Starting phenix.real_space_refine on Thu Dec 7 20:20:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kpw_22990/12_2023/7kpw_22990.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kpw_22990/12_2023/7kpw_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kpw_22990/12_2023/7kpw_22990.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kpw_22990/12_2023/7kpw_22990.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kpw_22990/12_2023/7kpw_22990.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kpw_22990/12_2023/7kpw_22990.pdb" } resolution = 4.9 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= 0.001 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/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: {'GLN:plan1': 43, 'HIS:plan': 17, 'TYR:plan': 32, 'ASN:plan1': 64, 'TRP:plan': 8, 'ASP:plan': 45, 'PHE:plan': 60, 'GLU:plan': 50, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 1540 Time building chain proxies: 3.25, per 1000 atoms: 0.75 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.58 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: 1.41 Time building geometry restraints manager: 2.01 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: 97.77 - 104.44: 2 104.44 - 111.10: 2057 111.10 - 117.76: 1321 117.76 - 124.42: 2583 124.42 - 131.09: 62 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 2.520 nonbonded pdb=" O LEU C1013 " pdb=" N ASP C1016 " model vdw 2.501 2.520 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 2.520 nonbonded pdb=" O ILE C1009 " pdb=" N LEU C1012 " model vdw 2.553 2.520 ... (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: 2.560 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: 11.120 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.570 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.360 ------------------------------------------------------------------------------- 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= 0.639 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 (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: 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 TRP 0.000 0.000 TRP C 477 PHE 0.000 0.000 PHE C 439 TYR 0.000 0.000 TYR C 480 *********************** 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 fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.502 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0439 time to fit residues: 2.8005 Evaluate side-chains 26 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.493 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 0.3980 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4311 Z= 0.145 Angle : 0.448 8.723 6025 Z= 0.299 Chirality : 0.038 0.139 853 Planarity : 0.003 0.017 863 Dihedral : 4.864 31.480 863 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 0.82 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.18 % Favored : 95.35 % 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 (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: 2.42 (0.30), residues: 861 helix: 2.78 (0.20), residues: 627 sheet: None (None), residues: 0 loop : -1.92 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP C 477 PHE 0.000 0.000 PHE C 439 TYR 0.000 0.000 TYR C 480 *********************** 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 fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.478 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0433 time to fit residues: 2.8501 Evaluate side-chains 26 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.513 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 53 optimal weight: 0.1980 chunk 21 optimal weight: 0.0000 chunk 78 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 overall best weight: 2.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.8235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 4311 Z= 0.394 Angle : 0.731 7.308 6025 Z= 0.524 Chirality : 0.041 0.142 853 Planarity : 0.006 0.023 863 Dihedral : 7.763 36.052 863 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 1.05 % Allowed : 10.45 % Favored : 88.50 % 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 (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: -1.53 (0.27), residues: 861 helix: 0.00 (0.20), residues: 606 sheet: None (None), residues: 0 loop : -3.51 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP C 477 PHE 0.000 0.000 PHE C 439 TYR 0.000 0.000 TYR C 480 *********************** 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 fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.461 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0405 time to fit residues: 2.6479 Evaluate side-chains 26 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.492 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.8412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4311 Z= 0.255 Angle : 0.533 6.765 6025 Z= 0.373 Chirality : 0.038 0.150 853 Planarity : 0.003 0.014 863 Dihedral : 6.139 33.623 863 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.46 % Allowed : 10.45 % Favored : 89.08 % 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 (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 (0.28), residues: 861 helix: 0.55 (0.20), residues: 620 sheet: None (None), residues: 0 loop : -3.57 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP C 477 PHE 0.000 0.000 PHE C 439 TYR 0.000 0.000 TYR C 480 *********************** 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 fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.560 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0436 time to fit residues: 2.9199 Evaluate side-chains 26 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 5.9990 chunk 47 optimal weight: 0.3980 chunk 1 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 42 optimal weight: 0.4980 chunk 74 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.8420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4311 Z= 0.130 Angle : 0.400 5.415 6025 Z= 0.272 Chirality : 0.037 0.129 853 Planarity : 0.002 0.011 863 Dihedral : 4.939 31.261 863 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.29 % Favored : 90.24 % 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 (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: 0.84 (0.31), residues: 861 helix: 1.87 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -3.56 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP C 477 PHE 0.000 0.000 PHE C 439 TYR 0.000 0.000 TYR C 480 *********************** 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 fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.523 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0455 time to fit residues: 2.9721 Evaluate side-chains 