Starting phenix.real_space_refine on Sat Aug 23 02:59:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qwd_18691/08_2025/8qwd_18691.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qwd_18691/08_2025/8qwd_18691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qwd_18691/08_2025/8qwd_18691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qwd_18691/08_2025/8qwd_18691.map" model { file = "/net/cci-nas-00/data/ceres_data/8qwd_18691/08_2025/8qwd_18691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qwd_18691/08_2025/8qwd_18691.cif" } resolution = 3.33 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= 0.000 sd= 0.021 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: 5 Type Number sf(0) Gaussians Mg 2 5.21 5 S 18 5.16 5 C 5895 2.51 5 N 1504 2.21 5 O 1785 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9204 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 9198 Classifications: {'peptide': 1103} Link IDs: {'PTRANS': 26, 'TRANS': 1076} Chain breaks: 8 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2, 'water': 4} Link IDs: {None: 5} Time building chain proxies: 2.04, per 1000 atoms: 0.22 Number of scatterers: 9204 At special positions: 0 Unit cell: (76.6134, 119.451, 128.513, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 Mg 2 11.99 O 1785 8.00 N 1504 7.00 C 5895 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: 0.80 Conformation dependent library (CDL) restraints added in 234.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 7 sheets defined 49.8% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 removed outlier: 4.183A pdb=" N ASN A 7 " --> pdb=" O LYS A 3 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE A 8 " --> pdb=" O MET A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 38 through 68 Processing helix chain 'A' and resid 71 through 76 Processing helix chain 'A' and resid 76 through 86 removed outlier: 3.567A pdb=" N TYR A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLU A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 112 Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 122 through 128 removed outlier: 3.657A pdb=" N LEU A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.531A pdb=" N LYS A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 149 through 153' Processing helix chain 'A' and resid 160 through 173 removed outlier: 3.789A pdb=" N PHE A 164 " --> pdb=" O TYR A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 186 Processing helix chain 'A' and resid 188 through 204 removed outlier: 4.093A pdb=" N LYS A 192 " --> pdb=" O GLU A 188 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS A 202 " --> pdb=" O LYS A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.653A pdb=" N ILE A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 235 " --> pdb=" O VAL A 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 230 through 235' Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 239 through 245 removed outlier: 4.045A pdb=" N THR A 243 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 258 Processing helix chain 'A' and resid 270 through 277 Processing helix chain 'A' and resid 278 through 282 removed outlier: 3.711A pdb=" N ASN A 282 " --> pdb=" O ARG A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 332 removed outlier: 3.602A pdb=" N LEU A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 351 removed outlier: 3.548A pdb=" N LYS A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 376 removed outlier: 3.667A pdb=" N ASP A 370 " --> pdb=" O THR A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 389 removed outlier: 3.629A pdb=" N ASN A 387 " --> pdb=" O LYS A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 430 Processing helix chain 'A' and resid 445 through 457 removed outlier: 3.762A pdb=" N GLN A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 510 Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' Processing helix chain 'A' and resid 527 through 543 removed outlier: 3.557A pdb=" N TYR A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLU A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU A 539 " --> pdb=" O GLU A 535 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU A 540 " --> pdb=" O ALA A 536 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN A 543 " --> pdb=" O GLU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 555 removed outlier: 3.549A pdb=" N ASN A 549 " --> pdb=" O ILE A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 607 removed outlier: 4.084A pdb=" N ASN A 607 " --> pdb=" O LYS A 604 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 604 through 607' Processing helix chain 'A' and resid 633 through 644 Proline residue: A 639 - end of helix removed outlier: 3.543A pdb=" N SER A 644 " --> pdb=" O LYS A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 652 removed outlier: 4.155A pdb=" N PHE A 651 " --> pdb=" O ASN A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 