Starting phenix.real_space_refine on Thu Jul 2 19:12:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zka_14760/07_2026/7zka_14760.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zka_14760/07_2026/7zka_14760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7zka_14760/07_2026/7zka_14760.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zka_14760/07_2026/7zka_14760.cif" model { file = "/net/cci-nas-00/data/ceres_data/7zka_14760/07_2026/7zka_14760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zka_14760/07_2026/7zka_14760.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zka_14760/07_2026/7zka_14760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zka_14760/07_2026/7zka_14760.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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 P 6 5.49 5 Mg 2 5.21 5 S 36 5.16 5 C 6053 2.51 5 N 1566 2.21 5 O 1743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9406 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 9133 Classifications: {'peptide': 1177} Link IDs: {'PTRANS': 29, 'TRANS': 1147} Chain breaks: 1 Chain: "A" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 273 Unusual residues: {' MG': 2, 'ATP': 2, 'JIZ': 1, 'LMN': 1, 'Y01': 3} Classifications: {'undetermined': 9, 'water': 4} Link IDs: {None: 12} Time building chain proxies: 1.82, per 1000 atoms: 0.19 Number of scatterers: 9406 At special positions: 0 Unit cell: (71.625, 85.377, 150.699, 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) S 36 16.00 P 6 15.00 Mg 2 11.99 O 1743 8.00 N 1566 7.00 C 6053 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 315.4 milliseconds 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 4 sheets defined 71.4% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 43 through 72 removed outlier: 4.269A pdb=" N LEU A 64 " --> pdb=" O HIS A 60 " (cutoff:3.500A) Proline residue: A 65 - end of helix Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 94 through 154 removed outlier: 3.565A pdb=" N TYR A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 164 through 180 removed outlier: 4.236A pdb=" N ASN A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 216 removed outlier: 3.910A pdb=" N GLY A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TRP A 208 " --> pdb=" O PHE A 204 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N LYS A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 256 removed outlier: 3.707A pdb=" N LEU A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 264 Processing helix chain 'A' and resid 265 through 319 removed outlier: 3.753A pdb=" N ASN A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 366 removed outlier: 4.473A pdb=" N ILE A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLY A 337 " --> pdb=" O SER A 333 " (cutoff:3.500A) Proline residue: A 346 - end of helix removed outlier: 3.857A pdb=" N TYR A 359 " --> pdb=" O ARG A 355 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLU A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 437 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 458 through 465 Processing helix chain 'A' and resid 479 through 486 Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 505 through 512 Processing helix chain 'A' and resid 514 through 518 Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 528 through 542 Processing helix chain 'A' and resid 558 through 572 removed outlier: 3.596A pdb=" N ALA A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 590 removed outlier: 3.739A pdb=" N VAL A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 616 through 624 Processing helix chain 'A' and resid 691 through 699 removed outlier: 3.620A pdb=" N LEU A 699 " --> pdb=" O ARG A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 702 No H-bonds generated for 'chain 'A' and resid 700 through 702' Processing helix chain 'A' and resid 703 through 737 removed outlier: 3.753A pdb=" N PHE A 707 " --> pdb=" O GLU A 703 " (cutoff:3.500A) Proline residue: A 722 - end of helix Processing helix chain 'A' and resid 742 through 747 Processing helix chain 'A' and resid 749 through 795 Processing helix chain 'A' and resid 796 through 802 removed outlier: 3.562A pdb=" N PHE A 800 " --> pdb=" O ASP A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 824 Processing helix chain 'A' and resid 828 through 850 Processing helix chain 'A' and resid 853 through 899 removed outlier: 3.588A pdb=" N LEU A 857 " --> pdb=" O LEU A 853 " (cutoff:3.500A) Proline residue: A 862 - end of helix removed outlier: 3.777A pdb=" N LEU A 880 " --> pdb=" O SER A 876 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LYS A 881 " --> pdb=" O GLY A 877 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN A 899 " --> pdb=" O GLU A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 907 Processing helix chain 'A' and resid 908 through 962 removed