Starting phenix.real_space_refine on Sat Aug 23 21:25:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pjj_17711/08_2025/8pjj_17711.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pjj_17711/08_2025/8pjj_17711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pjj_17711/08_2025/8pjj_17711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pjj_17711/08_2025/8pjj_17711.map" model { file = "/net/cci-nas-00/data/ceres_data/8pjj_17711/08_2025/8pjj_17711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pjj_17711/08_2025/8pjj_17711.cif" } resolution = 4.24 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7392 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 42 5.49 5 S 47 5.16 5 C 5137 2.51 5 N 1438 2.21 5 O 1684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8348 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7474 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 946, 7463 Classifications: {'peptide': 946} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 898} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 946, 7463 Classifications: {'peptide': 946} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 898} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 7593 Chain: "B" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 847 Classifications: {'RNA': 40} Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 19, 'rna3p_pyr': 18} Link IDs: {'rna2p': 2, 'rna3p': 37} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.63, per 1000 atoms: 0.32 Number of scatterers: 8348 At special positions: 0 Unit cell: (74.56, 102.52, 137.004, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 47 16.00 P 42 15.00 O 1684 8.00 N 1438 7.00 C 5137 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: 0.63 Conformation dependent library (CDL) restraints added in 458.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1810 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 7 sheets defined 47.1% alpha, 10.8% beta 10 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 171 through 181 Processing helix chain 'A' and resid 223 through 242 Processing helix chain 'A' and resid 268 through 283 Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 352 through 371 Processing helix chain 'A' and resid 371 through 384 Processing helix chain 'A' and resid 385 through 388 Processing helix chain 'A' and resid 389 through 400 removed outlier: 3.741A pdb=" N ASN A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 415 removed outlier: 3.601A pdb=" N THR A 415 " --> pdb=" O GLY A 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 416 through 428 removed outlier: 3.564A pdb=" N SER A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 458 Processing helix chain 'A' and resid 486 through 494 Processing helix chain 'A' and resid 513 through 530 removed outlier: 3.585A pdb=" N ASP A 525 " --> pdb=" O VAL A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 551 Processing helix chain 'A' and resid 570 through 578 Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 636 through 651 removed outlier: 3.737A pdb=" N LEU A 640 " --> pdb=" O SER A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 676 Processing helix chain 'A' and resid 695 through 703 removed outlier: 3.785A pdb=" N GLN A 699 " --> pdb=" O PRO A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 722 removed outlier: 3.554A pdb=" N GLU A 721 " --> pdb=" O THR A 717 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR A 722 " --> pdb=" O ASN A 718 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 717 through 722' Processing helix chain 'A' and resid 758 through 767 Processing helix chain 'A' and resid 782 through 789 removed outlier: 3.584A pdb=" N LEU A 789 " --> pdb=" O ARG A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 812 Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 829 through 842 removed outlier: 3.620A pdb=" N VAL A 833 " --> pdb=" O PRO A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 862 removed outlier: 3.739A pdb=" N ARG A 861 " --> pdb=" O ARG A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 878 removed outlier: 5.040A pdb=" N MET A 871 " --> pdb=" O ARG A 867 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU A 874 " --> pdb=" O LYS A 870 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 876 " --> pdb=" O MET A 872 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 877 " --> pdb=" O VAL A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 893 Processing helix chain 'A' and resid 908 through 914 Processing helix chain 'A' and resid 920 through 937 Processing helix chain 'A' and resid 940 through 950 removed outlier: 3.923A pdb=" N ARG A 945 " --> pdb=" O HIS