659 removed outlier: 3.805A pdb=" N LEU A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 654 through 659' Processing helix chain 'A' and resid 677 through 692 removed outlier: 3.715A pdb=" N ASN A 690 " --> pdb=" O LYS A 686 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 697 Processing helix chain 'A' and resid 710 through 723 removed outlier: 4.038A pdb=" N PHE A 714 " --> pdb=" O ASP A 710 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 717 " --> pdb=" O GLY A 713 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N TYR A 723 " --> pdb=" O GLU A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 742 Processing helix chain 'A' and resid 763 through 773 removed outlier: 4.195A pdb=" N PHE A 773 " --> pdb=" O TRP A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 779 removed outlier: 3.699A pdb=" N LYS A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 868 removed outlier: 4.295A pdb=" N GLU A 863 " --> pdb=" O ASP A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 872 Processing helix chain 'A' and resid 941 through 961 removed outlier: 4.014A pdb=" N HIS A 951 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL A 958 " --> pdb=" O ALA A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 972 removed outlier: 3.835A pdb=" N GLY A 972 " --> pdb=" O LEU A 969 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 969 through 972' Processing helix chain 'A' and resid 981 through 998 removed outlier: 3.886A pdb=" N LYS A 987 " --> pdb=" O GLN A 983 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS A 990 " --> pdb=" O GLN A 986 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A 995 " --> pdb=" O MET A 991 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1046 removed outlier: 4.055A pdb=" N LYS A1045 " --> pdb=" O ASN A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1072 removed outlier: 3.561A pdb=" N ASN A1071 " --> pdb=" O LYS A1067 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS A1072 " --> pdb=" O GLU A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1094 Processing helix chain 'A' and resid 1130 through 1142 Processing helix chain 'A' and resid 1152 through 1157 Processing helix chain 'A' and resid 1161 through 1176 removed outlier: 3.591A pdb=" N PHE A1165 " --> pdb=" O ASP A1161 " (cutoff:3.500A) Processing helix chain 'A' and resid 1216 through 1236 removed outlier: 3.535A pdb=" N ILE A1223 " --> pdb=" O GLY A1219 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS A1226 " --> pdb=" O HIS A1222 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A1228 " --> pdb=" O ALA A1224 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TRP A1229 " --> pdb=" O ARG A1225 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1257 Processing sheet with id=AA1, first strand: chain 'A' and resid 724 through 731 removed outlier: 5.278A pdb=" N LEU A 590 " --> pdb=" O MET A 626 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N TYR A 628 " --> pdb=" O SER A 588 " (cutoff:3.500A) removed outlier: 11.053A pdb=" N SER A 588 " --> pdb=" O TYR A 628 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN A 586 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 563 " --> pdb=" O TYR A 793 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR A 793 " --> pdb=" O GLU A 563 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLU A 788 " --> pdb=" O PRO A 844 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 724 through 731 removed outlier: 5.278A pdb=" N LEU A 590 " --> pdb=" O MET A 626 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N TYR A 628 " --> pdb=" O SER A 588 " (cutoff:3.500A) removed outlier: 11.053A pdb=" N SER A 588 " --> pdb=" O TYR A 628 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N THR A 587 " --> pdb=" O MET A 602 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TYR A 597 " --> pdb=" O ILE A 749 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 22 " --> pdb=" O PHE A 839 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE A 839 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 361 through 363 Processing sheet with id=AA4, first strand: chain 'A' and resid 896 through 900 removed outlier: 6.919A pdb=" N LEU A 889 " --> pdb=" O VAL A 897 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N GLN A 899 " --> pdb=" O LEU A 887 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU A 887 " --> pdb=" O GLN A 899 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 877 " --> pdb=" O VAL A 965 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLU A 967 " --> pdb=" O ILE A 877 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N ARG A 879 " --> pdb=" O GLU A 967 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1075 through 1079 Processing sheet with id=AA6, first strand: chain 'A' and resid 1111 through 1114 Processing sheet with id=AA7, first strand: chain 'A' and resid 1179 through 1181 removed outlier: 3.548A pdb=" N ASN A1180 " --> pdb=" O TYR A1189 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A1189 " --> pdb=" O ASN A1180 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 379 hydrogen bonds defined for protein. 