outlier: 4.537A pdb=" N ILE A 922 " --> pdb=" O GLN A 918 " (cutoff:3.500A) Proline residue: A 923 - end of helix Processing helix chain 'A' and resid 969 through 1010 Proline residue: A 992 - end of helix removed outlier: 3.956A pdb=" N VAL A 999 " --> pdb=" O ALA A 995 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER A1000 " --> pdb=" O LYS A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1080 removed outlier: 3.617A pdb=" N VAL A1076 " --> pdb=" O LYS A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1100 No H-bonds generated for 'chain 'A' and resid 1098 through 1100' Processing helix chain 'A' and resid 1101 through 1108 Processing helix chain 'A' and resid 1122 through 1129 Processing helix chain 'A' and resid 1137 through 1148 Processing helix chain 'A' and resid 1150 through 1157 Processing helix chain 'A' and resid 1159 through 1163 Processing helix chain 'A' and resid 1166 through 1170 Processing helix chain 'A' and resid 1173 through 1188 removed outlier: 4.099A pdb=" N ARG A1188 " --> pdb=" O ARG A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1217 removed outlier: 3.587A pdb=" N ALA A1217 " --> pdb=" O ALA A1213 " (cutoff:3.500A) Processing helix chain 'A' and resid 1229 through 1236 Processing helix chain 'A' and resid 1252 through 1259 removed outlier: 3.505A pdb=" N GLN A1259 " --> pdb=" O GLN A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1271 Processing sheet with id=AA1, first strand: chain 'A' and resid 406 through 412 removed outlier: 6.789A pdb=" N LYS A 407 " --> pdb=" O HIS A 394 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N HIS A 394 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU A 409 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N PHE A 390 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N SER A 448 " --> pdb=" O PHE A 390 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ASN A 392 " --> pdb=" O MET A 446 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N MET A 446 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 466 through 469 removed outlier: 6.444A pdb=" N GLY A 467 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ASP A 551 " --> pdb=" O GLY A 467 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 469 " --> pdb=" O ASP A 551 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU A 548 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ILE A 581 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU A 550 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE A 594 " --> pdb=" O GLN A 605 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN A 605 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY A 596 " --> pdb=" O VAL A 603 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1050 through 1056 removed outlier: 6.881A pdb=" N GLN A1050 " --> pdb=" O VAL A1037 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL A1037 " --> pdb=" O GLN A1050 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU A1052 " --> pdb=" O GLY A1035 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N PHE A1033 " --> pdb=" O PHE A1091 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N PHE A1091 " --> pdb=" O PHE A1033 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLY A1035 " --> pdb=" O SER A1089 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N SER A1089 " --> pdb=" O GLY A1035 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1109 through 1112 removed outlier: 6.379A pdb=" N GLY A1110 " --> pdb=" O LEU A1194 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ASP A1196 " --> pdb=" O GLY A1110 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL A1112 " --> pdb=" O ASP A1196 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU A1062 " --> pdb=" O VAL A1225 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N THR A1061 " --> pdb=" O LEU A1238 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL A1240 " --> pdb=" O THR A1061 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA A1063 " --> pdb=" O VAL A1240 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE A1242 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL A1065 " --> pdb=" O ILE A1242 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE A1239 " --> pdb=" O HIS A1250 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N HIS A1250 " --> pdb=" O ILE A1239 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL A1241 " --> pdb=" O LYS A1248 " (cutoff:3.500A) 635 hydrogen bonds defined for protein. 