A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 975 Processing helix chain 'A' and resid 977 through 981 removed outlier: 3.821A pdb=" N CYS A 980 " --> pdb=" O PRO A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1008 Processing helix chain 'A' and resid 1101 through 1110 removed outlier: 3.573A pdb=" N ALA A1105 " --> pdb=" O GLU A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1125 Processing helix chain 'A' and resid 1126 through 1129 removed outlier: 3.678A pdb=" N ILE A1129 " --> pdb=" O PRO A1126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1126 through 1129' Processing helix chain 'A' and resid 1133 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 192 removed outlier: 3.689A pdb=" N LEU A 204 " --> pdb=" O ALA A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 188 through 192 Processing sheet with id=AA3, first strand: chain 'A' and resid 465 through 468 removed outlier: 7.478A pdb=" N ILE A 436 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N CYS A 485 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A 504 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N MET A 538 " --> pdb=" O ILE A 504 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A 403 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N SER A 539 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE A 405 " --> pdb=" O SER A 539 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU A 557 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE A 404 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL A 559 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ARG A 406 " --> pdb=" O VAL A 559 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 568 through 569 removed outlier: 5.252A pdb=" N PHE A 569 " --> pdb=" O THR A 779 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A 730 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N PHE A 778 " --> pdb=" O VAL A 730 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL A 732 " --> pdb=" O PHE A 778 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ALA A 655 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE A 656 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N SER A 716 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL A 658 " --> pdb=" O SER A 716 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLN A 686 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU A 715 " --> pdb=" O GLN A 686 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU A 688 " --> pdb=" O LEU A 715 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 737 through 744 removed outlier: 3.861A pdb=" N ALA A 738 " --> pdb=" O VAL A 755 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL A 755 " --> pdb=" O ALA A 738 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A 753 " --> pdb=" O MET A 740 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1055 through 1056 removed outlier: 3.880A pdb=" N SER A1062 " --> pdb=" O ILE A1056 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N CYS A1063 " --> pdb=" O ALA A1028 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU A1030 " --> pdb=" O CYS A1063 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS A1027 " --> pdb=" O THR A1023 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LYS A1020 " --> pdb=" O LYS A1016 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1090 through 1092 325 hydrogen bonds defined for protein. 933 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 1.24 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2475 1.34 - 1.46: 1525 1.46 - 1.58: 4440 1.58 - 1.70: 81 1.70 - 1.82: 71 Bond restraints: 8592 Sorted by residual: bond pdb=" N ASP A 605 " pdb=" CA ASP A 605 " ideal model delta sigma weight residual 1.460 1.489 -0.029 1.02e-02 9.61e+03 8.03e+00 bond pdb=" N ASP A 603 " pdb=" CA ASP A 603 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.23e-02 6.61e+03 6.80e+00 bond pdb=" N LYS A 604 " pdb=" CA LYS A 604 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.27e+00 bond pdb=" N GLU A 608 " pdb=" CA GLU A 608 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.23e-02 6.61e+03 5.46e+00 bond pdb=" N GLU A 602 " pdb=" CA GLU A 602 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 5.17e+00 ... (remaining 8587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 11517 2.05 - 4.09: 252 4.09 - 6.14: 51 6.14 - 8.19: 12 8.19 - 10.23: 3 Bond angle restraints: 11835 Sorted by residual: angle pdb=" N GLU A 379 " pdb=" CA GLU A 379 " pdb=" CB GLU A 379 " ideal model delta sigma weight residual 110.39 117.65 -7.26 1.66e+00 3.63e-01 1.91e+01 angle pdb=" N LEU A 630 " pdb=" CA LEU A 630 " pdb=" CB LEU A 630 " ideal model delta sigma weight residual 110.49 116.86 -6.37 