Starting phenix.real_space_refine on Wed Sep 17 04:42:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kpw_22990/09_2025/7kpw_22990.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kpw_22990/09_2025/7kpw_22990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kpw_22990/09_2025/7kpw_22990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kpw_22990/09_2025/7kpw_22990.map" model { file = "/net/cci-nas-00/data/ceres_data/7kpw_22990/09_2025/7kpw_22990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kpw_22990/09_2025/7kpw_22990.cif" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 3 Type Number sf(0) Gaussians C 2583 2.51 5 N 865 2.21 5 O 865 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4313 Number of models: 1 Model: "" Number of chains: 1 Chain: "C" Number of atoms: 4313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 865, 4313 Classifications: {'peptide': 865} Incomplete info: {'truncation_to_alanine': 830} Link IDs: {'PTRANS': 22, 'TRANS': 842} Chain breaks: 1 Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 2975 Unresolved non-hydrogen angles: 3799 Unresolved non-hydrogen dihedrals: 2479 Unresolved non-hydrogen chiralities: 290 Planarities with less than four sites: {'ASN:plan1': 64, 'ARG:plan': 20, 'ASP:plan': 45, 'PHE:plan': 60, 'GLN:plan1': 43, 'GLU:plan': 50, 'TRP:plan': 8, 'TYR:plan': 32, 'HIS:plan': 17} Unresolved non-hydrogen planarities: 1540 Time building chain proxies: 1.54, per 1000 atoms: 0.36 Number of scatterers: 4313 At special positions: 0 Unit cell: (86.67, 86.67, 119.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 865 8.00 N 865 7.00 C 2583 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: 0.44 Conformation dependent library (CDL) restraints added in 216.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1706 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 0 sheets defined 82.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'C' and resid 421 through 428 removed outlier: 3.587A pdb=" N SER C 425 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE C 426 " --> pdb=" O ASN C 422 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG C 427 " --> pdb=" O ASN C 423 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN C 428 " --> pdb=" O SER C 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 421 through 428' Processing helix chain 'C' and resid 438 through 444 removed outlier: 3.524A pdb=" N ILE C 443 " --> pdb=" O PHE C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 466 removed outlier: 3.587A pdb=" N PHE C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR C 465 " --> pdb=" O ASP C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 476 removed outlier: 4.112A pdb=" N GLU C 474 " --> pdb=" O ASP C 470 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP C 476 " --> pdb=" O PRO C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 496 removed outlier: 3.537A pdb=" N LYS C 490 " --> pdb=" O LEU C 486 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE C 495 " --> pdb=" O ILE C 491 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU C 496 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 517 Processing helix chain 'C' and resid 524 through 543 removed outlier: 4.218A pdb=" N ASP C 528 " --> pdb=" O SER C 524 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU C 529 " --> pdb=" O THR C 525 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP C 539 " --> pdb=" O GLU C 535 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 542 " --> pdb=" O ILE C 538 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE C 543 " --> pdb=" O TRP C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 572 removed outlier: 3.521A pdb=" N GLN C 552 " --> pdb=" O ASN C 548 " (cutoff:3.500A) Proline residue: C 561 - end of helix removed outlier: 3.547A pdb=" N LEU C 570 " --> pdb=" O LEU C 566 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR C 572 " --> pdb=" O ASN C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 588 Proline residue: C 579 - end of helix removed outlier: 3.782A pdb=" N ILE C 586 " --> pdb=" O ILE C 582 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER C 587 " --> pdb=" O ARG C 583 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER C 588 " --> pdb=" O LYS C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 605 removed outlier: 3.636A pdb=" N SER C 596 " --> pdb=" O TYR C 592 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN C 597 " --> pdb=" O LEU C 593 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 624 removed outlier: 4.648A pdb=" N MET C 615 " --> pdb=" O ILE C 611 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS C 616 " --> pdb=" O SER C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 651 removed outlier: 3.951A pdb=" N MET C 651 " --> pdb=" O GLU C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 