1845 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1514 1.31 - 1.44: 2466 1.44 - 1.56: 5509 1.56 - 1.69: 34 1.69 - 1.82: 64 Bond restraints: 9587 Sorted by residual: bond pdb=" C03 JIZ A1401 " pdb=" N02 JIZ A1401 " ideal model delta sigma weight residual 1.367 1.639 -0.272 2.00e-02 2.50e+03 1.86e+02 bond pdb=" C08 JIZ A1401 " pdb=" N04 JIZ A1401 " ideal model delta sigma weight residual 1.366 1.616 -0.250 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C13 JIZ A1401 " pdb=" N06 JIZ A1401 " ideal model delta sigma weight residual 1.366 1.615 -0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C02 JIZ A1401 " pdb=" S01 JIZ A1401 " ideal model delta sigma weight residual 1.728 1.546 0.182 2.00e-02 2.50e+03 8.27e+01 bond pdb=" C03 JIZ A1401 " pdb=" C04 JIZ A1401 " ideal model delta sigma weight residual 1.360 1.520 -0.160 2.00e-02 2.50e+03 6.39e+01 ... (remaining 9582 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 12845 3.56 - 7.12: 130 7.12 - 10.68: 14 10.68 - 14.24: 1 14.24 - 17.80: 4 Bond angle restraints: 12994 Sorted by residual: angle pdb=" N ILE A 318 " pdb=" CA ILE A 318 " pdb=" C ILE A 318 " ideal model delta sigma weight residual 111.90 99.57 12.33 8.10e-01 1.52e+00 2.32e+02 angle pdb=" N PRO A 741 " pdb=" CA PRO A 741 " pdb=" C PRO A 741 " ideal model delta sigma weight residual 113.47 131.27 -17.80 1.43e+00 4.89e-01 1.55e+02 angle pdb=" N GLN A 746 " pdb=" CA GLN A 746 " pdb=" C GLN A 746 " ideal model delta sigma weight residual 111.28 103.00 8.28 1.09e+00 8.42e-01 5.77e+01 angle pdb=" N PRO A 740 " pdb=" CA PRO A 740 " pdb=" C PRO A 740 " ideal model delta sigma weight residual 110.70 102.31 8.39 1.22e+00 6.72e-01 4.73e+01 angle pdb=" N LYS A 86 " pdb=" CA LYS A 86 " pdb=" C LYS A 86 " ideal model delta sigma weight residual 112.57 105.01 7.56 1.13e+00 7.83e-01 4.47e+01 ... (remaining 12989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 5039 17.58 - 35.17: 454 35.17 - 52.75: 106 52.75 - 70.33: 27 70.33 - 87.91: 13 Dihedral angle restraints: 5639 sinusoidal: 2268 harmonic: 3371 Sorted by residual: dihedral pdb=" C LEU A 519 " pdb=" N LEU A 519 " pdb=" CA LEU A 519 " pdb=" CB LEU A 519 " ideal model delta harmonic sigma weight residual -122.60 -137.47 14.87 0 2.50e+00 1.60e-01 3.54e+01 dihedral pdb=" N LEU A 519 " pdb=" C LEU A 519 " pdb=" CA LEU A 519 " pdb=" CB LEU A 519 " ideal model delta harmonic sigma weight residual 122.80 135.32 -12.52 0 2.50e+00 1.60e-01 2.51e+01 dihedral pdb=" C PHE A 516 " pdb=" N PHE A 516 " pdb=" CA PHE A 516 " pdb=" CB PHE A 516 " ideal model delta harmonic sigma weight residual -122.60 -112.15 -10.45 0 2.50e+00 1.60e-01 1.75e+01 ... (remaining 5636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 1458 0.131 - 0.261: 33 0.261 - 0.392: 7 0.392 - 0.523: 2 0.523 - 0.653: 1 Chirality restraints: 1501 Sorted by residual: chirality pdb=" CA PRO A 741 " pdb=" N PRO A 741 " pdb=" C PRO A 741 " pdb=" CB PRO A 741 " both_signs ideal model delta sigma weight residual False 2.72 2.06 0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CA LEU A 519 " pdb=" N LEU A 519 " pdb=" C LEU A 519 " pdb=" CB LEU A 519 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.49e+00 chirality pdb=" CA ILE A 318 " pdb=" N ILE A 318 " pdb=" C ILE A 318 " pdb=" CB ILE A 318 " both_signs ideal model delta sigma weight residual False 2.43 2.83 -0.39 2.00e-01 2.50e+01 3.89e+00 ... (remaining 1498 not shown) Planarity restraints: 1613 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 736 " -0.016 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C THR A 736 " 0.059 2.00e-02 2.50e+03 pdb=" O THR A 736 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN A 737 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 218 " 0.052 5.00e-02 4.00e+02 7.87e-02 9.92e+00 pdb=" N PRO A 219 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 219 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 219 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 520 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.24e+00 pdb=" C VAL A 520 " 0.047 2.00e-02 2.50e+03 pdb=" O VAL A 520 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY A 521 " -0.016 2.00e-02 2.50e+03 ... (remaining 1610 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 95 2.61 - 3.18: 8453 3.18 - 3.75: 15131 3.75 - 4.33: 21212 4.33 - 4.90: 34202 Nonbonded interactions: 79093 Sorted by model distance: nonbonded pdb=" OG SER A1073 " pdb="MG MG A1405 " model vdw 2.034 2.170 nonbonded pdb=" O2G ATP A1404 " pdb="MG MG A1405 " model vdw 2.049 2.170 nonbonded pdb=" OG SER A 430 " pdb="MG MG A1403 " model vdw 2.063 2.170 nonbonded pdb=" OE1 GLN A1114 " pdb="MG MG A1405 " model vdw 2.066 2.170 nonbonded pdb=" O2B ATP A1404 " pdb="MG MG A1405 " model vdw 2.075 2.170 ... (remaining 79088 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.700 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 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 : 0.009 0.272 9588 Z= 0.496 Angle : 0.871 17.803 12994 Z= 0.522 Chirality : 0.057 0.653 1501 Planarity : 0.005 0.079 1613 Dihedral : 15.114 87.912 3479 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.24), residues: 1173 helix: 1.40 (0.18), residues: 795 sheet: -0.40 (0.61), residues: 70 