restraints weight = 18601.185| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.86 r_work: 0.3584 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 14566 Z= 0.193 Angle : 0.573 8.787 19903 Z= 0.297 Chirality : 0.042 0.155 2129 Planarity : 0.005 0.050 2426 Dihedral : 13.532 64.042 2240 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.08 % Allowed : 10.60 % Favored : 87.33 % 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 aren not related in a simple way. whole: 0.57 (0.21), residues: 1631 helix: 1.00 (0.20), residues: 692 sheet: -0.00 (0.32), residues: 256 loop : 0.05 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 638 TYR 0.013 0.002 TYR C 291 PHE 0.017 0.002 PHE C 403 TRP 0.015 0.001 TRP A 295 HIS 0.006 0.001 HIS A 783 Details of bonding type rmsd covalent geometry : bond 0.00453 (14566) covalent geometry : angle 0.57333 (19903) hydrogen bonds : bond 0.04593 ( 667) hydrogen bonds : angle 4.98541 ( 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 180 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8927 (mt) cc_final: 0.8635 (mp) REVERT: A 103 LEU cc_start: 0.8327 (tp) cc_final: 0.8027 (mp) REVERT: A 112 ARG cc_start: 0.6748 (ttt-90) cc_final: 0.6438 (mpp-170) REVERT: A 353 LYS cc_start: 0.8744 (ptpt) cc_final: 0.8289 (pptt) REVERT: A 365 ARG cc_start: 0.7116 (tpp-160) cc_final: 0.6584 (tpm170) REVERT: A 409 MET cc_start: 0.7037 (mtt) cc_final: 0.6645 (mtm) REVERT: A 441 MET cc_start: 0.7532 (tpt) cc_final: 0.7301 (ttp) REVERT: A 451 ASP cc_start: 0.7662 (m-30) cc_final: 0.7407 (m-30) REVERT: A 577 MET cc_start: 0.8336 (mtt) cc_final: 0.7976 (mmm) REVERT: A 639 LYS cc_start: 0.7690 (ttmt) cc_final: 0.7360 (tmmt) REVERT: A 736 ASN cc_start: 0.7808 (m110) cc_final: 0.7249 (t0) REVERT: A 801 ARG cc_start: 0.6971 (mmt-90) cc_final: 0.6738 (mpt90) REVERT: A 810 ASP cc_start: 0.7608 (t70) cc_final: 0.7369 (t0) REVERT: A 896 TRP cc_start: 0.8209 (t60) cc_final: 0.7857 (t60) REVERT: A 1099 GLU cc_start: 0.6668 (tt0) cc_final: 0.6442 (pt0) REVERT: A 1114 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7047 (mp0) REVERT: A 1203 GLU cc_start: 0.6668 (tt0) cc_final: 0.6347 (pt0) REVERT: B 253 ASP cc_start: 0.7844 (t70) cc_final: 0.7504 (t0) REVERT: B 280 ASP cc_start: 0.6285 (t0) cc_final: 0.5607 (t0) REVERT: B 281 GLU cc_start: 0.7664 (mp0) cc_final: 0.7452 (pm20) REVERT: B 313 HIS cc_start: 0.6695 (t-170) cc_final: 0.6339 (m-70) REVERT: C 236 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7696 (mt-10) REVERT: C 257 ARG cc_start: 0.6112 (tpm170) cc_final: 0.5649 (ttp80) REVERT: C 285 LYS cc_start: 0.7957 (mtpt) cc_final: 0.7743 (ptmt) REVERT: C 309 HIS cc_start: 0.7529 (m90) cc_final: 0.7015 (m90) REVERT: C 394 GLU cc_start: 0.6341 (mt-10) cc_final: 0.5615 (tp30) REVERT: C 396 ARG cc_start: 0.5733 (mtt180) cc_final: 0.5386 (mtp-110) REVERT: C 419 GLU cc_start: 0.6938 (mm-30) cc_final: 0.6516 (mm-30) outliers start: 30 outliers final: 12 residues processed: 170 average time/residue: 0.7290 time to fit residues: 134.7691 Evaluate side-chains 148 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 963 MET Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 185 LEU 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: 0.3980 chunk 67 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 114 optimal weight: 0.5980 chunk 140 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.157406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.121101 restraints weight = 18611.577| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.87 r_work: 0.3612 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14566 Z= 0.117 Angle : 0.496 7.585 19903 Z= 0.259 Chirality : 0.039 0.146 2129 Planarity : 0.004 0.047 2426 Dihedral : 13.300 63.295 2234 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.94 % Allowed : 12.26 % Favored : 85.80 % 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 aren not related in a simple way. whole: 0.93 (0.21), residues: 1631 helix: 1.29 (0.20), residues: 691 sheet: 0.25 (0.32), residues: 256 loop : 0.21 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 631 TYR 0.011 0.001 TYR C 291 PHE 0.016 0.001 PHE B 403 TRP 0.012 0.001 TRP A 203 HIS 0.005 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00259 (14566) covalent geometry : angle 0.49607 (19903) hydrogen bonds : bond 0.03638 ( 667) hydrogen bonds : angle 4.60595 ( 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 