Starting phenix.real_space_refine on Mon May 12 20:13:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qwd_18691/05_2025/8qwd_18691.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qwd_18691/05_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_18691/05_2025/8qwd_18691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qwd_18691/05_2025/8qwd_18691.map" model { file = "/net/cci-nas-00/data/ceres_data/8qwd_18691/05_2025/8qwd_18691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qwd_18691/05_2025/8qwd_18691.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.99, per 1000 atoms: 0.65 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: 2.40 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.28 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: 3.17 Time building geometry restraints manager: 2.81 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: 3.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.300 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.430 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.008 0.001 TRP A1124 HIS 0.004 0.000 HIS A 187 PHE 0.023 0.001 PHE A 85 TYR 0.019 0.001 TYR A 296 ARG 0.003 0.000 ARG A1116 Details of bonding type rmsd hydrogen bonds : bond 0.21193 ( 366) hydrogen bonds : angle 8.38878 ( 1092) covalent geometry : bond 0.00242 ( 9386) covalent geometry : angle 0.50760 (12601) *********************** 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 : 1.086 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: 0.2043 time to fit residues: 22.4787 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 : 0.959 ------------------------------------------------------------------------------- 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 92 optimal weight: 0.1980 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4407 r_free = 0.4407 target = 0.211939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.133672 restraints weight = 11224.827| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 3.22 r_work: 0.3304 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.0801 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= 0.127 Angle : 0.514 8.806 12601 Z= 0.279 Chirality : 0.040 0.154 1315 Planarity : 0.004 0.046 1633 Dihedral : 4.455 44.558 1184 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 2.57 % Allowed : 28.59 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.26), residues: 1085 helix: 0.77 (0.26), residues: 453 sheet: -1.17 (0.48), residues: 118 loop : -1.88 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1252 HIS 0.004 0.001 HIS A1222 PHE 0.022 0.001 PHE A 85 TYR 0.014 0.001 TYR A 750 ARG 0.002 0.000 ARG A1205 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 366) hydrogen bonds : angle 5.44793 ( 1092) covalent geometry : bond 0.00286 ( 9386) covalent geometry : angle 0.51400 (12601) *********************** 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 105 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.6990 (mp0) REVERT: A 449 ASP cc_start: 0.8158 (m-30) cc_final: 0.7608 (m-30) REVERT: A 637 MET cc_start: 0.7684 (tmm) cc_final: 0.6184 (tmm) REVERT: A 860 GLU cc_start: 0.7532 (mp0) cc_final: 0.7235 (mp0) REVERT: A 891 ASP cc_start: 0.8513 (t0) cc_final: 0.8248 (t0) REVERT: A 1111 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.7817 (mtt90) outliers start: 26 outliers final: 7 residues processed: 103 average time/residue: 0.1891 time to fit residues: 28.6834 Evaluate side-chains 84 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 8 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 78 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 = 0.4371 r_free = 0.4371 target = 0.207324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.129870 restraints weight = 11361.723| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 3.34 r_work: 0.3202 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 9386 Z= 0.294 Angle : 0.642 8.740 12601 Z= 0.339 Chirality : 0.045 0.161 1315 Planarity : 0.004 0.050 1633 Dihedral : 4.865 41.737 1181 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 3.36 % Allowed : 28.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.26), residues: 1085 helix: 0.56 (0.25), residues: 461 sheet: -1.37 (0.47), residues: 118 loop : -2.13 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1252 HIS 0.008 0.001 HIS A 389 PHE 0.027 0.002 PHE A 864 TYR 0.021 0.002 TYR A1221 ARG 0.002 0.000 ARG A1205 Details of bonding type rmsd hydrogen bonds : bond 0.04300 ( 366) hydrogen bonds : angle 5.53984 ( 1092) covalent geometry : bond 0.00711 ( 9386) covalent geometry : angle 0.64151 (12601) *********************** 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 103 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 69 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: A 433 CYS cc_start: 0.7385 (t) cc_final: 0.7040 (t) REVERT: A 449 ASP cc_start: 0.8184 (m-30) cc_final: 0.7633 (m-30) REVERT: A 637 MET cc_start: 0.7632 (tmm) cc_final: 0.6122 (tmm) REVERT: A 716 