664 Processing helix chain 'C' and resid 667 through 685 removed outlier: 4.275A pdb=" N LYS C 671 " --> pdb=" O PRO C 667 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU C 676 " --> pdb=" O ILE C 672 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP C 677 " --> pdb=" O MET C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 704 removed outlier: 3.603A pdb=" N LEU C 695 " --> pdb=" O ASN C 691 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE C 704 " --> pdb=" O LYS C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 721 removed outlier: 3.538A pdb=" N HIS C 711 " --> pdb=" O GLU C 707 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE C 712 " --> pdb=" O VAL C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 740 removed outlier: 3.637A pdb=" N LEU C 734 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET C 735 " --> pdb=" O LEU C 731 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP C 736 " --> pdb=" O GLU C 732 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS C 740 " --> pdb=" O ASP C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 747 removed outlier: 4.064A pdb=" N SER C 746 " --> pdb=" O GLN C 742 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN C 747 " --> pdb=" O LYS C 743 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 742 through 747' Processing helix chain 'C' and resid 748 through 763 Processing helix chain 'C' and resid 773 through 788 Proline residue: C 782 - end of helix Processing helix chain 'C' and resid 791 through 813 removed outlier: 3.501A pdb=" N LYS C 796 " --> pdb=" O PRO C 792 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C 803 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU C 804 " --> pdb=" O ASP C 800 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU C 805 " --> pdb=" O LEU C 801 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS C 813 " --> pdb=" O TYR C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 827 removed outlier: 4.024A pdb=" N LYS C 818 " --> pdb=" O LEU C 814 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 825 " --> pdb=" O ASN C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 854 removed outlier: 4.641A pdb=" N THR C 843 " --> pdb=" O ALA C 839 " (cutoff:3.500A) Proline residue: C 847 - end of helix removed outlier: 3.762A pdb=" N VAL C 852 " --> pdb=" O GLU C 848 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE C 854 " --> pdb=" O PHE C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 878 removed outlier: 4.686A pdb=" N ILE C 864 " --> pdb=" O ASN C 860 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP C 865 " --> pdb=" O SER C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 893 Processing helix chain 'C' and resid 896 through 907 removed outlier: 3.621A pdb=" N LYS C 906 " --> pdb=" O ASP C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 916 Processing helix chain 'C' and resid 918 through 927 removed outlier: 3.585A pdb=" N GLN C 923 " --> pdb=" O PHE C 919 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY C 927 " --> pdb=" O GLN C 923 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 948 removed outlier: 3.815A pdb=" N ASN C 941 " --> pdb=" O ILE C 937 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 948 " --> pdb=" O GLY C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 949 through 963 removed outlier: 3.781A pdb=" N PHE C 962 " --> pdb=" O ILE C 958 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU C 963 " --> pdb=" O LYS C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 983 Processing helix chain 'C' and resid 986 through 1004 removed outlier: 3.502A pdb=" N LYS C 991 " --> pdb=" O GLU C 987 " (cutoff:3.500A) Proline residue: C1000 - end of helix Processing helix chain 'C' and resid 1006 through 1023 removed outlier: 3.793A pdb=" N LEU C1014 " --> pdb=" O ILE C1010 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN C1015 " --> pdb=" O MET C1011 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1072 through 1083 removed outlier: 4.261A pdb=" N GLU C1076 " --> pdb=" O ILE C1072 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE C1083 " --> pdb=" O VAL C1079 " (cutoff:3.500A) Processing helix chain 'C' and resid 1087 through 1103 Processing helix chain 'C' and resid 1106 through 1126 removed outlier: 3.749A pdb=" N GLU C1111 " --> pdb=" O ALA C1107 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE C1116 " --> pdb=" O ASP C1112 " (cutoff:3.500A) Processing helix chain 'C' and resid 1128 through 1146 Processing helix chain 'C' and resid 1146 through 1172 removed outlier: 3.998A pdb=" N ASN C1169 " --> pdb=" O LYS C1165 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR C1170 " --> pdb=" O ILE C1166 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL C1172 " --> pdb=" O ASP C1168 " (cutoff:3.500A) Processing helix chain 'C' and resid 