1092 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: 1.52 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2966 1.34 - 1.46: 1895 1.46 - 1.58: 4493 1.58 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 9386 Sorted by residual: bond pdb=" C ALA A 869 " pdb=" N PRO A 870 " ideal model delta sigma weight residual 1.336 1.360 -0.025 1.08e-02 8.57e+03 5.21e+00 bond pdb=" CB LYS A 621 " pdb=" CG LYS A 621 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.20e+00 bond pdb=" CG LYS A 621 " pdb=" CD LYS A 621 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" CB MET A 171 " pdb=" CG MET A 171 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.13e-01 bond pdb=" CA PHE A 85 " pdb=" CB PHE A 85 " ideal model delta sigma weight residual 1.532 1.547 -0.015 1.78e-02 3.16e+03 7.39e-01 ... (remaining 9381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 12461 2.03 - 4.06: 123 4.06 - 6.10: 11 6.10 - 8.13: 3 8.13 - 10.16: 3 Bond angle restraints: 12601 Sorted by residual: angle pdb=" CB LYS A 621 " pdb=" CG LYS A 621 " pdb=" CD LYS A 621 " ideal model delta sigma weight residual 111.30 120.57 -9.27 2.30e+00 1.89e-01 1.62e+01 angle pdb=" CA GLU A 188 " pdb=" CB GLU A 188 " pdb=" CG GLU A 188 " ideal model delta sigma weight residual 114.10 121.64 -7.54 2.00e+00 2.50e-01 1.42e+01 angle pdb=" CB MET A 171 " pdb=" CG MET A 171 " pdb=" SD MET A 171 " ideal model delta sigma weight residual 112.70 122.86 -10.16 3.00e+00 1.11e-01 1.15e+01 angle pdb=" N ASN A1122 " pdb=" CA ASN A1122 " pdb=" C ASN A1122 " ideal model delta sigma weight residual 110.42 105.37 5.05 1.55e+00 4.16e-01 1.06e+01 angle pdb=" CA MET A 171 " pdb=" CB MET A 171 " pdb=" CG MET A 171 " ideal model delta sigma weight residual 114.10 120.58 -6.48 2.00e+00 2.50e-01 1.05e+01 ... (remaining 12596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4649 17.91 - 35.81: 761 35.81 - 53.71: 238 53.71 - 71.62: 35 71.62 - 89.52: 15 Dihedral angle restraints: 5698 sinusoidal: 2433 harmonic: 3265 Sorted by residual: dihedral pdb=" CA TYR A1115 " pdb=" C TYR A1115 " pdb=" N ARG A1116 " pdb=" CA ARG A1116 " ideal model delta harmonic sigma weight residual 180.00 -159.26 -20.74 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA ASN A1121 " pdb=" C ASN A1121 " pdb=" N ASN A1122 " pdb=" CA ASN A1122 " ideal model delta harmonic sigma weight residual 180.00 160.17 19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA CYS A 622 " pdb=" C CYS A 622 " pdb=" N TYR A 623 " pdb=" CA TYR A 623 " ideal model delta harmonic sigma weight residual 180.00 162.18 17.82 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 5695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 713 0.025 - 0.051: 374 0.051 - 0.076: 147 0.076 - 0.102: 49 0.102 - 0.127: 32 Chirality restraints: 1315 Sorted by residual: chirality pdb=" CA GLU A 188 " pdb=" N GLU A 188 " pdb=" C GLU A 188 " pdb=" CB GLU A 188 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CA ASN A1122 " pdb=" N ASN A1122 " pdb=" C ASN A1122 " pdb=" CB ASN A1122 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.12 2.00e-01 2.50e+01 3.74e-01 chirality pdb=" CA ILE A 875 " pdb=" N ILE A 875 " pdb=" C ILE A 875 " pdb=" CB ILE A 875 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.67e-01 ... (remaining 1312 not shown) Planarity restraints: 1633 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 703 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO A 704 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 704 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 704 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 510 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO A 511 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 511 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 511 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A1008 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO A1009 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A1009 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A1009 " 0.020 5.00e-02 4.00e+02 ... (remaining 1630 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 97 2.64 - 3.20: 8288 3.20 - 3.77: 13679 3.77 - 4.33: 18756 4.33 - 4.90: 30957 Nonbonded interactions: 71777 Sorted by model distance: nonbonded pdb=" OG SER A1044 " pdb="MG MG A1401 " model vdw 2.070 2.170 nonbonded pdb=" O PRO A 704 " pdb=" OG SER A 707 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR A 628 " pdb=" O LEU A 785 " model vdw 2.231 3.040 nonbonded pdb=" OG SER A 703 " pdb=" OE2 GLU A 717 " model vdw 2.237 3.040 nonbonded pdb=" OD1 ASP A 878 " pdb="MG MG A1402 " model vdw 2.238 2.170 ... (remaining 71772 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: 