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7352 (mtm-85) REVERT: A 891 ASP cc_start: 0.8643 (t0) cc_final: 0.8400 (t0) REVERT: A 1111 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8040 (mpt180) REVERT: A 1123 GLN cc_start: 0.6504 (OUTLIER) cc_final: 0.6282 (pm20) outliers start: 34 outliers final: 15 residues processed: 99 average time/residue: 0.2060 time to fit residues: 29.6319 Evaluate side-chains 80 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 62 PHE 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 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 1013 LEU 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 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 38 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 chunk 84 optimal weight: 0.4980 chunk 4 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 33 optimal weight: 0.0980 chunk 85 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 = 0.4384 r_free = 0.4384 target = 0.209637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.136590 restraints weight = 11275.781| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 3.20 r_work: 0.3301 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9386 Z= 0.120 Angle : 0.511 8.918 12601 Z= 0.274 Chirality : 0.040 0.148 1315 Planarity : 0.004 0.049 1633 Dihedral : 4.579 43.256 1181 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.87 % Allowed : 29.77 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.26), residues: 1085 helix: 0.75 (0.25), residues: 464 sheet: -1.28 (0.46), residues: 123 loop : -2.04 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1252 HIS 0.006 0.001 HIS A 389 PHE 0.023 0.001 PHE A 85 TYR 0.020 0.001 TYR A 750 ARG 0.002 0.000 ARG A1116 Details of bonding type rmsd hydrogen bonds : bond 0.03363 ( 366) hydrogen bonds : angle 5.07697 ( 1092) covalent geometry : bond 0.00269 ( 9386) covalent geometry : angle 0.51132 (12601) *********************** 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 99 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7257 (tm-30) cc_final: 0.6868 (tm-30) REVERT: A 425 LEU cc_start: 0.5971 (OUTLIER) cc_final: 0.5748 (mp) REVERT: A 449 ASP cc_start: 0.8159 (m-30) cc_final: 0.7625 (m-30) REVERT: A 716 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7175 (mtm-85) REVERT: A 891 ASP cc_start: 0.8489 (t0) cc_final: 0.8174 (t0) REVERT: A 1123 GLN cc_start: 0.6349 (OUTLIER) cc_final: 0.6126 (pm20) outliers start: 29 outliers final: 17 residues processed: 97 average time/residue: 0.2132 time to fit residues: 30.4178 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 : 0.958 ------------------------------------------------------------------------------- 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 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 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 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 55 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 31 optimal weight: 6.9990 chunk 80 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 23 optimal weight: 20.0000 chunk 85 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4374 r_free = 0.4374 target = 0.208526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.135242 restraints weight = 11297.765| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 3.55 r_work: 0.3241 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9386 Z= 0.149 Angle : 0.521 8.772 12601 Z= 0.278 Chirality : 0.041 0.149 1315 Planarity : 0.004 0.050 1633 Dihedral : 4.570 42.425 1181 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 2.97 % Allowed : 29.67 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.26), residues: 1085 helix: 0.79 (0.25), residues: 464 sheet: -1.26 (0.46), residues: 121 loop : -2.03 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1252 HIS 0.005 0.001 HIS A 389 PHE 0.023 0.001 PHE A 85 TYR 0.018 0.001 TYR A 750 ARG 0.002 0.000 ARG A1205 Details of bonding type rmsd hydrogen bonds : bond 0.03351 ( 366) hydrogen bonds : angle 5.00853 ( 1092) covalent geometry : bond 0.00354 ( 9386) covalent geometry : angle 0.52094 (12601) *********************** 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 100 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 70 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7276 (tm-30) cc_final: 0.6868 (tm-30) REVERT: A 355 TYR cc_start: 0.7134 (m-80) cc_final: 0.6884 (m-80) REVERT: A 425 LEU cc_start: 0.6290 (OUTLIER) cc_final: 0.6027 (mp) REVERT: A 433 CYS cc_start: 0.7416 (t) cc_final: 0.7072 (t) REVERT: A 449 ASP cc_start: 0.8253 (m-30) cc_final: 0.7712 (m-30) REVERT: A 660 ILE cc_start: 0.6979 (OUTLIER) cc_final: 0.6747 (pp) REVERT: A 716 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7357 (mtm-85) REVERT: A 891 ASP cc_start: 0.8553 (t0) cc_final: 0.8255 (t0) REVERT: A 1022 PHE cc_start: 0.7312 (t80) cc_final: 0.7076 (t80) REVERT: A 1025 PHE cc_start: 0.7182 (OUTLIER) cc_final: 0.6876 (t80) REVERT: A 1111 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.7954 (mtt90) REVERT: A 1123 GLN cc_start: 0.6411 (OUTLIER) cc_final: 0.6179 (pm20) outliers start: 30 outliers final: 17 residues processed: 95 average time/residue: 0.2190 time to fit residues: 29.8051 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 : 1.154 ------------------------------------------------------------------------------- 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 574 LEU 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 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 1025 PHE Chi-restraints excluded: chain A residue 1111 ARG Chi-restraints excluded: chain A residue 1117 ASN Chi-restraints excluded: chain A residue 1123 GLN 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 108 optimal weight: 0.0170 chunk 15 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 77 optimal weight: 0.0030 chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 0.0570 chunk 87 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.3946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 848 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.210937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.138878 restraints weight = 11230.200| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 3.22 r_work: 0.3326 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9386 Z= 0.105 Angle : 0.505 8.903 12601 Z= 0.268 Chirality : 0.040 0.151 1315 Planarity : 0.003 0.049 1633 Dihedral : 4.443 42.670 1181 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 3.46 % Allowed : 29.57 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.26), residues: 1085 helix: 0.93 (0.25), residues: 465 sheet: -1.02 (0.47), residues: 120 loop : -1.98 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1252 HIS 0.005 0.001 HIS A 389 PHE 0.023 0.001 PHE A 85 TYR 0.017 0.001 TYR A 750 ARG 0.005 0.000 ARG A1116 Details of bonding type rmsd hydrogen bonds : bond 0.03041 ( 366) hydrogen bonds : angle 4.84257 ( 1092) covalent geometry : bond 0.00233 ( 9386) covalent geometry : angle 0.50525 (12601) *********************** 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 110 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 75 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7201 (tm-30) cc_final: 0.6744 (tm-30) REVERT: A 355 TYR cc_start: 0.7151 (m-80) cc_final: 0.6866 (m-80) REVERT: A 425 LEU cc_start: 0.5881 (OUTLIER) cc_final: 0.5656 (mp) REVERT: A 449 ASP cc_start: 0.8117 (m-30) cc_final: 0.7641 (m-30) REVERT: A 660 ILE cc_start: 0.6943 (OUTLIER) cc_final: 0.6729 (pp) REVERT: A 716 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7181 (mtm-85) REVERT: A 891 ASP cc_start: 0.8497 (t0) cc_final: 0.8192 (t0) REVERT: A 1022 PHE cc_start: 0.7216 (t80) cc_final: 0.7009 (t80) REVERT: A 1025 PHE cc_start: 0.7120 (OUTLIER) cc_final: 0.6818 (t80) REVERT: A 1111 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.7862 (mmt-90) outliers start: 35 outliers final: 14 residues processed: 107 average time/residue: 0.2013 time to fit residues: 30.9406 Evaluate side-chains 89 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 616 SER 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 837 ASP 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 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 42 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 7 optimal weight: 0.0470 chunk 91 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- 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 = 0.4380 r_free = 0.4380 target = 0.209153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.130872 restraints weight = 11466.137| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 3.33 r_work: 0.3272 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9386 Z= 0.145 Angle : 0.527 9.230 12601 Z= 0.277 Chirality : 0.041 0.148 1315 Planarity : 0.003 0.050 1633 Dihedral : 4.496 41.912 1181 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 3.66 % Allowed : 29.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.26), residues: 1085 helix: 0.98 (0.25), residues: 463 sheet: -1.00 (0.48), residues: 115 loop : -2.00 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1252 HIS 0.005 0.001 HIS A1222 PHE 0.023 0.001 PHE A 85 TYR 0.016 0.001 TYR A 750 ARG 0.002 0.000 ARG A1116 Details of bonding type rmsd hydrogen bonds : bond 0.03168 ( 366) hydrogen bonds : angle 4.85595 ( 1092) covalent geometry : bond 0.00344 ( 9386) covalent geometry : angle 0.52706 (12601) *********************** 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 111 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 74 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7221 (tm-30) cc_final: 0.6739 (tm-30) REVERT: A 355 TYR cc_start: 0.7190 (m-80) cc_final: 0.6868 (m-80) REVERT: A 425 LEU cc_start: 0.5932 (OUTLIER) cc_final: 0.5675 (mp) REVERT: A 433 CYS cc_start: 0.7299 (t) cc_final: 0.6988 (t) REVERT: A 660 ILE cc_start: 0.7034 (OUTLIER) cc_final: 0.6820 (pp) REVERT: A 716 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7241 (mtm-85) REVERT: A 891 ASP cc_start: 0.8522 (t0) cc_final: 0.8174 (t0) REVERT: A 1022 PHE cc_start: 0.7255 (t80) cc_final: 0.7017 (t80) REVERT: A 1025 PHE cc_start: 0.7265 (OUTLIER) cc_final: 0.6807 (t80) REVERT: A 1111 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7789 (mtt90) outliers start: 37 outliers final: 26 residues processed: 107 average time/residue: 0.1998 time to fit residues: 30.9370 Evaluate side-chains 100 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 69 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 298 GLN 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 753 ASP 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 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 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 36 optimal weight: 4.9990 chunk 88 optimal weight: 0.0970 chunk 44 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 74 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.4414 r_free = 0.4414 target = 0.212439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.139883 restraints weight = 11558.207| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 3.40 r_work: 0.3297 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1664 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= 0.117 Angle : 0.507 9.032 12601 Z= 0.268 Chirality : 0.040 0.149 1315 Planarity : 0.003 0.050 1633 Dihedral : 4.446 41.940 1181 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 3.17 % Allowed : 29.87 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.26), residues: 1085 helix: 0.92 (0.25), residues: 475 sheet: -0.90 (0.49), residues: 115 loop : -2.06 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1252 HIS 0.005 0.001 HIS A 389 PHE 0.023 0.001 PHE A 85 TYR 0.016 0.001 TYR A 750 ARG 0.001 0.000 ARG A1116 Details of bonding type rmsd hydrogen bonds : bond 0.03033 ( 366) hydrogen bonds : angle 4.79437 ( 1092) covalent geometry : bond 0.00270 ( 9386) covalent geometry : angle 0.50747 (12601) *********************** 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 103 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 71 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6770 (tm-30) REVERT: A 197 MET cc_start: 0.8137 (mmm) cc_final: 0.7894 (mmp) REVERT: A 355 TYR cc_start: 0.7221 (m-80) cc_final: 0.6916 (m-80) REVERT: A 425 LEU cc_start: 0.5895 (OUTLIER) cc_final: 0.5651 (mp) REVERT: A 433 CYS cc_start: 0.7248 (t) cc_final: 0.6909 (t) REVERT: A 660 ILE cc_start: 0.7033 (OUTLIER) cc_final: 0.6823 (pp) REVERT: A 716 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7227 (mtm-85) REVERT: A 879 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7779 (mtm180) REVERT: A 891 ASP cc_start: 0.8450 (t0) cc_final: 0.8122 (t0) REVERT: A 1025 PHE cc_start: 0.7297 (OUTLIER) cc_final: 0.6988 (t80) REVERT: A 1060 TYR cc_start: 0.6032 (t80) cc_final: 0.5718 (t80) REVERT: A 1111 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7803 (mmt-90) outliers start: 32 outliers final: 22 residues processed: 99 average time/residue: 0.2149 time to fit residues: 30.3906 Evaluate side-chains 99 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 298 GLN 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 616 SER 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 753 ASP Chi-restraints excluded: chain A residue 834 TYR Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 879 ARG 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 100 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 25 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 107 optimal weight: 0.5980 chunk 8 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 52 optimal weight: 0.0020 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 848 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.211052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.139453 restraints weight = 11376.643| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 3.41 r_work: 0.3314 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9386 Z= 0.110 Angle : 0.497 8.752 12601 Z= 0.264 Chirality : 0.040 0.151 1315 Planarity : 0.003 0.050 1633 Dihedral : 4.399 41.723 1181 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 3.07 % Allowed : 30.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.26), residues: 1085 helix: 0.96 (0.25), residues: 475 sheet: -0.93 (0.47), residues: 120 loop : -2.03 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1252 HIS 0.004 0.001 HIS A 389 PHE 0.023 0.001 PHE A 85 TYR 0.015 0.001 TYR A 750 ARG 0.003 0.000 ARG A1116 Details of bonding type rmsd hydrogen bonds : bond 0.02976 ( 366) hydrogen bonds : angle 4.75213 ( 1092) covalent geometry : bond 0.00250 ( 9386) covalent geometry : angle 0.49716 (12601) *********************** 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 105 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7147 (tm-30) cc_final: 0.6618 (tm-30) REVERT: A 197 MET cc_start: 0.8138 (mmm) cc_final: 0.7888 (mmp) REVERT: A 355 TYR cc_start: 0.7183 (m-80) cc_final: 