1174 through 1196 removed outlier: 3.547A pdb=" N LEU C1181 " --> pdb=" O ILE C1177 " (cutoff:3.500A) Processing helix chain 'C' and resid 1204 through 1218 removed outlier: 3.614A pdb=" N ARG C1208 " --> pdb=" O ILE C1204 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU C1218 " --> pdb=" O ASN C1214 " (cutoff:3.500A) Processing helix chain 'C' and resid 1218 through 1224 Processing helix chain 'C' and resid 1225 through 1239 removed outlier: 4.166A pdb=" N ILE C1239 " --> pdb=" O HIS C1235 " (cutoff:3.500A) Processing helix chain 'C' and resid 1239 through 1251 removed outlier: 4.433A pdb=" N ILE C1243 " --> pdb=" O ILE C1239 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C1245 " --> pdb=" O GLN C1241 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP C1250 " --> pdb=" O ASP C1246 " (cutoff:3.500A) Processing helix chain 'C' and resid 1259 through 1272 Processing helix chain 'C' and resid 1276 through 1296 Processing helix chain 'C' and resid 1307 through 1314 Processing helix chain 'C' and resid 1319 through 1326 removed outlier: 3.673A pdb=" N VAL C1323 " --> pdb=" O VAL C1319 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR C1326 " --> pdb=" O PHE C1322 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1278 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: 0.74 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.27: 858 1.27 - 1.35: 870 1.35 - 1.42: 0 1.42 - 1.49: 862 1.49 - 1.56: 1721 Bond restraints: 4311 Sorted by residual: bond pdb=" C LEU C 661 " pdb=" O LEU C 661 " ideal model delta sigma weight residual 1.237 1.296 -0.059 1.17e-02 7.31e+03 2.56e+01 bond pdb=" C ARG C 802 " pdb=" O ARG C 802 " ideal model delta sigma weight residual 1.237 1.293 -0.056 1.17e-02 7.31e+03 2.30e+01 bond pdb=" C GLY C 944 " pdb=" O GLY C 944 " ideal model delta sigma weight residual 1.234 1.290 -0.056 1.20e-02 6.94e+03 2.20e+01 bond pdb=" C VAL C 808 " pdb=" O VAL C 808 " ideal model delta sigma weight residual 1.237 1.288 -0.050 1.17e-02 7.31e+03 1.85e+01 bond pdb=" C ILE C 912 " pdb=" O ILE C 912 " ideal model delta sigma weight residual 1.237 1.283 -0.046 1.17e-02 7.31e+03 1.56e+01 ... (remaining 4306 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.29: 5778 3.29 - 6.58: 203 6.58 - 9.88: 38 9.88 - 13.17: 5 13.17 - 16.46: 1 Bond angle restraints: 6025 Sorted by residual: angle pdb=" N LEU C 494 " pdb=" CA LEU C 494 " pdb=" C LEU C 494 " ideal model delta sigma weight residual 111.14 127.60 -16.46 1.08e+00 8.57e-01 2.32e+02 angle pdb=" N ILE C 495 " pdb=" CA ILE C 495 " pdb=" C ILE C 495 " ideal model delta sigma weight residual 113.20 124.91 -11.71 9.60e-01 1.09e+00 1.49e+02 angle pdb=" N ASP C1073 " pdb=" CA ASP C1073 " pdb=" C ASP C1073 " ideal model delta sigma weight residual 111.28 123.07 -11.79 1.09e+00 8.42e-01 1.17e+02 angle pdb=" N ILE C1171 " pdb=" CA ILE C1171 " pdb=" C ILE C1171 " ideal model delta sigma weight residual 110.53 119.35 -8.82 9.40e-01 1.13e+00 8.81e+01 angle pdb=" N LEU C 939 " pdb=" CA LEU C 939 " pdb=" C LEU C 939 " ideal model delta sigma weight residual 111.36 121.37 -10.01 1.09e+00 8.42e-01 8.44e+01 ... (remaining 6020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 3.23: 2373 3.23 - 6.46: 145 6.46 - 9.70: 38 9.70 - 12.93: 10 12.93 - 16.16: 3 Dihedral angle restraints: 2569 sinusoidal: 0 harmonic: 2569 Sorted by residual: dihedral pdb=" N PRO C 613 " pdb=" C PRO C 613 " pdb=" CA PRO C 613 " pdb=" CB PRO C 613 " ideal model delta harmonic sigma weight residual 115.10 129.00 -13.90 0 2.50e+00 1.60e-01 3.09e+01 dihedral pdb=" N PRO C1255 " pdb=" C PRO C1255 " pdb=" CA PRO C1255 " pdb=" CB PRO C1255 " ideal model delta harmonic sigma weight residual 115.10 127.95 -12.85 0 2.50e+00 1.60e-01 2.64e+01 dihedral pdb=" N PRO C 472 " pdb=" C PRO C 472 " pdb=" CA PRO C 472 " pdb=" CB PRO C 472 " ideal model delta harmonic sigma weight residual 115.10 127.10 -12.00 0 2.50e+00 1.60e-01 2.30e+01 ... (remaining 2566 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 704 0.122 - 0.245: 116 0.245 - 0.367: 24 0.367 - 0.490: 7 0.490 - 0.612: 2 Chirality restraints: 853 Sorted by residual: chirality pdb=" CA LEU C 494 " pdb=" N LEU C 494 " pdb=" C LEU C 494 " pdb=" CB LEU C 494 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.37e+00 chirality pdb=" CA PRO C 613 " pdb=" N PRO C 613 " pdb=" C PRO C 613 " pdb=" CB PRO C 613 " both_signs ideal model delta sigma weight residual False 2.72 2.18 0.54 2.00e-01 2.50e+01 7.21e+00 chirality pdb=" CA PRO C1255 " pdb=" N PRO C1255 " pdb=" C PRO C1255 " pdb=" CB PRO C1255 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.75e+00 ... (remaining 850 not shown) Planarity restraints: 863 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C1082 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C ASP C1082 " -0.061 2.00e-02 2.50e+03 pdb=" O ASP C1082 