173 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8915 (mt) cc_final: 0.8571 (mp) REVERT: A 103 LEU cc_start: 0.8299 (tp) cc_final: 0.8030 (mp) REVERT: A 112 ARG cc_start: 0.6792 (ttt-90) cc_final: 0.6498 (mpp-170) REVERT: A 353 LYS cc_start: 0.8699 (ptpt) cc_final: 0.8234 (pptt) REVERT: A 365 ARG cc_start: 0.7121 (tpp-160) cc_final: 0.6553 (tpm170) REVERT: A 409 MET cc_start: 0.7001 (mtt) cc_final: 0.6645 (mtm) REVERT: A 441 MET cc_start: 0.7538 (tpt) cc_final: 0.7322 (ttp) REVERT: A 447 ASP cc_start: 0.7367 (m-30) cc_final: 0.6994 (m-30) REVERT: A 451 ASP cc_start: 0.7523 (m-30) cc_final: 0.7212 (m-30) REVERT: A 556 LYS cc_start: 0.7549 (mtmt) cc_final: 0.6731 (mmtt) REVERT: A 577 MET cc_start: 0.8345 (mtt) cc_final: 0.8030 (mmm) REVERT: A 639 LYS cc_start: 0.7656 (ttmt) cc_final: 0.7344 (tmmt) REVERT: A 736 ASN cc_start: 0.7744 (m110) cc_final: 0.7129 (t0) REVERT: A 801 ARG cc_start: 0.6938 (mmt-90) cc_final: 0.6693 (mpt90) REVERT: A 896 TRP cc_start: 0.8200 (t60) cc_final: 0.7856 (t60) REVERT: A 1099 GLU cc_start: 0.6619 (tt0) cc_final: 0.6408 (pt0) REVERT: A 1114 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7133 (mp0) REVERT: B 253 ASP cc_start: 0.7820 (t70) cc_final: 0.7465 (t0) REVERT: B 280 ASP cc_start: 0.6245 (t0) cc_final: 0.5746 (t0) REVERT: B 281 GLU cc_start: 0.7727 (mp0) cc_final: 0.7429 (pm20) REVERT: B 313 HIS cc_start: 0.6532 (t-170) cc_final: 0.6192 (m-70) REVERT: C 236 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7679 (mt-10) REVERT: C 257 ARG cc_start: 0.5805 (tpm170) cc_final: 0.5342 (ttp80) REVERT: C 285 LYS cc_start: 0.7952 (mtpt) cc_final: 0.7739 (ptmm) REVERT: C 394 GLU cc_start: 0.6267 (mt-10) cc_final: 0.5617 (tp30) REVERT: C 396 ARG cc_start: 0.5659 (mtt180) cc_final: 0.5303 (mtp-110) REVERT: C 419 GLU cc_start: 0.6906 (mm-30) cc_final: 0.6490 (mm-30) outliers start: 28 outliers final: 9 residues processed: 163 average time/residue: 0.7350 time to fit residues: 130.1963 Evaluate side-chains 139 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 460 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 158 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 151 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1076 ASN C 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.156599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.120130 restraints weight = 18601.928| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.86 r_work: 0.3603 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14566 Z= 0.153 Angle : 0.512 8.825 19903 Z= 0.265 Chirality : 0.040 0.149 2129 Planarity : 0.004 0.048 2426 Dihedral : 13.262 61.926 2234 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.35 % Allowed : 13.30 % Favored : 84.35 % 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 aren not related in a simple way. whole: 0.99 (0.21), residues: 1631 helix: 1.28 (0.20), residues: 693 sheet: 0.36 (0.32), residues: 256 loop : 0.27 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 631 TYR 0.013 0.001 TYR C 291 PHE 0.015 0.001 PHE B 403 TRP 0.011 0.001 TRP A 295 HIS 0.005 0.001 HIS A 783 Details of bonding type rmsd covalent geometry : bond 0.00357 (14566) covalent geometry : angle 0.51201 (19903) hydrogen bonds : bond 0.03731 ( 667) hydrogen bonds : angle 4.49129 ( 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 168 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 0.598 Fit side-chains REVERT: A 95 LEU cc_start: 0.8902 (mt) cc_final: 0.8518 (mp) REVERT: A 98 GLN cc_start: 0.8656 (tp-100) cc_final: 0.8378 (tp-100) REVERT: A 103 LEU cc_start: 0.8355 (tp) cc_final: 0.8080 (mp) REVERT: A 112 ARG cc_start: 0.6776 (ttt-90) cc_final: 0.6477 (mpp-170) REVERT: A 353 LYS cc_start: 0.8728 (ptpt) cc_final: 0.8273 (pptt) REVERT: A 365 ARG cc_start: 0.7117 (tpp-160) cc_final: 0.6574 (tpm170) REVERT: A 409 MET cc_start: 0.7016 (mtt) cc_final: 0.6642 (mtm) REVERT: A 441 MET cc_start: 0.7515 (tpt) cc_final: 0.7288 (ttp) REVERT: A 446 MET cc_start: 0.7766 (mtp) cc_final: 0.7536 (mtm) REVERT: A 447 ASP cc_start: 0.7357 (m-30) cc_final: 0.6987 (m-30) REVERT: A 451 ASP cc_start: 0.7543 (m-30) cc_final: 0.7231 (m-30) REVERT: A 556 LYS cc_start: 0.7526 (mtmt) cc_final: 0.6711 (mmtt) REVERT: A 577 MET cc_start: 0.8357 (mtt) cc_final: 0.8004 (mmm) REVERT: A 639 LYS cc_start: 0.7672 (ttmt) cc_final: 0.7346 (tmmt) REVERT: A 736 ASN cc_start: 0.7776 (m110) cc_final: 0.7183 (t0) REVERT: A 896 TRP cc_start: 0.8158 (t60) cc_final: 0.7857 (t60) REVERT: A 1099 GLU cc_start: 0.6647 (tt0) cc_final: 0.6433 (pt0) REVERT: A 1114 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7125 (mp0) REVERT: A 1141 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6269 (tpt) REVERT: B 253 ASP cc_start: 0.7850 (t70) cc_final: 0.7503 (t0) REVERT: B 280 ASP cc_start: 0.6269 (t0) cc_final: 0.5780 (t0) REVERT: B 281 GLU cc_start: 0.7766 (mp0) cc_final: 0.7450 (pm20) REVERT: B 313 HIS cc_start: 0.6556 (t-170) cc_final: 0.6181 (m-70) REVERT: C 129 ASP cc_start: 0.7630 (t70) cc_final: 0.7421 (t0) REVERT: C 236 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7655 (mt-10) REVERT: C 257 ARG cc_start: 0.6192 (tpm170) cc_final: 0.5731 (ttp80) REVERT: C 285 LYS cc_start: 0.8029 (mtpt) cc_final: 0.7804 (ptmm) REVERT: C 394 GLU cc_start: 0.6195 (mt-10) cc_final: 0.5538 (tp30) REVERT: C 396 ARG cc_start: 0.5628 (mtt180) cc_final: 0.5275 (mtp-110) REVERT: C 419 GLU cc_start: 0.6892 (mm-30) cc_final: 0.6526 (mm-30) outliers start: 34 outliers final: 19 residues processed: 159 average time/residue: 0.7403 time to fit residues: 127.9113 Evaluate side-chains 149 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 770 LEU Chi-restraints excluded: chain A residue 833 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 93 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 76 optimal weight: 0.2980 chunk 85 optimal weight: 0.8980 chunk 164 optimal weight: 0.2980 chunk 130 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 71 optimal weight: 20.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1076 ASN C 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.157909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.121519 restraints weight = 18706.619| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.88 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: 0.6925 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14566 Z= 0.122 Angle : 0.490 9.504 19903 Z= 0.254 Chirality : 0.039 0.151 2129 Planarity : 0.004 0.047 2426 Dihedral : 13.160 60.824 2234 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.49 % Allowed : 14.06 % Favored : 83.45 % 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 aren not related in a simple way. whole: 1.18 (0.21), residues: 1631 helix: 1.48 (0.20), residues: 686 sheet: 0.47 (0.32), residues: 256 loop : 0.33 (0.25), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 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 96 HIS 0.004 0.001 HIS A 783 Details of bonding type rmsd covalent geometry : bond 0.00279 (14566) covalent geometry : angle 0.49013 (19903) hydrogen bonds : bond 0.03360 ( 667) hydrogen bonds : angle 4.35229 ( 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 173 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8950 (mt) cc_final: 0.8571 (mp) REVERT: A 98 GLN cc_start: 0.8700 (tp-100) cc_final: 0.8461 (tp-100) REVERT: A 103 LEU cc_start: 0.8340 (tp) cc_final: 0.8075 (mp) REVERT: A 112 ARG cc_start: 0.6800 (ttt-90) cc_final: 0.6512 (mpp-170) REVERT: A 353 LYS cc_start: 0.8712 (ptpt) cc_final: 0.8208 (pptt) REVERT: A 365 ARG cc_start: 0.7094 (tpp-160) cc_final: 0.6507 (tpm170) REVERT: A 409 MET cc_start: 0.7001 (mtt) cc_final: 0.6625 (mtm) REVERT: A 441 MET cc_start: 0.7563 (tpt) cc_final: 0.7339 (ttp) REVERT: A 446 MET cc_start: 0.7793 (mtp) cc_final: 0.7536 (mtm) REVERT: A 447 ASP cc_start: 0.7388 (m-30) cc_final: 0.7017 (m-30) REVERT: A 451 ASP cc_start: 0.7509 (m-30) cc_final: 0.7218 (m-30) REVERT: A 556 LYS cc_start: 0.7529 (mtmt) cc_final: 0.6702 (mmtt) REVERT: A 577 MET cc_start: 0.8309 (mtt) cc_final: 0.7942 (mmm) REVERT: A 639 LYS cc_start: 0.7706 (ttmt) cc_final: 0.7376 (tmmt) REVERT: A 736 ASN cc_start: 0.7699 (m110) cc_final: 0.7094 (t0) REVERT: A 801 ARG cc_start: 0.7460 (pmm-80) cc_final: 0.7040 (mpt90) REVERT: A 896 TRP cc_start: 0.8122 (t60) cc_final: 0.7889 (t60) REVERT: A 945 MET cc_start: 0.2352 (OUTLIER) cc_final: 0.1927 (mpp) REVERT: A 1099 GLU cc_start: 0.6623 (tt0) cc_final: 0.6408 (pt0) REVERT: A 1114 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7120 (mp0) REVERT: A 1141 MET cc_start: 0.7178 (OUTLIER) cc_final: 0.6348 (tpt) REVERT: B 253 ASP cc_start: 0.7850 (t70) cc_final: 0.7486 (t0) REVERT: B 280 ASP cc_start: 0.6283 (t0) cc_final: 0.5822 (t0) REVERT: B 281 GLU cc_start: 0.7796 (mp0) cc_final: 0.7480 (pm20) REVERT: B 313 HIS cc_start: 0.6518 (t-170) cc_final: 0.6176 (m-70) REVERT: C 129 ASP cc_start: 0.7567 (t70) cc_final: 0.7363 (t0) REVERT: C 236 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7676 (mt-10) REVERT: C 257 ARG cc_start: 0.6095 (tpm170) cc_final: 0.5655 (ttp80) REVERT: C 328 ARG cc_start: 0.6120 (mmp80) cc_final: 0.5873 (mmp80) REVERT: C 346 MET cc_start: 0.5968 (OUTLIER) cc_final: 0.5693 (mtp) REVERT: C 394 GLU cc_start: 0.6177 (mt-10) cc_final: 0.5609 (tp30) REVERT: C 396 ARG cc_start: 0.5652 (mtt180) cc_final: 0.5290 (mtp-110) REVERT: C 419 GLU cc_start: 0.6904 (mm-30) cc_final: 0.6550 (mm-30) REVERT: C 421 MET cc_start: 0.7320 (ppp) cc_final: 0.7018 (ppp) REVERT: C 445 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6574 (mt-10) outliers start: 36 outliers final: 16 residues processed: 160 average time/residue: 0.7251 time to fit residues: 126.2752 Evaluate side-chains 150 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 770 LEU 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 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 256 LEU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 346 MET 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: 2.9990 chunk 71 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 116 optimal weight: 0.0270 chunk 130 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 overall best weight: 2.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1076 ASN B 309 HIS C 318 ASN C 409 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.155198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.118676 restraints weight = 18557.847| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.85 r_work: 0.3577 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14566 Z= 0.207 Angle : 0.554 12.094 19903 Z= 0.285 Chirality : 0.042 0.158 2129 Planarity : 0.005 0.049 2426 Dihedral : 13.261 60.709 2233 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.84 % Allowed : 14.34 % 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 aren not related in a simple way. whole: 0.94 (0.21), residues: 1631 helix: 1.22 (0.20), residues: 688 sheet: 0.50 (0.32), residues: 250 loop : 0.21 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 631 TYR 0.015 0.002 TYR C 291 PHE 0.016 0.002 PHE A 728 TRP 0.011 0.001 TRP A 295 HIS 0.007 0.001 HIS A 783 Details of bonding type rmsd covalent geometry : bond 0.00494 (14566) covalent geometry : angle 0.55436 (19903) hydrogen bonds : bond 0.04027 ( 667) hydrogen bonds : angle 4.48397 ( 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 171 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8938 (mt) cc_final: 0.8612 (mp) REVERT: A 98 GLN cc_start: 0.8677 (tp-100) cc_final: 0.8439 (tp-100) REVERT: A 103 LEU cc_start: 0.8351 (tp) cc_final: 0.8069 (mp) REVERT: A 112 ARG cc_start: 0.6732 (ttt-90) cc_final: 0.6419 (mpp-170) REVERT: A 353 LYS cc_start: 0.8700 (ptpt) cc_final: 0.8206 (pptt) REVERT: A 365 ARG cc_start: 0.7071 (tpp-160) cc_final: 0.6553 (tpt170) REVERT: A 441 MET cc_start: 0.7540 (tpt) cc_final: 0.7248 (ttp) REVERT: A 447 ASP cc_start: 0.7241 (m-30) cc_final: 0.7023 (m-30) REVERT: A 577 MET cc_start: 0.8259 (mtt) cc_final: 0.7897 (mmm) REVERT: A 639 LYS cc_start: 0.7648 (ttmt) cc_final: 0.7337 (tmmt) REVERT: A 736 ASN cc_start: 0.7786 (m110) cc_final: 0.7149 (t0) REVERT: A 801 ARG cc_start: 0.7418 (pmm-80) cc_final: 0.6988 (mpt90) REVERT: A 896 TRP cc_start: 0.8116 (t60) cc_final: 0.7897 (t60) REVERT: A 945 MET cc_start: 0.2205 (OUTLIER) cc_final: 0.1852 (mpp) REVERT: A 1099 GLU cc_start: 0.6640 (tt0) cc_final: 0.6401 (pt0) REVERT: A 1114 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7143 (mp0) REVERT: A 1141 MET cc_start: 0.6987 (OUTLIER) cc_final: 0.6152 (tpt) REVERT: B 253 ASP cc_start: 0.7810 (t70) cc_final: 0.7472 (t0) REVERT: B 280 ASP cc_start: 0.6306 (t0) cc_final: 0.5823 (t0) REVERT: B 281 GLU cc_start: 0.7793 (mp0) cc_final: 0.7446 (pm20) REVERT: B 313 HIS cc_start: 0.6584 (t-170) cc_final: 0.6227 (m-70) REVERT: C 129 ASP cc_start: 0.7569 (t70) cc_final: 0.7331 (t0) REVERT: C 236 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7573 (mt-10) REVERT: C 257 ARG cc_start: 0.6099 (tpm170) cc_final: 0.5648 (ttp80) REVERT: C 394 GLU cc_start: 0.6133 (mt-10) cc_final: 0.5523 (tp30) REVERT: C 396 ARG cc_start: 0.5587 (mtt180) cc_final: 0.5221 (mtp-110) REVERT: C 419 GLU cc_start: 0.6818 (mm-30) cc_final: 0.6587 (mm-30) REVERT: C 421 MET cc_start: 0.7298 (ppp) cc_final: 0.7074 (ppp) REVERT: C 445 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6557 (mt-10) outliers start: 41 outliers final: 20 residues processed: 160 average time/residue: 0.7065 time to fit residues: 123.3587 Evaluate side-chains 149 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 833 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 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: 0.1980 chunk 88 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 163 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.156136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.119610 restraints weight = 18540.176| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.86 r_work: 0.3592 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14566 Z= 0.157 Angle : 0.522 13.128 19903 Z= 0.269 Chirality : 0.040 0.149 2129 Planarity : 0.004 0.058 2426 Dihedral : 13.247 60.978 2233 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.63 % Allowed : 15.03 % Favored : 82.34 % 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 aren not related in a simple way. whole: 0.99 (0.21), residues: 1631 helix: 1.27 (0.20), residues: 693 sheet: 0.50 (0.32), residues: 250 loop : 0.22 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 631 TYR 0.013 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 covalent geometry : bond 0.00371 (14566) covalent geometry : angle 0.52238 (19903) hydrogen bonds : bond 0.03702 ( 667) hydrogen bonds : angle 4.41039 ( 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 168 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 130 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.8652 (tp-100) cc_final: 0.8384 (tp-100) REVERT: A 103 LEU cc_start: 0.8404 (tp) cc_final: 0.8124 (mp) REVERT: A 112 ARG cc_start: 0.6770 (ttt-90) cc_final: 0.6470 (mpp-170) REVERT: A 353 LYS cc_start: 0.8711 (ptpt) cc_final: 0.8247 (pptt) REVERT: A 365 ARG cc_start: 0.7112 (tpp-160) cc_final: 0.6599 (tpt170) REVERT: A 409 MET cc_start: 0.6998 (mtt) cc_final: 0.6624 (mtm) REVERT: A 441 MET cc_start: 0.7575 (tpt) cc_final: 0.7296 (ttp) REVERT: A 446 MET cc_start: 0.7743 (mtp) cc_final: 0.7527 (mtm) REVERT: A 447 ASP cc_start: 0.7326 (m-30) cc_final: 0.6966 (m-30) REVERT: A 451 ASP cc_start: 0.7492 (m-30) cc_final: 0.7213 (m-30) REVERT: A 556 LYS cc_start: 0.7466 (mtmt) cc_final: 0.6690 (mmtt) REVERT: A 577 MET cc_start: 0.8304 (mtt) cc_final: 0.7974 (mmm) REVERT: A 639 LYS cc_start: 0.7675 (ttmt) cc_final: 0.7364 (tmmt) REVERT: A 736 ASN cc_start: 0.7735 (m110) cc_final: 0.7116 (t0) REVERT: A 752 MET cc_start: 0.7075 (ttm) cc_final: 0.6849 (ttt) REVERT: A 801 ARG cc_start: 0.7383 (pmm-80) cc_final: 0.6991 (mpt90) REVERT: A 888 MET cc_start: 0.6658 (mtm) cc_final: 0.6380 (ttm) REVERT: A 945 MET cc_start: 0.2393 (OUTLIER) cc_final: 0.2040 (mpp) REVERT: A 1099 GLU cc_start: 0.6648 (tt0) cc_final: 0.6423 (pt0) REVERT: A 1114 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7194 (mp0) REVERT: A 1141 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6306 (tpt) REVERT: B 253 ASP cc_start: 0.7836 (t70) cc_final: 0.7476 (t0) REVERT: B 280 ASP cc_start: 0.6305 (t0) cc_final: 0.5861 (t0) REVERT: B 281 GLU cc_start: 0.7838 (mp0) cc_final: 0.7496 (pm20) REVERT: B 313 HIS cc_start: 0.6515 (t-170) cc_final: 0.6175 (m-70) REVERT: C 129 ASP cc_start: 0.7652 (t70) cc_final: 0.7418 (t0) REVERT: C 236 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7662 (mt-10) REVERT: C 257 ARG cc_start: 0.6093 (tpm170) cc_final: 0.5637 (ttp80) REVERT: C 346 MET cc_start: 0.5989 (OUTLIER) cc_final: 0.5668 (mtp) REVERT: C 394 GLU cc_start: 0.6194 (mt-10) cc_final: 0.5576 (tp30) REVERT: C 396 ARG cc_start: 0.5635 (mtt180) cc_final: 0.5262 (mtp-110) REVERT: C 409 ASN cc_start: 0.7125 (m-40) cc_final: 0.6812 (m110) REVERT: C 419 GLU cc_start: 0.6860 (mm-30) cc_final: 0.6497 (mm-30) REVERT: C 421 MET cc_start: 0.7281 (ppp) cc_final: 0.7080 (ppp) outliers start: 38 outliers final: 24 residues processed: 160 average time/residue: 0.6958 time to fit residues: 121.6264 Evaluate side-chains 156 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 217 SER 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 945 MET Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1072 THR 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 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 