0.6818 (m-80) REVERT: A 433 CYS cc_start: 0.7215 (t) cc_final: 0.6879 (t) REVERT: A 716 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.7196 (mtm-85) REVERT: A 879 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7787 (mtm180) REVERT: A 891 ASP cc_start: 0.8435 (t0) cc_final: 0.8119 (t0) REVERT: A 1025 PHE cc_start: 0.7270 (OUTLIER) cc_final: 0.6942 (t80) REVERT: A 1060 TYR cc_start: 0.6112 (t80) cc_final: 0.5874 (t80) REVERT: A 1111 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7779 (mmt-90) outliers start: 31 outliers final: 21 residues processed: 100 average time/residue: 0.2133 time to fit residues: 30.6039 Evaluate side-chains 97 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 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 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 860 GLU Chi-restraints excluded: chain A residue 879 ARG 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 54 optimal weight: 0.0670 chunk 89 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 57 optimal weight: 0.0050 chunk 8 optimal weight: 20.0000 chunk 24 optimal weight: 8.9990 chunk 44 optimal weight: 0.0370 overall best weight: 1.0214 ------------------------------------------------------------------------------- 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 = 0.4405 r_free = 0.4405 target = 0.211293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.135850 restraints weight = 11573.507| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.83 r_work: 0.3210 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9386 Z= 0.153 Angle : 0.533 8.632 12601 Z= 0.281 Chirality : 0.041 0.147 1315 Planarity : 0.003 0.050 1633 Dihedral : 4.509 41.176 1181 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 2.57 % Allowed : 30.07 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.26), residues: 1085 helix: 0.89 (0.25), residues: 475 sheet: -0.99 (0.47), residues: 116 loop : -2.06 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1252 HIS 0.005 0.001 HIS A1222 PHE 0.023 0.001 PHE A 85 TYR 0.015 0.001 TYR A 750 ARG 0.002 0.000 ARG A1116 Details of bonding type rmsd hydrogen bonds : bond 0.03185 ( 366) hydrogen bonds : angle 4.83818 ( 1092) covalent geometry : bond 0.00368 ( 9386) covalent geometry : angle 0.53291 (12601) ********************** 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: 26 poor density : 71 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7167 (tm-30) cc_final: 0.6616 (tm-30) REVERT: A 197 MET cc_start: 0.8152 (mmm) cc_final: 0.7895 (mmp) REVERT: A 355 TYR cc_start: 0.7370 (m-80) cc_final: 0.7056 (m-80) REVERT: A 433 CYS cc_start: 0.7317 (t) cc_final: 0.7019 (t) REVERT: A 716 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7401 (mtm-85) REVERT: A 879 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.8018 (mtm180) REVERT: A 891 ASP cc_start: 0.8582 (t0) cc_final: 0.8291 (t0) REVERT: A 1025 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.6991 (t80) REVERT: A 1111 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8015 (mtt90) outliers start: 26 outliers final: 22 residues processed: 94 average time/residue: 0.2230 time to fit residues: 29.8734 Evaluate side-chains 95 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 69 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 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 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 860 GLU Chi-restraints excluded: chain A residue 879 ARG 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 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 93 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 86 optimal weight: 0.3980 chunk 17 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 10 optimal weight: 20.0000 chunk 70 optimal weight: 1.9990 chunk 25 optimal weight: 20.0000 chunk 98 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 HIS ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.209269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.133054 restraints weight = 11439.377| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 3.41 r_work: 0.3249 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9386 Z= 0.195 Angle : 0.578 10.575 12601 Z= 0.303 Chirality : 0.042 0.140 1315 Planarity : 0.004 0.050 1633 Dihedral : 4.709 40.940 1181 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 2.67 % Allowed : 30.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.26), residues: 1085 helix: 0.78 (0.25), residues: 474 sheet: -1.07 (0.47), residues: 116 loop : -2.08 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1252 HIS 0.005 0.001 HIS A1222 PHE 0.023 0.001 PHE A 85 TYR 0.019 0.002 TYR A 327 ARG 0.003 0.000 ARG A1116 Details of bonding type rmsd hydrogen bonds : bond 0.03436 ( 366) hydrogen bonds : angle 4.98837 ( 1092) covalent geometry : bond 0.00475 ( 9386) covalent geometry : angle 0.57840 (12601) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5647.96 seconds wall clock time: 98 minutes 31.27 seconds (5911.27 seconds total)