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE C1083 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 667 " 0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C PRO C 667 " -0.061 2.00e-02 2.50e+03 pdb=" O PRO C 667 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU C 668 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 945 " 0.016 2.00e-02 2.50e+03 3.28e-02 1.07e+01 pdb=" C SER C 945 " -0.057 2.00e-02 2.50e+03 pdb=" O SER C 945 " 0.021 2.00e-02 2.50e+03 pdb=" N TYR C 946 " 0.019 2.00e-02 2.50e+03 ... (remaining 860 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1604 2.84 - 3.36: 4890 3.36 - 3.87: 6576 3.87 - 4.39: 6002 4.39 - 4.90: 9978 Nonbonded interactions: 29050 Sorted by model distance: nonbonded pdb=" O ASP C 526 " pdb=" N LEU C 529 " model vdw 2.327 3.120 nonbonded pdb=" O LEU C1013 " pdb=" N ASP C1016 " model vdw 2.501 3.120 nonbonded pdb=" O ASP C 526 " pdb=" C GLU C 527 " model vdw 2.528 3.270 nonbonded pdb=" O ALA C 733 " pdb=" N ASP C 736 " model vdw 2.528 3.120 nonbonded pdb=" O ILE C1009 " pdb=" N LEU C1012 " model vdw 2.553 3.120 ... (remaining 29045 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 group one per residue 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: 4.960 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.180 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.059 4311 Z= 0.672 Angle : 1.535 16.459 6025 Z= 1.270 Chirality : 0.105 0.612 853 Planarity : 0.007 0.035 863 Dihedral : 1.886 16.161 863 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 1.16 % Allowed : 3.95 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.47 % 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: 4.09 (0.30), residues: 861 helix: 4.33 (0.19), residues: 602 sheet: None (None), residues: 0 loop : -1.61 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR C 480 PHE 0.000 0.000 PHE C 439 TRP 0.000 0.000 TRP C 477 Details of bonding type rmsd covalent geometry : bond 0.00863 ( 4311) covalent geometry : angle 1.53506 ( 6025) hydrogen bonds : bond 0.23192 ( 426) hydrogen bonds : angle 6.18171 ( 1278) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.178 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0214 time to fit residues: 1.2789 Evaluate side-chains 26 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.0070 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.093396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.080519 restraints weight = 28431.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.080310 restraints weight = 29895.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.080457 restraints weight = 29796.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.080509 restraints weight = 28484.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.080571 restraints weight = 27623.358| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4311 Z= 0.146 Angle : 0.435 8.065 6025 Z= 0.292 Chirality : 0.037 0.126 853 Planarity : 0.003 0.016 863 Dihedral : 4.826 32.586 863 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 0.33 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.07 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 2.46 (0.30), residues: 861 helix: 2.79 (0.20), residues: 633 sheet: None (None), residues: 0 loop : -1.98 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR C 480 PHE 0.000 0.000 PHE C 439 TRP 0.000 0.000 TRP C 477 Details of bonding type rmsd covalent geometry : bond 0.00188 ( 4311) covalent geometry : angle 0.43491 ( 6025) hydrogen bonds : bond 0.03914 ( 426) hydrogen bonds : angle 4.25752 ( 1278) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.165 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0199 time to fit residues: 1.1833 Evaluate side-chains 26 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 68 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 42 optimal weight: 0.1980 chunk 83 optimal weight: 5.9990 chunk 53 optimal weight: 0.2980 chunk 0 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.3296 r_free = 0.3296 target = 0.077252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.065421 restraints weight = 28553.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.065072 restraints weight = 31489.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.065208 restraints weight = 31623.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.065267 restraints weight = 29882.