loop : -0.55 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 925 TYR 0.010 0.001 TYR A 440 PHE 0.025 0.001 PHE A 953 TRP 0.008 0.001 TRP A 311 HIS 0.003 0.001 HIS A 932 Details of bonding type rmsd/Z covalent geometry : bond 0.00923 / 0.50 ( 9587) covalent geometry : angle 0.87115 / 0.52 (12994) hydrogen bonds : bond 0.13289 / 8.54 ( 635) hydrogen bonds : angle 5.59472 / 4.08 ( 1845) Misc. bond : bond 0.02901 / 1.53 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.275 Fit side-chains REVERT: A 193 MET cc_start: 0.6753 (mmp) cc_final: 0.6482 (mmp) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.5193 time to fit residues: 80.3444 Evaluate side-chains 105 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.0870 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 GLN A 90 GLN A 515 GLN A 749 ASN A 835 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.169262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.125728 restraints weight = 10100.267| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.70 r_work: 0.3211 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9588 Z= 0.139 Angle : 0.539 7.043 12994 Z= 0.280 Chirality : 0.041 0.188 1501 Planarity : 0.004 0.065 1613 Dihedral : 6.943 53.618 1360 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.96 % Favored : 97.95 % Rotamer: Outliers : 1.76 % Allowed : 9.83 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.24), residues: 1173 helix: 1.77 (0.18), residues: 800 sheet: 0.00 (0.62), residues: 70 loop : -0.48 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 745 TYR 0.008 0.001 TYR A 440 PHE 0.023 0.001 PHE A 508 TRP 0.006 0.001 TRP A 311 HIS 0.005 0.001 HIS A 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 ( 9587) covalent geometry : angle 0.53852 / 0.28 (12994) hydrogen bonds : bond 0.05005 / 3.42 ( 635) hydrogen bonds : angle 4.42858 / 3.19 ( 1845) Misc. bond : bond 0.00113 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.324 Fit side-chains REVERT: A 392 ASN cc_start: 0.7202 (p0) cc_final: 0.6721 (t0) REVERT: A 831 VAL cc_start: 0.7511 (OUTLIER) cc_final: 0.7307 (t) REVERT: A 1009 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7312 (mp0) REVERT: A 1152 GLN cc_start: 0.7548 (mt0) cc_final: 0.6602 (mp-120) REVERT: A 1164 ARG cc_start: 0.7467 (tmt170) cc_final: 0.7196 (tmm-80) REVERT: A 1189 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7986 (mt0) REVERT: A 1215 ASP cc_start: 0.7096 (m-30) cc_final: 0.6872 (m-30) outliers start: 17 outliers final: 3 residues processed: 120 average time/residue: 0.5417 time to fit residues: 69.3876 Evaluate side-chains 107 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 1189 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 106 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 86 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 99 optimal weight: 0.1980 chunk 51 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.169441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.126441 restraints weight = 10098.156| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.69 r_work: 0.3120 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9588 Z= 0.125 Angle : 0.496 6.972 12994 Z= 0.259 Chirality : 0.040 0.177 1501 Planarity : 0.004 0.062 1613 Dihedral : 6.731 55.401 1360 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.28 % Allowed : 11.70 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.24), residues: 1173 helix: 1.95 (0.18), residues: 800 sheet: 0.18 (0.62), residues: 70 loop : -0.49 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 589 TYR 0.010 0.001 TYR A 306 PHE 0.018 0.001 PHE A 619 TRP 0.005 0.001 TRP A 158 HIS 0.008 0.001 HIS A 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 9587) covalent geometry : angle 0.49573 / 0.26 (12994) hydrogen bonds : bond 0.04727 / 3.26 ( 635) hydrogen bonds : angle 4.17360 / 3.02 ( 1845) Misc. bond : bond 0.00025 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 188 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.6419 (mpp) REVERT: A 392 ASN cc_start: 0.6926 (p0) cc_final: 0.6492 (t0) REVERT: A 619 PHE cc_start: 0.6162 (t80) cc_final: 0.5933 (t80) REVERT: A 940 PHE cc_start: 0.7125 (t80) cc_final: 0.6921 (t80) REVERT: A 1009 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7162 (mp0) REVERT: A 1152 GLN cc_start: 0.7406 (mt0) cc_final: 0.6440 (mp-120) REVERT: A 1164 ARG cc_start: 0.7477 (tmt170) cc_final: 0.7151 (tmm-80) REVERT: A 1189 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7905 (mt0) REVERT: A 1215 ASP cc_start: 0.7018 (m-30) cc_final: 0.6815 (m-30) outliers start: 22 outliers final: 10 residues processed: 117 average time/residue: 0.5194 time to fit residues: 65.0237 Evaluate side-chains 111 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1189 GLN Chi-restraints excluded: chain A residue 1232 