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: 6.9990 chunk 14 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 72 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 140 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN B 309 HIS 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 = 0.4132 r_free = 0.4132 target = 0.157704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.121246 restraints weight = 18499.123| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.87 r_work: 0.3617 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.1945 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= 0.116 Angle : 0.491 13.203 19903 Z= 0.254 Chirality : 0.038 0.147 2129 Planarity : 0.004 0.052 2426 Dihedral : 13.139 60.450 2233 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.42 % Allowed : 15.37 % 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 aren not related in a simple way. whole: 1.20 (0.21), residues: 1631 helix: 1.51 (0.20), residues: 685 sheet: 0.54 (0.32), residues: 256 loop : 0.31 (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 0.026 0.001 TRP A 896 HIS 0.006 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00264 (14566) covalent geometry : angle 0.49098 (19903) hydrogen bonds : bond 0.03317 ( 667) hydrogen bonds : angle 4.28381 ( 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 171 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.8387 (tp) cc_final: 0.8119 (mp) REVERT: A 112 ARG cc_start: 0.6778 (ttt-90) cc_final: 0.6441 (mpp-170) REVERT: A 353 LYS cc_start: 0.8701 (ptpt) cc_final: 0.8226 (pptt) REVERT: A 365 ARG cc_start: 0.7087 (tpp-160) cc_final: 0.6544 (tpt170) REVERT: A 409 MET cc_start: 0.6986 (mtt) cc_final: 0.6598 (mtm) REVERT: A 441 MET cc_start: 0.7566 (tpt) cc_final: 0.7322 (ttp) REVERT: A 446 MET cc_start: 0.7757 (mtp) cc_final: 0.7504 (mtm) REVERT: A 447 ASP cc_start: 0.7362 (m-30) cc_final: 0.6996 (m-30) REVERT: A 451 ASP cc_start: 0.7473 (m-30) cc_final: 0.7171 (m-30) REVERT: A 556 LYS cc_start: 0.7535 (mtmt) cc_final: 0.6714 (mmtt) REVERT: A 577 MET cc_start: 0.8287 (mtt) cc_final: 0.7968 (mmm) REVERT: A 639 LYS cc_start: 0.7708 (ttmt) cc_final: 0.7368 (tmmt) REVERT: A 736 ASN cc_start: 0.7667 (m110) cc_final: 0.6997 (t0) REVERT: A 752 MET cc_start: 0.7012 (ttm) cc_final: 0.6771 (ttt) REVERT: A 801 ARG cc_start: 0.7386 (pmm-80) cc_final: 0.7001 (mpt90) REVERT: A 888 MET cc_start: 0.6655 (mtm) cc_final: 0.6379 (ttm) REVERT: A 896 TRP cc_start: 0.8406 (t60) cc_final: 0.7883 (t60) REVERT: A 1099 GLU cc_start: 0.6629 (tt0) cc_final: 0.6407 (pt0) REVERT: A 1114 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7106 (mp0) REVERT: A 1141 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.6290 (tpt) REVERT: B 253 ASP cc_start: 0.7821 (t70) cc_final: 0.7440 (t0) REVERT: B 280 ASP cc_start: 0.6347 (t0) cc_final: 0.5914 (t0) REVERT: B 281 GLU cc_start: 0.7845 (mp0) cc_final: 0.7492 (pm20) REVERT: B 313 HIS cc_start: 0.6484 (t-170) cc_final: 0.6175 (m-70) REVERT: C 129 ASP cc_start: 0.7667 (t70) cc_final: 0.7445 (t0) REVERT: C 236 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7641 (mt-10) REVERT: C 257 ARG cc_start: 0.5810 (tpm170) cc_final: 0.5342 (ttp80) REVERT: C 394 GLU cc_start: 0.6199 (mt-10) cc_final: 0.5609 (tp30) REVERT: C 396 ARG cc_start: 0.5655 (mtt180) cc_final: 0.5277 (mtp-110) REVERT: C 409 ASN cc_start: 0.7117 (m-40) cc_final: 0.6854 (m-40) REVERT: C 419 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6496 (mm-30) outliers start: 35 outliers final: 17 residues processed: 163 average time/residue: 0.6810 time to fit residues: 121.4251 Evaluate side-chains 150 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 1065 VAL Chi-restraints excluded: chain A residue 1078 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 256 LEU Chi-restraints excluded: chain C residue 306 LEU 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: 0.4980 chunk 10 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 146 optimal weight: 0.0870 chunk 130 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4123 r_free = 0.4123 target = 0.156813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.120228 restraints weight = 18589.173| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.87 r_work: 0.3601 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.1951 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= 0.151 Angle : 0.531 13.708 19903 