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.065478 restraints weight = 29092.172| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.6377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4311 Z= 0.268 Angle : 0.548 6.769 6025 Z= 0.390 Chirality : 0.038 0.130 853 Planarity : 0.004 0.019 863 Dihedral : 5.849 31.824 863 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 0.49 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.43 % Favored : 91.99 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.36 (0.29), residues: 861 helix: 1.41 (0.20), residues: 637 sheet: None (None), residues: 0 loop : -3.35 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR C 480 PHE 0.000 0.000 PHE C 439 TRP 0.000 0.000 TRP C 477 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 4311) covalent geometry : angle 0.54784 ( 6025) hydrogen bonds : bond 0.05612 ( 426) hydrogen bonds : angle 5.72577 ( 1278) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.165 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0198 time to fit residues: 1.1734 Evaluate side-chains 26 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 21 optimal weight: 0.0050 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 71 optimal weight: 9.9990 overall best weight: 1.9400 ------------------------------------------------------------------------------- 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 = 0.3222 r_free = 0.3222 target = 0.072945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.061415 restraints weight = 28969.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.061444 restraints weight = 28726.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.061514 restraints weight = 28347.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.061600 restraints weight = 26907.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.061620 restraints weight = 26759.450| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.8764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4311 Z= 0.277 Angle : 0.563 8.171 6025 Z= 0.394 Chirality : 0.039 0.138 853 Planarity : 0.004 0.015 863 Dihedral : 6.335 34.654 863 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 0.49 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.76 % Favored : 89.66 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.64 (0.29), residues: 861 helix: 0.61 (0.20), residues: 632 sheet: None (None), residues: 0 loop : -3.42 (0.38), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR C 480 PHE 0.000 0.000 PHE C 439 TRP 0.000 0.000 TRP C 477 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 4311) covalent geometry : angle 0.56321 ( 6025) hydrogen bonds : bond 0.05474 ( 426) hydrogen bonds : angle 5.90182 ( 1278) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.159 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0197 time to fit residues: 1.1678 Evaluate side-chains 26 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 71 optimal weight: 9.9990 chunk 12 optimal weight: 0.0070 chunk 52 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- 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 = 0.3201 r_free = 0.3201 target = 0.071969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.060556 restraints weight = 29106.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.060544 restraints weight = 28687.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.060584 restraints weight = 27085.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.060668 restraints weight = 26467.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.060790 restraints weight = 25618.124| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.9619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4311 Z= 0.260 Angle : 0.524 5.763 6025 Z= 0.370 Chirality : 0.038 0.141 853 Planarity : 0.003 0.017 863 Dihedral : 6.086 33.185 863 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 0.49 Ramachandran Plot: Outliers : 0.70 % Allowed : 9.87 % Favored : 89.43 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.64 (0.29), residues: 861 helix: 0.67 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -3.67 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR C 480 PHE 0.000 0.000 PHE C 439 TRP 0.000 0.000 TRP C 477 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 4311) covalent geometry : angle 0.52436 ( 6025) hydrogen bonds : bond 0.05144 ( 426) hydrogen bonds : angle 5.69909 ( 1278) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.159 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0198 time to fit residues: 1.1828 Evaluate side-chains 26 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 76 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 32 optimal weight: 0.0870 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 overall best weight: 2.5364 ------------------------------------------------------------------------------- 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 = 0.3105 r_free = 0.3105 target = 0.068251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.057179 restraints weight = 30034.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.057210 restraints weight = 29351.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.057304 restraints weight = 27368.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.057486 restraints weight = 26269.