26 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.541 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 83 optimal weight: 0.0040 chunk 69 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.0020 chunk 43 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.8484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.014 4311 Z= 0.088 Angle : 0.351 5.092 6025 Z= 0.234 Chirality : 0.036 0.124 853 Planarity : 0.002 0.011 863 Dihedral : 4.129 26.962 863 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 0.82 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.25 % Favored : 91.29 % 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 : 0.00 % 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: 1.88 (0.32), residues: 861 helix: 2.56 (0.21), residues: 646 sheet: None (None), residues: 0 loop : -3.19 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP C 477 PHE 0.000 0.000 PHE C 439 TYR 0.000 0.000 TYR C 480 *********************** 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 fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.541 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0493 time to fit residues: 3.1221 Evaluate side-chains 26 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.527 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.8978 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= 0.144 Angle : 0.390 5.077 6025 Z= 0.267 Chirality : 0.037 0.128 853 Planarity : 0.002 0.010 863 Dihedral : 4.633 28.153 863 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.99 % Favored : 89.55 % 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 : 0.00 % 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: 1.52 (0.31), residues: 861 helix: 2.36 (0.21), residues: 641 sheet: None (None), residues: 0 loop : -3.42 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP C 477 PHE 0.000 0.000 PHE C 439 TYR 0.000 0.000 TYR C 480 *********************** 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 fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.512 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0435 time to fit residues: 2.8325 Evaluate side-chains 26 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.446 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 0.0570 chunk 65 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.5902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 1.0013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4311 Z= 0.236 Angle : 0.506 5.885 6025 Z= 0.355 Chirality : 0.038 0.142 853 Planarity : 0.003 0.015 863 Dihedral : 5.910 32.913 863 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.46 % Allowed : 10.80 % Favored : 88.73 % 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 (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: -0.02 (0.30), residues: 861 helix: 1.20 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -3.78 (0.38), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP C 477 PHE 0.000 0.000 PHE C 439 TYR 0.000 0.000 TYR C 480 *********************** 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 fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.447 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0434 time to fit residues: 2.7593 Evaluate side-chains 26 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.486 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 60 optimal weight: 0.4980 chunk 23 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 1.0359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4311 Z= 0.200 Angle : 0.449 5.197 6025 Z= 0.313 Chirality : 0.037 0.140 853 Planarity : 0.003 0.015 863 Dihedral : 5.358 30.778 863 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.58 % Allowed : 10.92 % Favored : 88.50 % 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 (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: 0.21 (0.30), residues: 861 helix: 1.41 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -3.81 (0.38), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP C 477 PHE 0.000 0.000 PHE C 439 TYR 0.000 0.000 TYR C 480 *********************** 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 fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.508 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0427 time to fit residues: 2.8080 Evaluate side-chains 26 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.510 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 85 optimal weight: 0.0970 chunk 78 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 1.0758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4311 Z= 0.225 Angle : 0.484 5.422 6025 Z= 0.338 Chirality : 0.038 0.145 853 Planarity : 0.003 0.016 863 Dihedral : 5.766 32.299 863 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.58 % Allowed : 11.38 % 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 : 0.12 % 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: -0.26 (0.30), residues: 861 helix: 1.03 (0.21), residues: 642 sheet: None (None), residues: 0 loop : -3.97 (0.38), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP C 477 PHE 0.000 0.000 PHE C 439 TYR 0.000 0.000 TYR C 480 ********************** 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 fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.501 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0435 time to fit residues: 2.8506 Evaluate side-chains 26 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.534 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 49 optimal weight: 0.5980 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 = 0.3155 r_free = 0.3155 target = 0.070424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.059075 restraints weight = 28914.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.059416 restraints weight = 26613.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.059462 restraints weight = 23659.217| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 1.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4311 Z= 0.227 Angle : 0.488 5.388 6025 Z= 0.341 Chirality : 0.038 0.145 853 Planarity : 0.003 0.017 863 Dihedral : 5.850 32.304 863 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.58 % Allowed : 11.61 % Favored : 87.80 % 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 (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: -0.50 (0.30), residues: 861 helix: 0.85 (0.21), residues: 646 sheet: None (None), residues: 0 loop : -4.13 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP C 477 PHE 0.000 0.000 PHE C 439 TYR 0.000 0.000 TYR C 480 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 993.27 seconds wall clock time: 18 minutes 34.70 seconds (1114.70 seconds total)