2.440 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.100 Find NCS groups from input model: 0.130 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 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 : 0.002 0.044 9386 Z= 0.111 Angle : 0.508 10.161 12601 Z= 0.268 Chirality : 0.039 0.127 1315 Planarity : 0.003 0.052 1633 Dihedral : 19.138 89.524 3586 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.30 % Allowed : 30.46 % Favored : 69.24 % 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 aren not related in a simple way. whole: -1.20 (0.26), residues: 1085 helix: 0.38 (0.25), residues: 444 sheet: -0.89 (0.53), residues: 109 loop : -1.83 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1116 TYR 0.019 0.001 TYR A 296 PHE 0.023 0.001 PHE A 85 TRP 0.008 0.001 TRP A1124 HIS 0.004 0.000 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9386) covalent geometry : angle 0.50760 (12601) hydrogen bonds : bond 0.21193 ( 366) hydrogen bonds : angle 8.38878 ( 1092) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 ASP cc_start: 0.8256 (m-30) cc_final: 0.7708 (m-30) outliers start: 3 outliers final: 3 residues processed: 74 average time/residue: 0.0918 time to fit residues: 10.0298 Evaluate side-chains 73 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 739 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.0170 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.0170 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.0970 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.6056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** 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 = 0.4407 r_free = 0.4407 target = 0.211993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.133429 restraints weight = 11312.858| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 3.22 r_work: 0.3323 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9386 Z= 0.124 Angle : 0.513 8.814 12601 Z= 0.279 Chirality : 0.040 0.155 1315 Planarity : 0.004 0.045 1633 Dihedral : 4.436 44.776 1184 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.57 % Allowed : 28.68 % Favored : 68.74 % 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 aren not related in a simple way. whole: -0.97 (0.26), residues: 1085 helix: 0.77 (0.26), residues: 453 sheet: -1.06 (0.49), residues: 116 loop : -1.88 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1205 TYR 0.015 0.001 TYR A 750 PHE 0.022 0.001 PHE A 85 TRP 0.013 0.001 TRP A1252 HIS 0.005 0.001 HIS A1222 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9386) covalent geometry : angle 0.51277 (12601) hydrogen bonds : bond 0.04139 ( 366) hydrogen bonds : angle 5.44631 ( 1092) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.6989 (mp0) REVERT: A 449 ASP cc_start: 0.8120 (m-30) cc_final: 0.7583 (m-30) REVERT: A 637 MET cc_start: 0.7634 (tmm) cc_final: 0.6147 (tmm) REVERT: A 750 TYR cc_start: 0.7917 (p90) cc_final: 0.7699 (p90) REVERT: A 860 GLU cc_start: 0.7505 (mp0) cc_final: 0.7203 (mp0) REVERT: A 891 ASP cc_start: 0.8486 (t0) cc_final: 0.8213 (t0) REVERT: A 1111 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.7510 (mtt90) outliers start: 26 outliers final: 7 residues processed: 104 average time/residue: 0.0931 time to fit residues: 14.3485 Evaluate side-chains 82 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 1111 ARG Chi-restraints excluded: chain A residue 1122 ASN Chi-restraints excluded: chain A residue 1248 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 78 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 848 ASN ** 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 = 0.4376 r_free = 0.4376 target = 0.208654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.135066 restraints weight = 11309.832| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 3.25 r_work: 0.3278 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9386 Z= 0.181 Angle : 0.549 8.744 12601 Z= 0.292 Chirality : 0.042 0.149 1315 Planarity : 0.004 0.049 1633 Dihedral : 4.523 42.652 1181 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 2.47 % Allowed : 29.48 % Favored : 68.05 % 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 aren not related in a simple way. whole: -1.06 (0.26), residues: 1085 helix: 0.78 (0.25), residues: 463 sheet: -1.16 (0.47), residues: 121 loop : -2.08 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1205 TYR 0.016 0.001 TYR A 750 PHE 0.024 0.001 PHE A 85 TRP 0.014 0.001 TRP A1252 HIS 0.007 0.001 HIS A 389 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 9386) covalent geometry : angle 0.54929 (12601) hydrogen bonds : bond 0.03789 ( 366) hydrogen bonds : angle 5.26506 ( 1092) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6797 (tm-30) REVERT: A 449 ASP cc_start: 0.8204 (m-30) cc_final: 0.7683 (m-30) REVERT: A 637 MET cc_start: 0.7715 (tmm) cc_final: 0.6170 (tmm) REVERT: A 716 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7233 (mtm-85) REVERT: A 891 ASP cc_start: 0.8499 (t0) cc_final: 0.8174 (t0) REVERT: A 1111 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.7848 (mmt-90) REVERT: A 1123 GLN cc_start: 0.6445 (OUTLIER) cc_final: 0.6224 (pm20) outliers start: 25 outliers final: 13 residues processed: 97 average time/residue: 0.0975 time to fit residues: 13.7522 Evaluate side-chains 84 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 1111 ARG Chi-restraints excluded: chain A residue 1122 ASN Chi-restraints excluded: chain A residue 1123 GLN Chi-restraints excluded: chain A residue 1191 ILE Chi-restraints excluded: chain A residue 1247 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 81 optimal weight: 0.8980 chunk 10 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** 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 = 0.4391 r_free = 0.4391 target = 0.209798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.135841 restraints weight = 11437.767| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.43 r_work: 0.3243 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9386 Z= 0.184 Angle : 0.545 8.686 12601 Z= 0.290 Chirality : 0.042 0.144 1315 Planarity : 0.004 0.050 1633 Dihedral : 4.614 42.482 1181 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 3.56 % Allowed : 28.59 % Favored : 67.85 % 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 aren not related in a simple way. whole: -1.07 (0.26), residues: 1085 helix: 0.75 (0.25), residues: 464 sheet: -1.16 (0.48), residues: 118 loop : -2.05 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1116 TYR 0.018 0.001 TYR A 750 PHE 0.023 0.001 PHE A 85 TRP 0.014 0.001 TRP A1252 HIS 0.006 0.001 HIS A 389 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 9386) covalent geometry : angle 0.54493 (12601) hydrogen bonds : bond 0.03561 ( 366) hydrogen bonds : angle 5.13238 ( 1092) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 69 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7212 (tm-30) cc_final: 0.6827 (tm-30) REVERT: A 197 MET cc_start: 0.8179 (mmm) cc_final: 0.7952 (mmp) REVERT: A 355 TYR cc_start: 0.7198 (m-80) cc_final: 0.6961 (m-80) REVERT: A 449 ASP cc_start: 0.8126 (m-30) cc_final: 0.7586 (m-30) REVERT: A 891 ASP cc_start: 0.8538 (t0) cc_final: 0.8235 (t0) REVERT: A 1025 PHE cc_start: 0.7167 (OUTLIER) cc_final: 0.6844 (t80) REVERT: A 1111 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.7803 (mmt-90) REVERT: A 1123 GLN cc_start: 0.6334 (OUTLIER) cc_final: 0.6111 (pm20) REVERT: A 1166 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8132 (ttmt) outliers start: 36 outliers final: 16 residues processed: 102 average time/residue: 0.0895 time to fit residues: 13.5416 Evaluate side-chains 85 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1025 PHE Chi-restraints excluded: chain A residue 1111 ARG Chi-restraints excluded: chain A residue 1123 GLN Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1166 LYS Chi-restraints excluded: chain A residue 1191 ILE Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain A residue 1248 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 76 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 16 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1180 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.208776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.133781 restraints weight = 11415.914| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 3.42 r_work: 0.3225 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9386 Z= 0.206 Angle : 0.567 8.759 12601 Z= 0.301 Chirality : 0.042 0.143 1315 Planarity : 0.004 0.050 1633 Dihedral : 4.755 41.967 1181 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 3.76 % Allowed : 28.78 % Favored : 67.46 % 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 aren not related in a simple way. whole: -1.15 (0.26), residues: 1085 helix: 0.69 (0.25), residues: 464 sheet: -1.22 (0.47), residues: 118 loop : -2.09 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1116 TYR 0.017 0.002 TYR A1221 PHE 0.023 0.002 PHE A 85 TRP 0.015 0.001 TRP A1252 HIS 0.006 0.001 HIS A 389 Details of bonding type rmsd covalent geometry : bond 0.00499 ( 9386) covalent geometry : angle 0.56678 (12601) hydrogen bonds : bond 0.03600 ( 366) hydrogen bonds : angle 5.14565 ( 1092) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 66 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7222 (tm-30) cc_final: 0.6809 (tm-30) REVERT: A 355 TYR cc_start: 0.7303 (m-80) cc_final: 0.7054 (m-80) REVERT: A 425 LEU cc_start: 0.6149 (OUTLIER) cc_final: 0.5878 (mp) REVERT: A 433 CYS cc_start: 0.7525 (t) cc_final: 0.7213 (t) REVERT: A 449 ASP cc_start: 0.8184 (m-30) cc_final: 0.7643 (m-30) REVERT: A 660 ILE cc_start: 0.7064 (OUTLIER) cc_final: 0.6840 (pp) REVERT: A 716 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7342 (mtm-85) REVERT: A 891 ASP cc_start: 0.8595 (t0) cc_final: 