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.057552 restraints weight = 25406.910| |-----------------------------------------------------------------------------| r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 1.0640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 4311 Z= 0.377 Angle : 0.652 8.295 6025 Z= 0.463 Chirality : 0.040 0.153 853 Planarity : 0.005 0.018 863 Dihedral : 7.086 36.358 863 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.58 % Allowed : 11.03 % Favored : 88.39 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.95 (0.28), residues: 861 helix: -0.30 (0.20), residues: 642 sheet: None (None), residues: 0 loop : -4.22 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR C 480 PHE 0.000 0.000 PHE C 439 TRP 0.000 0.000 TRP C 477 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 4311) covalent geometry : angle 0.65178 ( 6025) hydrogen bonds : bond 0.06426 ( 426) hydrogen bonds : angle 6.77788 ( 1278) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.170 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0199 time to fit residues: 1.1794 Evaluate side-chains 26 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 71 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.3067 r_free = 0.3067 target = 0.066466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.055702 restraints weight = 29632.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.055938 restraints weight = 28331.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.055920 restraints weight = 26231.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.055936 restraints weight = 26156.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.055960 restraints weight = 25497.984| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 1.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4311 Z= 0.370 Angle : 0.666 6.210 6025 Z= 0.472 Chirality : 0.040 0.158 853 Planarity : 0.005 0.020 863 Dihedral : 7.459 35.733 863 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.58 % Allowed : 13.36 % Favored : 86.06 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -2.74 (0.27), residues: 861 helix: -0.83 (0.19), residues: 642 sheet: None (None), residues: 0 loop : -4.68 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR C 480 PHE 0.000 0.000 PHE C 439 TRP 0.000 0.000 TRP C 477 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 4311) covalent geometry : angle 0.66582 ( 6025) hydrogen bonds : bond 0.06505 ( 426) hydrogen bonds : angle 7.05872 ( 1278) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.134 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0190 time to fit residues: 1.0472 Evaluate side-chains 26 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 60 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 0.1980 chunk 4 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 17 optimal weight: 0.0670 chunk 41 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.4322 ------------------------------------------------------------------------------- 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 = 0.3144 r_free = 0.3144 target = 0.069808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.058509 restraints weight = 29481.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.058667 restraints weight = 27981.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.058734 restraints weight = 25307.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.058786 restraints weight = 24955.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.058863 restraints weight = 24245.373| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 1.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4311 Z= 0.213 Angle : 0.497 5.988 6025 Z= 0.343 Chirality : 0.038 0.148 853 Planarity : 0.003 0.017 863 Dihedral : 6.180 35.660 863 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.70 % Allowed : 11.27 % Favored : 88.04 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.53 (0.29), residues: 861 helix: 0.11 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -4.56 (0.37), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR C 480 PHE 0.000 0.000 PHE C 439 TRP 0.000 0.000 TRP C 477 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 4311) covalent geometry : angle 0.49676 ( 6025) hydrogen bonds : bond 0.04611 ( 426) hydrogen bonds : angle 5.72848 ( 1278) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.151 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0199 time to fit residues: 1.1593 Evaluate side-chains 26 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 chunk 12 optimal weight: 0.0870 chunk 32 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.0362 ------------------------------------------------------------------------------- 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 = 0.3189 r_free = 0.3189 target = 0.072001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.060297 restraints weight = 29231.