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 47 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 43 optimal weight: 0.1980 chunk 106 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.160947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.116428 restraints weight = 10314.722| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.74 r_work: 0.3103 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9588 Z= 0.141 Angle : 0.511 7.231 12994 Z= 0.265 Chirality : 0.041 0.179 1501 Planarity : 0.004 0.059 1613 Dihedral : 6.735 59.581 1360 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.47 % Favored : 97.44 % Rotamer: Outliers : 2.90 % Allowed : 13.98 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.24), residues: 1173 helix: 1.93 (0.18), residues: 804 sheet: 0.20 (0.60), residues: 70 loop : -0.60 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 785 TYR 0.011 0.001 TYR A 306 PHE 0.020 0.001 PHE A 508 TRP 0.006 0.001 TRP A 158 HIS 0.008 0.001 HIS A 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 9587) covalent geometry : angle 0.51113 / 0.27 (12994) hydrogen bonds : bond 0.04956 / 3.44 ( 635) hydrogen bonds : angle 4.09127 / 2.97 ( 1845) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 188 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.6508 (mpp) REVERT: A 392 ASN cc_start: 0.7014 (p0) cc_final: 0.6566 (t0) REVERT: A 424 ASN cc_start: 0.8219 (m-40) cc_final: 0.7747 (m110) REVERT: A 619 PHE cc_start: 0.6289 (t80) cc_final: 0.6026 (t80) REVERT: A 831 VAL cc_start: 0.7309 (OUTLIER) cc_final: 0.7100 (t) REVERT: A 884 LYS cc_start: 0.6651 (mtpp) cc_final: 0.6331 (mtmm) REVERT: A 940 PHE cc_start: 0.7107 (t80) cc_final: 0.6834 (t80) REVERT: A 953 PHE cc_start: 0.7082 (OUTLIER) cc_final: 0.6765 (t80) REVERT: A 1009 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7189 (mp0) REVERT: A 1152 GLN cc_start: 0.7492 (mt0) cc_final: 0.6524 (mp-120) REVERT: A 1189 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7971 (mt0) REVERT: A 1215 ASP cc_start: 0.7108 (m-30) cc_final: 0.6884 (m-30) REVERT: A 1237 ASP cc_start: 0.7913 (t0) cc_final: 0.7692 (t0) outliers start: 28 outliers final: 11 residues processed: 122 average time/residue: 0.5214 time to fit residues: 68.2377 Evaluate side-chains 117 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1189 GLN Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1238 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 0.4980 chunk 38 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 114 optimal weight: 9.9990 chunk 110 optimal weight: 0.1980 chunk 102 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 GLN A 514 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.167464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.124415 restraints weight = 10209.037| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.70 r_work: 0.3093 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9588 Z= 0.117 Angle : 0.481 7.057 12994 Z= 0.249 Chirality : 0.039 0.191 1501 Planarity : 0.004 0.057 1613 Dihedral : 6.647 57.191 1360 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.69 % Allowed : 15.11 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.24), residues: 1173 helix: 2.06 (0.18), residues: 803 sheet: 0.23 (0.61), residues: 70 loop : -0.60 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 355 TYR 0.011 0.001 TYR A 306 PHE 0.014 0.001 PHE A 508 TRP 0.005 0.001 TRP A1104 HIS 0.006 0.001 HIS A 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 ( 9587) covalent geometry : angle 0.48137 / 0.25 (12994) hydrogen bonds : bond 0.04567 / 3.17 ( 635) hydrogen bonds : angle 3.98716 / 2.90 ( 1845) Misc. bond : bond 0.00004 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.232 Fit side-chains REVERT: A 188 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.6416 (mpp) REVERT: A 392 ASN cc_start: 0.6797 (p0) cc_final: 0.6414 (t0) REVERT: A 424 ASN cc_start: 0.8108 (m-40) cc_final: 0.7642 (m110) REVERT: A 619 PHE cc_start: 0.6185 (t80) cc_final: 0.5909 (t80) REVERT: A 884 LYS cc_start: 0.6469 (mtpp) cc_final: 0.6144 (mtmm) REVERT: A 940 PHE cc_start: 0.6971 (t80) cc_final: 0.6708 (t80) REVERT: A 1009 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7102 (mp0) REVERT: A 1086 MET cc_start: 0.8353 (ptp) cc_final: 0.8101 (ptm) REVERT: A 1152 GLN cc_start: 0.7387 (mt0) cc_final: 0.6376 (mp-120) REVERT: A 1164 ARG cc_start: 0.7488 (tmt170) cc_final: 0.7016 (tmm-80) REVERT: A 1189 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7927 (mt0) REVERT: A 1215 ASP cc_start: 0.7069 (m-30) cc_final: 0.6851 (m-30) REVERT: A 1237 ASP cc_start: 0.7867 (t0) cc_final: 0.7628 (t0) outliers start: 26 outliers final: 8 residues processed: 121 average time/residue: 0.4995 time to fit residues: 64.6713 Evaluate side-chains 111 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1189 