0.8292 (t0) REVERT: A 1025 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.6971 (t80) REVERT: A 1111 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.7788 (mmt-90) REVERT: A 1166 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8166 (ttmt) outliers start: 38 outliers final: 22 residues processed: 102 average time/residue: 0.0960 time to fit residues: 14.0495 Evaluate side-chains 90 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 62 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1025 PHE Chi-restraints excluded: chain A residue 1111 ARG Chi-restraints excluded: chain A residue 1117 ASN Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1166 LYS Chi-restraints excluded: chain A residue 1191 ILE Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain A residue 1248 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 51 optimal weight: 0.8980 chunk 23 optimal weight: 20.0000 chunk 7 optimal weight: 0.0040 chunk 42 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 17 optimal weight: 10.0000 chunk 99 optimal weight: 0.0770 chunk 107 optimal weight: 0.5980 overall best weight: 0.4550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.209920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.134528 restraints weight = 11330.087| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 3.32 r_work: 0.3307 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9386 Z= 0.109 Angle : 0.512 8.877 12601 Z= 0.272 Chirality : 0.040 0.152 1315 Planarity : 0.003 0.050 1633 Dihedral : 4.534 42.646 1181 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 3.07 % Allowed : 29.38 % Favored : 67.56 % 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 aren not related in a simple way. whole: -0.92 (0.26), residues: 1085 helix: 0.88 (0.25), residues: 465 sheet: -0.94 (0.49), residues: 115 loop : -2.02 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1116 TYR 0.016 0.001 TYR A 750 PHE 0.023 0.001 PHE A 85 TRP 0.016 0.001 TRP A1252 HIS 0.005 0.001 HIS A 389 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 9386) covalent geometry : angle 0.51173 (12601) hydrogen bonds : bond 0.03133 ( 366) hydrogen bonds : angle 4.90458 ( 1092) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 72 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6780 (tm-30) REVERT: A 355 TYR cc_start: 0.7232 (m-80) cc_final: 0.7008 (m-80) REVERT: A 425 LEU cc_start: 0.5881 (OUTLIER) cc_final: 0.5656 (mp) REVERT: A 449 ASP cc_start: 0.8141 (m-30) cc_final: 0.7642 (m-30) REVERT: A 553 ASN cc_start: 0.8123 (t0) cc_final: 0.7531 (t0) REVERT: A 660 ILE cc_start: 0.7024 (OUTLIER) cc_final: 0.6820 (pp) REVERT: A 716 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7163 (mtm-85) REVERT: A 891 ASP cc_start: 0.8507 (t0) cc_final: 0.8199 (t0) REVERT: A 1022 PHE cc_start: 0.7215 (t80) cc_final: 0.6982 (t80) REVERT: A 1025 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.6917 (t80) outliers start: 31 outliers final: 17 residues processed: 98 average time/residue: 0.1021 time to fit residues: 14.4268 Evaluate side-chains 87 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 834 TYR Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1025 PHE Chi-restraints excluded: chain A residue 1191 ILE Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain A residue 1248 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 82 optimal weight: 0.0670 chunk 66 optimal weight: 4.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 848 ASN ** 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 = 0.4390 r_free = 0.4390 target = 0.209593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.137421 restraints weight = 11529.613| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 3.44 r_work: 0.3255 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9386 Z= 0.193 Angle : 0.560 9.140 12601 Z= 0.295 Chirality : 0.042 0.145 1315 Planarity : 0.004 0.050 1633 Dihedral : 4.667 41.706 1181 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 2.97 % Allowed : 29.77 % Favored : 67.26 % 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 aren not related in a simple way. whole: -1.01 (0.26), residues: 1085 helix: 0.84 (0.25), residues: 463 sheet: -1.05 (0.48), residues: 118 loop : -2.08 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1116 TYR 0.016 0.001 TYR A1221 PHE 0.023 0.001 PHE A 85 TRP 0.014 0.001 TRP A1252 HIS 0.005 0.001 HIS A1222 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 9386) covalent geometry : angle 0.56002 (12601) hydrogen bonds : bond 0.03415 ( 366) hydrogen bonds : angle 5.00653 ( 1092) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 63 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7177 (tm-30) cc_final: 0.6677 (tm-30) REVERT: A 197 MET cc_start: 0.8180 (mmm) cc_final: 0.7955 (mmp) REVERT: A 355 TYR cc_start: 0.7301 (m-80) cc_final: 0.7023 (m-80) REVERT: A 425 LEU cc_start: 0.6006 (OUTLIER) cc_final: 0.5744 (mp) REVERT: A 433 CYS cc_start: 0.7487 (t) cc_final: 0.7156 (t) REVERT: A 553 ASN cc_start: 0.8181 (t0) cc_final: 0.7596 (t0) REVERT: A 716 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7313 (mtm-85) REVERT: A 891 ASP cc_start: 0.8553 (t0) cc_final: 0.8203 (t0) REVERT: A 1022 PHE cc_start: 0.7285 (t80) cc_final: 0.7068 (t80) REVERT: A 1025 PHE cc_start: 0.7334 (OUTLIER) cc_final: 0.6915 (t80) REVERT: A 1111 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.7841 (mmt-90) outliers start: 30 outliers final: 18 residues processed: 91 average time/residue: 0.0990 time to fit residues: 12.8382 Evaluate side-chains 84 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 834 TYR Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1025 PHE Chi-restraints excluded: chain A residue 1111 ARG Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1191 ILE Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain A residue 1248 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 4 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 5 optimal weight: 20.0000 chunk 3 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.209274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.133831 restraints weight = 11384.820| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 3.54 r_work: 0.3254 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9386 Z= 0.119 Angle : 0.518 9.211 12601 Z= 0.274 Chirality : 0.040 0.152 1315 Planarity : 0.003 0.050 1633 Dihedral : 4.538 42.154 1181 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 2.97 % Allowed : 29.87 % Favored : 67.16 % 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 aren not related in a simple way. whole: -0.91 (0.26), residues: 1085 helix: 0.89 (0.25), residues: 468 sheet: -0.91 (0.49), residues: 116 loop : -2.04 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1116 TYR 0.015 0.001 TYR A 750 PHE 0.023 0.001 PHE A 85 TRP 0.015 0.001 TRP A1252 HIS 0.005 0.001 HIS A 389 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9386) covalent geometry : angle 0.51850 (12601) hydrogen bonds : bond 0.03131 ( 366) hydrogen bonds : angle 4.87049 ( 1092) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 67 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7177 (tm-30) cc_final: 0.6657 (tm-30) REVERT: A 425 LEU cc_start: 0.6031 (OUTLIER) cc_final: 0.5773 (mp) REVERT: A 433 CYS cc_start: 0.7337 (t) cc_final: 0.6970 (t) REVERT: A 553 ASN cc_start: 0.8210 (t0) cc_final: 0.7618 (t0) REVERT: A 716 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7267 (mtm-85) REVERT: A 891 ASP cc_start: 0.8569 (t0) cc_final: 0.8246 (t0) REVERT: A 1022 PHE cc_start: 0.7249 (t80) cc_final: 0.7017 (t80) REVERT: A 1025 PHE cc_start: 0.7369 (OUTLIER) cc_final: 0.7029 (t80) REVERT: A 1111 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.7783 (mmt-90) outliers start: 30 outliers final: 21 residues processed: 94 average time/residue: 0.0949 time to fit residues: 12.9498 Evaluate side-chains 92 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 834 TYR Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1025 PHE Chi-restraints excluded: chain A residue 1111 ARG Chi-restraints excluded: chain A residue 1117 ASN Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain A residue 1248 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 36 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 83 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 26 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 848 ASN ** 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 = 0.4373 r_free = 0.4373 target = 0.208290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.134575 restraints weight = 11203.598| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 3.38 r_work: 0.3252 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9386 Z= 0.151 Angle : 0.535 8.752 12601 Z= 0.282 Chirality : 0.041 0.149 1315 Planarity : 0.004 0.050 1633 Dihedral : 4.559 41.777 1181 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 2.77 % Allowed : 30.07 % Favored : 67.16 % 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 aren not related in a simple way. whole: -0.99 (0.26), residues: 1085 helix: 0.80 (0.25), residues: 475 sheet: -0.95 (0.48), residues: 116 loop : -2.11 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1116 TYR 0.014 0.001 TYR A 750 PHE 0.023 0.001 PHE A 85 TRP 0.014 0.001 TRP A1252 HIS 0.005 0.001 HIS A1222 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 9386) covalent geometry : angle 0.53456 (12601) hydrogen bonds : bond 0.03226 ( 366) hydrogen bonds : angle 4.89284 ( 1092) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7179 (tm-30) cc_final: 0.6670 (tm-30) REVERT: A 355 TYR cc_start: 0.7214 (m-80) cc_final: 0.6736 (m-80) REVERT: A 425 LEU cc_start: 0.5961 (OUTLIER) cc_final: 0.5698 (mp) REVERT: A 433 CYS cc_start: 0.7430 (t) cc_final: 0.7090 (t) REVERT: A 553 ASN cc_start: 0.8201 (t0) cc_final: 