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.060423 restraints weight = 29081.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.060787 restraints weight = 27325.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.060772 restraints weight = 26090.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.060853 restraints weight = 24650.824| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 1.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 4311 Z= 0.154 Angle : 0.431 5.459 6025 Z= 0.293 Chirality : 0.037 0.143 853 Planarity : 0.002 0.015 863 Dihedral : 5.358 31.865 863 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 0.66 Ramachandran Plot: Outliers : 0.58 % Allowed : 11.03 % Favored : 88.39 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.36 (0.30), residues: 861 helix: 1.00 (0.21), residues: 650 sheet: None (None), residues: 0 loop : -4.38 (0.37), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR C 480 PHE 0.000 0.000 PHE C 439 TRP 0.000 0.000 TRP C 477 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 4311) covalent geometry : angle 0.43075 ( 6025) hydrogen bonds : bond 0.03832 ( 426) hydrogen bonds : angle 4.96789 ( 1278) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.237 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0199 time to fit residues: 1.2010 Evaluate side-chains 26 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 47 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 6 optimal weight: 0.0980 chunk 68 optimal weight: 5.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- 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 = 0.3027 r_free = 0.3027 target = 0.064630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.054140 restraints weight = 30153.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.054045 restraints weight = 28685.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.054043 restraints weight = 27624.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.054153 restraints weight = 27575.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.054206 restraints weight = 26263.958| |-----------------------------------------------------------------------------| r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 1.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 4311 Z= 0.456 Angle : 0.747 7.901 6025 Z= 0.537 Chirality : 0.041 0.160 853 Planarity : 0.006 0.024 863 Dihedral : 7.619 35.779 863 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.81 % Allowed : 16.26 % Favored : 82.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.80 (0.27), residues: 861 helix: -0.83 (0.20), residues: 626 sheet: None (None), residues: 0 loop : -4.61 (0.35), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR C 480 PHE 0.000 0.000 PHE C 439 TRP 0.000 0.000 TRP C 477 Details of bonding type rmsd covalent geometry : bond 0.00601 ( 4311) covalent geometry : angle 0.74730 ( 6025) hydrogen bonds : bond 0.07409 ( 426) hydrogen bonds : angle 7.52562 ( 1278) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.176 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0185 time to fit residues: 1.1112 Evaluate side-chains 26 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 4 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 0.0970 chunk 47 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 = 0.3130 r_free = 0.3130 target = 0.069366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.058369 restraints weight = 28543.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.058519 restraints weight = 26807.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.058506 restraints weight = 25358.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.058620 restraints weight = 25160.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.058695 restraints weight = 24029.428| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 1.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 4311 Z= 0.204 Angle : 0.490 5.715 6025 Z= 0.339 Chirality : 0.038 0.148 853 Planarity : 0.003 0.018 863 Dihedral : 6.105 34.103 863 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.81 % Allowed : 11.73 % Favored : 87.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.48 (0.29), residues: 861 helix: 0.17 (0.21), residues: 633 sheet: None (None), residues: 0 loop : -4.34 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR C 480 PHE 0.000 0.000 PHE C 439 TRP 0.000 0.000 TRP C 477 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 4311) covalent geometry : angle 0.48987 ( 6025) hydrogen bonds : bond 0.04542 ( 426) hydrogen bonds : angle 5.66141 ( 1278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 704.51 seconds wall clock time: 12 minutes 46.01 seconds (766.01 seconds total)