GLN Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1238 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 94 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 7 optimal weight: 9.9990 chunk 39 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 514 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.161196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.116695 restraints weight = 10289.575| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.73 r_work: 0.3120 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9588 Z= 0.121 Angle : 0.488 6.978 12994 Z= 0.251 Chirality : 0.040 0.235 1501 Planarity : 0.004 0.057 1613 Dihedral : 6.612 58.898 1360 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.28 % Allowed : 15.73 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.24), residues: 1173 helix: 2.11 (0.18), residues: 803 sheet: 0.23 (0.62), residues: 70 loop : -0.59 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 925 TYR 0.011 0.001 TYR A 306 PHE 0.017 0.001 PHE A 508 TRP 0.005 0.001 TRP A 704 HIS 0.005 0.001 HIS A 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 9587) covalent geometry : angle 0.48819 / 0.25 (12994) hydrogen bonds : bond 0.04572 / 3.17 ( 635) hydrogen bonds : angle 3.95864 / 2.89 ( 1845) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.373 Fit side-chains REVERT: A 188 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.6526 (mpp) REVERT: A 392 ASN cc_start: 0.6890 (p0) cc_final: 0.6497 (t0) REVERT: A 424 ASN cc_start: 0.8201 (m-40) cc_final: 0.7751 (m110) REVERT: A 592 ASP cc_start: 0.7663 (m-30) cc_final: 0.7380 (m-30) REVERT: A 619 PHE cc_start: 0.6352 (t80) cc_final: 0.6104 (t80) REVERT: A 884 LYS cc_start: 0.6587 (mtpp) cc_final: 0.6266 (mtmm) REVERT: A 940 PHE cc_start: 0.7068 (t80) cc_final: 0.6806 (t80) REVERT: A 953 PHE cc_start: 0.7084 (OUTLIER) cc_final: 0.6750 (t80) REVERT: A 1009 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7145 (mp0) REVERT: A 1055 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7376 (tt0) REVERT: A 1086 MET cc_start: 0.8336 (ptp) cc_final: 0.8096 (ptm) REVERT: A 1152 GLN cc_start: 0.7500 (mt0) cc_final: 0.6507 (mp-120) REVERT: A 1164 ARG cc_start: 0.7553 (tmt170) cc_final: 0.7246 (tmm-80) REVERT: A 1189 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7953 (mt0) REVERT: A 1215 ASP cc_start: 0.7113 (m-30) cc_final: 0.6878 (m-30) REVERT: A 1237 ASP cc_start: 0.7887 (t0) cc_final: 0.7649 (t0) outliers start: 22 outliers final: 9 residues processed: 120 average time/residue: 0.6358 time to fit residues: 81.6326 Evaluate side-chains 118 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1055 GLU Chi-restraints excluded: chain A residue 1189 GLN Chi-restraints excluded: chain A residue 1232 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 7 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 514 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.154950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.109377 restraints weight = 10350.590| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.75 r_work: 0.3008 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9588 Z= 0.184 Angle : 0.550 8.197 12994 Z= 0.284 Chirality : 0.042 0.197 1501 Planarity : 0.004 0.057 1613 Dihedral : 6.878 59.589 1360 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.17 % Allowed : 16.15 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.24), residues: 1173 helix: 1.90 (0.18), residues: 805 sheet: 0.12 (0.62), residues: 70 loop : -0.63 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 925 TYR 0.011 0.001 TYR A 126 PHE 0.023 0.002 PHE A 508 TRP 0.007 0.001 TRP A 158 HIS 0.005 0.001 HIS A 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 ( 9587) covalent geometry : angle 0.54953 / 0.28 (12994) hydrogen bonds : bond 0.05481 / 3.82 ( 635) hydrogen bonds : angle 4.14850 / 3.02 ( 1845) Misc. bond : bond 0.00008 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.388 Fit side-chains REVERT: A 74 MET cc_start: 0.3344 (mpp) cc_final: 0.2751 (mmt) REVERT: A 188 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7092 (mpp) REVERT: A 392 ASN cc_start: 0.7035 (p0) cc_final: 0.6807 (p0) REVERT: A 424 ASN cc_start: 0.8165 (m-40) cc_final: 0.7791 (m110) REVERT: A 511 LYS cc_start: 0.8042 (mtpp) cc_final: 0.7817 (ttmm) REVERT: A 619 PHE cc_start: 0.6238 (t80) cc_final: 0.5904 (t80) REVERT: A 836 ILE cc_start: 0.7109 (mm) cc_final: 0.6871 (mt) REVERT: A 884 LYS cc_start: 0.6609 (mtpp) cc_final: 0.6259 (mtmm) REVERT: A 948 SER cc_start: 0.8196 (t) cc_final: 0.7805 (p) REVERT: A 1009 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7492 (mm-30) REVERT: A 1055 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7396 (tt0) REVERT: A 1152 GLN cc_start: 0.7490 (mt0) cc_final: 0.6504 (mp-120) REVERT: A 1189 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7970 (mt0) REVERT: A 1203 ASP