Z= 0.272 Chirality : 0.040 0.150 2129 Planarity : 0.004 0.052 2426 Dihedral : 13.146 60.410 2233 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.15 % Allowed : 15.86 % Favored : 81.99 % 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 aren not related in a simple way. whole: 1.10 (0.21), residues: 1631 helix: 1.39 (0.20), residues: 691 sheet: 0.54 (0.32), residues: 250 loop : 0.27 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 631 TYR 0.012 0.001 TYR C 291 PHE 0.023 0.001 PHE A 809 TRP 0.016 0.001 TRP A 896 HIS 0.005 0.001 HIS A 783 Details of bonding type rmsd covalent geometry : bond 0.00358 (14566) covalent geometry : angle 0.53084 (19903) hydrogen bonds : bond 0.03561 ( 667) hydrogen bonds : angle 4.32295 ( 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 164 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.8755 (mt0) cc_final: 0.8096 (mp10) REVERT: A 103 LEU cc_start: 0.8386 (tp) cc_final: 0.8121 (mp) REVERT: A 112 ARG cc_start: 0.6786 (ttt-90) cc_final: 0.6428 (mpp-170) REVERT: A 353 LYS cc_start: 0.8701 (ptpt) cc_final: 0.8241 (pptt) REVERT: A 365 ARG cc_start: 0.7094 (tpp-160) cc_final: 0.6594 (tpt170) REVERT: A 409 MET cc_start: 0.7007 (mtt) cc_final: 0.6631 (mtm) REVERT: A 441 MET cc_start: 0.7530 (tpt) cc_final: 0.7266 (ttp) REVERT: A 446 MET cc_start: 0.7747 (mtp) cc_final: 0.7538 (mtm) REVERT: A 447 ASP cc_start: 0.7354 (m-30) cc_final: 0.6993 (m-30) REVERT: A 451 ASP cc_start: 0.7453 (m-30) cc_final: 0.7162 (m-30) REVERT: A 556 LYS cc_start: 0.7546 (mtmt) cc_final: 0.6733 (mmtt) REVERT: A 577 MET cc_start: 0.8283 (mtt) cc_final: 0.7941 (mmm) REVERT: A 639 LYS cc_start: 0.7724 (ttmt) cc_final: 0.7401 (tmmt) REVERT: A 736 ASN cc_start: 0.7693 (m110) cc_final: 0.7057 (t0) REVERT: A 752 MET cc_start: 0.7040 (ttm) cc_final: 0.6827 (ttt) REVERT: A 801 ARG cc_start: 0.7394 (pmm-80) cc_final: 0.6998 (mpt90) REVERT: A 896 TRP cc_start: 0.8327 (t60) cc_final: 0.7620 (t60) REVERT: A 1032 GLU cc_start: 0.6021 (pm20) cc_final: 0.5443 (pm20) REVERT: A 1099 GLU cc_start: 0.6634 (tt0) cc_final: 0.6406 (pt0) REVERT: A 1114 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7158 (mp0) REVERT: A 1141 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6285 (tpt) REVERT: B 253 ASP cc_start: 0.7814 (t70) cc_final: 0.7444 (t0) REVERT: B 280 ASP cc_start: 0.6351 (t0) cc_final: 0.5755 (t0) REVERT: B 281 GLU cc_start: 0.7834 (mp0) cc_final: 0.7320 (mp0) REVERT: B 313 HIS cc_start: 0.6513 (t-170) cc_final: 0.6179 (m-70) REVERT: B 421 MET cc_start: 0.7146 (tmt) cc_final: 0.6850 (tmm) REVERT: C 129 ASP cc_start: 0.7659 (t70) cc_final: 0.7429 (t0) REVERT: C 236 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7644 (mt-10) REVERT: C 257 ARG cc_start: 0.6078 (tpm170) cc_final: 0.5637 (ttp80) REVERT: C 394 GLU cc_start: 0.6218 (mt-10) cc_final: 0.5628 (tp30) REVERT: C 396 ARG cc_start: 0.5664 (mtt180) cc_final: 0.5289 (mtp-110) REVERT: C 409 ASN cc_start: 0.7087 (m-40) cc_final: 0.6807 (m-40) REVERT: C 419 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6517 (mm-30) REVERT: C 421 MET cc_start: 0.7379 (ppp) cc_final: 0.6930 (ppp) outliers start: 31 outliers final: 23 residues processed: 158 average time/residue: 0.7640 time to fit residues: 131.2057 Evaluate side-chains 149 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 217 SER 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 574 SER Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1072 THR 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 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 132 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 44 optimal weight: 0.0370 chunk 121 optimal weight: 0.1980 chunk 67 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.4464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN B 309 HIS 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 = 0.4113 r_free = 0.4113 target = 0.156121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.119650 restraints weight = 18583.805| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.86 r_work: 0.3590 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14566 Z= 0.163 Angle : 0.546 14.066 19903 Z= 0.280 Chirality : 0.040 0.150 2129 Planarity : 0.004 0.050 2426 Dihedral : 13.180 60.485 2233 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.15 % Allowed : 16.07 % 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 aren not related in