0.7621 (t0) REVERT: A 716 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7279 (mtm-85) REVERT: A 891 ASP cc_start: 0.8514 (t0) cc_final: 0.8176 (t0) REVERT: A 1022 PHE cc_start: 0.7279 (t80) cc_final: 0.7024 (t80) REVERT: A 1025 PHE cc_start: 0.7375 (OUTLIER) cc_final: 0.7033 (t80) REVERT: A 1111 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.7762 (mmt-90) outliers start: 28 outliers final: 20 residues processed: 91 average time/residue: 0.0998 time to fit residues: 13.0748 Evaluate side-chains 90 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 834 TYR Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1025 PHE Chi-restraints excluded: chain A residue 1096 GLU Chi-restraints excluded: chain A residue 1111 ARG Chi-restraints excluded: chain A residue 1117 ASN Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain A residue 1248 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 10 optimal weight: 20.0000 chunk 74 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 42 optimal weight: 8.9990 chunk 105 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 0.0370 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1180 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.212791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.131576 restraints weight = 11406.868| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.84 r_work: 0.3337 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9386 Z= 0.110 Angle : 0.506 8.901 12601 Z= 0.267 Chirality : 0.040 0.152 1315 Planarity : 0.003 0.050 1633 Dihedral : 4.436 41.909 1181 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 2.37 % Allowed : 30.56 % Favored : 67.06 % 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 aren not related in a simple way. whole: -0.88 (0.26), residues: 1085 helix: 0.91 (0.25), residues: 475 sheet: -0.91 (0.46), residues: 120 loop : -2.07 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1116 TYR 0.014 0.001 TYR A 750 PHE 0.023 0.001 PHE A 85 TRP 0.015 0.001 TRP A1252 HIS 0.004 0.001 HIS A 389 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 9386) covalent geometry : angle 0.50642 (12601) hydrogen bonds : bond 0.02979 ( 366) hydrogen bonds : angle 4.77194 ( 1092) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7168 (tm-30) cc_final: 0.6640 (tm-30) REVERT: A 355 TYR cc_start: 0.7239 (m-80) cc_final: 0.6798 (m-80) REVERT: A 425 LEU cc_start: 0.5809 (OUTLIER) cc_final: 0.5569 (mp) REVERT: A 433 CYS cc_start: 0.7171 (t) cc_final: 0.6834 (t) REVERT: A 553 ASN cc_start: 0.8158 (t0) cc_final: 0.7606 (t0) REVERT: A 716 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7151 (mtm-85) REVERT: A 891 ASP cc_start: 0.8438 (t0) cc_final: 0.8113 (t0) REVERT: A 1025 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.6965 (t80) REVERT: A 1111 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7722 (mmt-90) outliers start: 24 outliers final: 19 residues processed: 94 average time/residue: 0.1011 time to fit residues: 13.5178 Evaluate side-chains 90 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 834 TYR Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1025 PHE Chi-restraints excluded: chain A residue 1111 ARG Chi-restraints excluded: chain A residue 1117 ASN Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain A residue 1248 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 6.9990 chunk 106 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 108 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 55 optimal weight: 7.9990 chunk 90 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 74 optimal weight: 0.6980 chunk 13 optimal weight: 20.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 848 ASN ** 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 = 0.4413 r_free = 0.4413 target = 0.212238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.138701 restraints weight = 11263.295| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 3.17 r_work: 0.3319 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9386 Z= 0.122 Angle : 0.524 9.247 12601 Z= 0.275 Chirality : 0.040 0.152 1315 Planarity : 0.003 0.050 1633 Dihedral : 4.421 41.351 1181 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 2.57 % Allowed : 30.56 % Favored : 66.86 % 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 aren not related in a simple way. whole: -0.84 (0.26), residues: 1085 helix: 0.96 (0.25), residues: 475 sheet: -0.83 (0.48), residues: 115 loop : -2.07 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1116 TYR 0.014 0.001 TYR A 750 PHE 0.023 0.001 PHE A 85 TRP 0.014 0.001 TRP A1252 HIS 0.004 0.001 HIS A1222 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9386) covalent geometry : angle 0.52361 (12601) hydrogen bonds : bond 0.02999 ( 366) hydrogen bonds : angle 4.74350 ( 1092) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2798.66 seconds wall clock time: 48 minutes 48.01 seconds (2928.01 seconds total)