cc_start: 0.5964 (m-30) cc_final: 0.5711 (m-30) REVERT: A 1215 ASP cc_start: 0.7013 (m-30) cc_final: 0.6776 (m-30) REVERT: A 1237 ASP cc_start: 0.7858 (t0) cc_final: 0.7598 (t0) outliers start: 21 outliers final: 9 residues processed: 119 average time/residue: 0.6341 time to fit residues: 80.6390 Evaluate side-chains 118 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1055 GLU Chi-restraints excluded: chain A residue 1189 GLN Chi-restraints excluded: chain A residue 1232 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 104 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 514 HIS A1020 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.158199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.113120 restraints weight = 10296.635| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.75 r_work: 0.3090 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9588 Z= 0.125 Angle : 0.493 7.235 12994 Z= 0.255 Chirality : 0.040 0.206 1501 Planarity : 0.004 0.056 1613 Dihedral : 6.715 58.951 1360 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.07 % Allowed : 16.56 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.24), residues: 1173 helix: 2.04 (0.18), residues: 807 sheet: 0.09 (0.63), residues: 70 loop : -0.59 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 925 TYR 0.011 0.001 TYR A 306 PHE 0.016 0.001 PHE A 508 TRP 0.005 0.001 TRP A1104 HIS 0.004 0.001 HIS A 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 ( 9587) covalent geometry : angle 0.49318 / 0.26 (12994) hydrogen bonds : bond 0.04786 / 3.34 ( 635) hydrogen bonds : angle 4.00069 / 2.92 ( 1845) Misc. bond : bond 0.00011 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.324 Fit side-chains REVERT: A 74 MET cc_start: 0.3240 (mpp) cc_final: 0.2647 (mmt) REVERT: A 188 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.6977 (mpp) REVERT: A 295 MET cc_start: 0.8295 (ttt) cc_final: 0.8030 (ttt) REVERT: A 392 ASN cc_start: 0.7029 (p0) cc_final: 0.6455 (t0) REVERT: A 424 ASN cc_start: 0.8207 (m-40) cc_final: 0.7710 (m110) REVERT: A 511 LYS cc_start: 0.8081 (mtpp) cc_final: 0.7870 (ttmm) REVERT: A 619 PHE cc_start: 0.6421 (t80) cc_final: 0.6155 (t80) REVERT: A 884 LYS cc_start: 0.6619 (mtpp) cc_final: 0.6289 (mtmm) REVERT: A 940 PHE cc_start: 0.7154 (t80) cc_final: 0.6943 (t80) REVERT: A 948 SER cc_start: 0.8270 (t) cc_final: 0.7907 (p) REVERT: A 1009 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7200 (mp0) REVERT: A 1055 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7383 (tt0) REVERT: A 1152 GLN cc_start: 0.7488 (mt0) cc_final: 0.6484 (mp-120) REVERT: A 1189 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7985 (mt0) REVERT: A 1215 ASP cc_start: 0.7048 (m-30) cc_final: 0.6809 (m-30) REVERT: A 1237 ASP cc_start: 0.7878 (t0) cc_final: 0.7640 (t0) outliers start: 20 outliers final: 8 residues processed: 117 average time/residue: 0.6125 time to fit residues: 76.5688 Evaluate side-chains 114 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1055 GLU Chi-restraints excluded: chain A residue 1189 GLN Chi-restraints excluded: chain A residue 1232 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 5 optimal weight: 30.0000 chunk 6 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 514 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.157321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.112252 restraints weight = 10285.682| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.74 r_work: 0.3077 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9588 Z= 0.141 Angle : 0.503 7.245 12994 Z= 0.261 Chirality : 0.040 0.215 1501 Planarity : 0.004 0.057 1613 Dihedral : 6.691 57.870 1360 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.86 % Allowed : 17.18 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.24), residues: 1173 helix: 2.01 (0.18), residues: 807 sheet: 0.12 (0.64), residues: 70 loop : -0.57 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 925 TYR 0.011 0.001 TYR A 306 PHE 0.019 0.001 PHE A 508 TRP 0.005 0.001 TRP A 158 HIS 0.005 0.001 HIS A 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 9587) covalent geometry : angle 0.50311 / 0.26 (12994) hydrogen bonds : bond 0.04924 / 3.44 ( 635) hydrogen bonds : angle 4.00792 / 2.93 ( 1845) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.371 Fit side-chains REVERT: A 74 MET cc_start: 0.3290 (mpp) cc_final: 0.2711 (mmt) REVERT: A 188 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7118 (mpp) REVERT: A 295 MET cc_start: 0.8297 (ttt) cc_final: 0.8029 (ttt) REVERT: A 392 ASN cc_start: 0.7027 (p0) cc_final: 0.6418 (t0) REVERT: A 424 ASN cc_start: 0.8203 (m-40) cc_final: 0.7711 (m110) REVERT: A 511 LYS cc_start: 0.8116 (mtpp) cc_final: 0.7900 (ttmm) REVERT: A 619 PHE cc_start: 0.6381 (t80) cc_final: 0.6124 (t80) REVERT: A 884 LYS cc_start: 0.6626 (mtpp) cc_final: 0.6289 (mtmm) REVERT: A 940 PHE cc_start: 0.7130 (t80) cc_final: 0.6752 (t80) REVERT: A 948 SER cc_start: 0.8282 (t) cc_final: 0.7898 (p) REVERT: A 1009 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7386 (mm-30) REVERT: A 1055 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7392 (tt0) REVERT: A 1152 GLN cc_start: 0.7499 (mt0) cc_final: 0.6528 (mp-120) REVERT: A 1189 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7978 (mt0) REVERT: A 1215 ASP cc_start: 0.7059 (m-30) cc_final: 0.6828 (m-30) REVERT: A 1237 ASP cc_start: 0.7865 (t0) cc_final: 0.7591 (t0) outliers start: 18 outliers final: 9 residues processed: 114 average time/residue: 0.6421 time to fit residues: 78.0667 Evaluate side-chains 116 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1055 GLU Chi-restraints excluded: chain A residue 1189 GLN Chi-restraints excluded: chain A residue 1232 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN A 514 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.156814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.111859 restraints weight = 10275.196| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.73 r_work: 0.3025 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9588 Z= 0.154 Angle : 0.520 7.391 12994 Z= 0.269 Chirality : 0.041 0.216 1501 Planarity : 0.004 0.057 1613 Dihedral : 6.784 57.915 1360 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.76 % Allowed : 17.29 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.24), residues: 1173 helix: 1.98 (0.18), residues: 806 sheet: 0.03 (0.64), residues: 70 loop : -0.56 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 925 TYR 0.011 0.001 TYR A 306 PHE 0.021 0.001 PHE A 508 TRP 0.006 0.001 TRP A 158 HIS 0.005 0.001 HIS A 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 9587) covalent geometry : angle 0.51957 / 0.27 (12994) hydrogen bonds : bond 0.05140 / 3.59 ( 635) hydrogen bonds : angle 4.05627 / 2.96 ( 1845) Misc. bond : bond 0.00011 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.366 Fit side-chains REVERT: A 74 MET cc_start: 0.3291 (mpp) cc_final: 0.2719 (mmt) REVERT: A 91 MET cc_start: 0.4884 (mmt) cc_final: 0.4484 (mmm) REVERT: A 188 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7131 (mpp) REVERT: A 392 ASN cc_start: 0.7028 (p0) cc_final: 0.6775 (p0) REVERT: A 424 ASN cc_start: 0.8156 (m-40) cc_final: 0.7655 (m110) REVERT: A 511 LYS cc_start: 0.8053 (mtpp) cc_final: 0.7844 (ttmm) REVERT: A 619 PHE cc_start: 0.6255 (t80) cc_final: 0.6013 (t80) REVERT: A 884 LYS cc_start: 0.6577 (mtpp) cc_final: 0.6229 (mtmm) REVERT: A 940 PHE cc_start: 0.7068 (t80) cc_final: 0.6667 (t80) REVERT: A 948 SER cc_start: 0.8243 (t) cc_final: 0.7821 (p) REVERT: A 982 MET cc_start: 0.7237 (ttm) cc_final: 0.7023 (mtp) REVERT: A 1009 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7431 (mm-30) REVERT: A 1055 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7400 (tt0) REVERT: A 1086 MET cc_start: 0.8369 (ptp) cc_final: 0.8083 (ptm) REVERT: A 1152 GLN cc_start: 0.7470 (mt0) cc_final: 0.6482 (mp-120) REVERT: A 1189 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7987 (mt0) REVERT: A 1215 ASP cc_start: 0.7029 (m-30) cc_final: 0.6808 (m-30) REVERT: A 1237 ASP cc_start: 0.7878 (t0) cc_final: 0.7607 (t0) outliers start: 17 outliers final: 9 residues processed: 113 average time/residue: 0.6650 time to fit residues: 80.0491 Evaluate side-chains 116 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1055 GLU Chi-restraints excluded: chain A residue 1189 GLN Chi-restraints excluded: chain A residue 1232 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 45 optimal weight: 0.5980 chunk 55 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 514 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.155344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.110148 restraints weight = 10273.288| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.74 r_work: 0.3056 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9588 Z= 0.169 Angle : 0.533 7.499 12994 Z= 0.276 Chirality : 0.041 0.213 1501 Planarity : 0.004 0.057 1613 Dihedral : 6.836 58.255 1360 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.76 % Allowed : 17.49 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.24), residues: 1173 helix: 1.93 (0.18), residues: 806 sheet: -0.06 (0.64), residues: 70 loop : -0.58 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 925 TYR 0.011 0.001 TYR A 306 PHE 0.022 0.001 PHE A 508 TRP 0.006 0.001 TRP A 158 HIS 0.005 0.001 HIS A 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 9587) covalent geometry : angle 0.53290 / 0.28 (12994) hydrogen bonds : bond 0.05316 / 3.72 ( 635) hydrogen bonds : angle 4.10313 / 3.00 ( 1845) Misc. bond : bond 0.00003 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3550.34 seconds wall clock time: 61 minutes 17.86 seconds (3677.86 seconds total)