a simple way. whole: 1.07 (0.21), residues: 1631 helix: 1.35 (0.20), residues: 691 sheet: 0.56 (0.32), residues: 250 loop : 0.26 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 631 TYR 0.012 0.001 TYR C 291 PHE 0.014 0.001 PHE B 403 TRP 0.015 0.001 TRP A 896 HIS 0.006 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00387 (14566) covalent geometry : angle 0.54602 (19903) hydrogen bonds : bond 0.03628 ( 667) hydrogen bonds : angle 4.35065 ( 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 161 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.8804 (mt0) cc_final: 0.8170 (mp10) REVERT: A 103 LEU cc_start: 0.8368 (tp) cc_final: 0.8119 (mp) REVERT: A 112 ARG cc_start: 0.6810 (ttt-90) cc_final: 0.6449 (mpp-170) REVERT: A 353 LYS cc_start: 0.8699 (ptpt) cc_final: 0.8224 (pptt) REVERT: A 365 ARG cc_start: 0.7113 (tpp-160) cc_final: 0.6617 (tpt170) REVERT: A 409 MET cc_start: 0.7037 (mtt) cc_final: 0.6662 (mtm) REVERT: A 441 MET cc_start: 0.7556 (tpt) cc_final: 0.7256 (ttp) REVERT: A 446 MET cc_start: 0.7743 (mtp) cc_final: 0.7539 (mtm) REVERT: A 447 ASP cc_start: 0.7395 (m-30) cc_final: 0.7018 (m-30) REVERT: A 451 ASP cc_start: 0.7497 (m-30) cc_final: 0.7198 (m-30) REVERT: A 556 LYS cc_start: 0.7515 (mtmt) cc_final: 0.6738 (mmtt) REVERT: A 577 MET cc_start: 0.8274 (mtt) cc_final: 0.7936 (mmm) REVERT: A 639 LYS cc_start: 0.7752 (ttmt) cc_final: 0.7441 (tmmt) REVERT: A 736 ASN cc_start: 0.7736 (m110) cc_final: 0.7100 (t0) REVERT: A 752 MET cc_start: 0.7064 (ttm) cc_final: 0.6799 (ttt) REVERT: A 801 ARG cc_start: 0.7385 (pmm-80) cc_final: 0.6996 (mpt90) REVERT: A 896 TRP cc_start: 0.8357 (t60) cc_final: 0.7665 (t60) REVERT: A 1032 GLU cc_start: 0.6026 (pm20) cc_final: 0.5451 (pm20) REVERT: A 1099 GLU cc_start: 0.6656 (tt0) cc_final: 0.6431 (pt0) REVERT: A 1114 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7156 (mp0) REVERT: A 1141 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.6297 (tpt) REVERT: B 253 ASP cc_start: 0.7815 (t70) cc_final: 0.7441 (t0) REVERT: B 280 ASP cc_start: 0.6353 (t0) cc_final: 0.5573 (t0) REVERT: B 281 GLU cc_start: 0.7829 (mp0) cc_final: 0.7298 (mp0) REVERT: B 313 HIS cc_start: 0.6509 (t-170) cc_final: 0.6182 (m-70) REVERT: C 129 ASP cc_start: 0.7632 (t70) cc_final: 0.7405 (t0) REVERT: C 236 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7680 (mt-10) REVERT: C 257 ARG cc_start: 0.6094 (tpm170) cc_final: 0.5633 (ttp80) REVERT: C 394 GLU cc_start: 0.6198 (mt-10) cc_final: 0.5607 (tp30) REVERT: C 396 ARG cc_start: 0.5675 (mtt180) cc_final: 0.5294 (mtp-110) REVERT: C 409 ASN cc_start: 0.7076 (m-40) cc_final: 0.6808 (m-40) REVERT: C 419 GLU cc_start: 0.6890 (mm-30) cc_final: 0.6611 (mm-30) REVERT: C 421 MET cc_start: 0.7381 (ppp) cc_final: 0.6925 (ppp) outliers start: 31 outliers final: 22 residues processed: 156 average time/residue: 0.7147 time to fit residues: 121.5790 Evaluate side-chains 150 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 217 SER 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 574 SER 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 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: 3.9990 chunk 0 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 139 optimal weight: 0.0040 chunk 50 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.155250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.118605 restraints weight = 18608.098| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.86 r_work: 0.3574 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14566 Z= 0.206 Angle : 0.582 14.002 19903 Z= 0.297 Chirality : 0.042 0.153 2129 Planarity : 0.005 0.047 2426 Dihedral : 13.271 60.444 2233 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.29 % Allowed : 16.20 % Favored : 81.51 % 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 aren not related in a simple way. whole: 0.92 (0.21), residues: 1631 helix: 1.20 (0.20), residues: 691 sheet: 0.52 (0.32), residues: 250 loop : 0.18 (0.24), residues: 690 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 809 TRP 0.014 0.001 TRP A 896 HIS 0.007 0.001 HIS A 783 Details of bonding type rmsd covalent geometry : bond 0.00495 (14566) covalent geometry : angle 0.58157 (19903) hydrogen bonds : bond 0.03996 ( 667) hydrogen bonds : angle 4.46595 ( 1846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5084.88 seconds wall clock time: 87 minutes 35.93 seconds (5255.93 seconds total)