1.69e+00 3.50e-01 1.42e+01 angle pdb=" C MET A 629 " pdb=" N LEU A 630 " pdb=" CA LEU A 630 " ideal model delta sigma weight residual 121.54 128.60 -7.06 1.91e+00 2.74e-01 1.37e+01 angle pdb=" C GLU A 608 " pdb=" N ILE A 609 " pdb=" CA ILE A 609 " ideal model delta sigma weight residual 123.14 118.37 4.77 1.31e+00 5.83e-01 1.33e+01 angle pdb=" C LEU A 378 " pdb=" N GLU A 379 " pdb=" CA GLU A 379 " ideal model delta sigma weight residual 120.72 114.76 5.96 1.67e+00 3.59e-01 1.27e+01 ... (remaining 11830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 5117 35.95 - 71.89: 165 71.89 - 107.84: 21 107.84 - 143.79: 3 143.79 - 179.73: 2 Dihedral angle restraints: 5308 sinusoidal: 2528 harmonic: 2780 Sorted by residual: dihedral pdb=" O4' C B 45 " pdb=" C1' C B 45 " pdb=" N1 C B 45 " pdb=" C2 C B 45 " ideal model delta sinusoidal sigma weight residual -128.00 51.73 -179.73 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O1B ADP A1201 " pdb=" O3A ADP A1201 " pdb=" PB ADP A1201 " pdb=" PA ADP A1201 " ideal model delta sinusoidal sigma weight residual 300.00 170.25 129.75 1 2.00e+01 2.50e-03 3.93e+01 dihedral pdb=" O4' U B 4 " pdb=" C1' U B 4 " pdb=" N1 U B 4 " pdb=" C2 U B 4 " ideal model delta sinusoidal sigma weight residual -160.00 -77.44 -82.56 1 1.50e+01 4.44e-03 3.71e+01 ... (remaining 5305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 950 0.035 - 0.071: 289 0.071 - 0.106: 113 0.106 - 0.142: 35 0.142 - 0.177: 4 Chirality restraints: 1391 Sorted by residual: chirality pdb=" C1' U B 9 " pdb=" O4' U B 9 " pdb=" C2' U B 9 " pdb=" N1 U B 9 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.18 2.00e-01 2.50e+01 7.86e-01 chirality pdb=" CA GLU A 608 " pdb=" N GLU A 608 " pdb=" C GLU A 608 " pdb=" CB GLU A 608 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CB ILE A 735 " pdb=" CA ILE A 735 " pdb=" CG1 ILE A 735 " pdb=" CG2 ILE A 735 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.85e-01 ... (remaining 1388 not shown) Planarity restraints: 1374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A1134 " -0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO A1135 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A1135 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1135 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U B 9 " -0.024 2.00e-02 2.50e+03 1.20e-02 3.22e+00 pdb=" N1 U B 9 " 0.025 2.00e-02 2.50e+03 pdb=" C2 U B 9 " 0.001 2.00e-02 2.50e+03 pdb=" O2 U B 9 " 0.003 2.00e-02 2.50e+03 pdb=" N3 U B 9 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U B 9 " -0.003 2.00e-02 2.50e+03 pdb=" O4 U B 9 " -0.007 2.00e-02 2.50e+03 pdb=" C5 U B 9 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U B 9 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 8 " -0.018 2.00e-02 2.50e+03 8.11e-03 1.81e+00 pdb=" N9 A B 8 " 0.017 2.00e-02 2.50e+03 pdb=" C8 A B 8 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A B 8 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A B 8 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A B 8 " 0.000 2.00e-02 2.50e+03 pdb=" N6 A B 8 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A B 8 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A B 8 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A B 8 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A B 8 " 0.005 2.00e-02 2.50e+03 ... (remaining 1371 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 289 2.68 - 3.23: 8761 3.23 - 3.79: 14214 3.79 - 4.34: 18337 4.34 - 4.90: 27342 Nonbonded interactions: 68943 Sorted by model distance: nonbonded pdb=" O GLN A 332 " pdb=" OH TYR A 479 " model vdw 2.120 3.040 nonbonded pdb=" NH1 ARG A 198 " pdb=" O2 U B 29 " model vdw 2.171 3.120 nonbonded pdb=" OG BSER A1070 " pdb=" OE1 GLN A1073 " model vdw 2.189 3.040 nonbonded pdb=" OG1 THR A 744 " pdb=" OD1 ASN A 747 " model vdw 2.212 3.040 nonbonded pdb=" OG SER A 548 " pdb=" O CYS A 554 " model vdw 2.226 3.040 ... (remaining 68938 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.00 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.550 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.010 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 : 0.003 0.032 8592 Z= 0.153 Angle : 0.755 10.234 11835 Z= 0.384 Chirality : 0.042 0.177 1391 Planarity : 0.004 0.046 1374 Dihedral : 17.529 179.735 3498 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.57 % Favored : 90.11 % Rotamer: Outliers : 0.72 % Allowed : 0.24 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.28), residues: 942 helix: -0.09 (0.26), residues: 415 sheet: -1.24 (0.51), residues: 113 loop : -1.20 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 375 TYR 0.009 0.001 TYR A 530 PHE 0.009 0.001 PHE A 518 TRP 0.018 0.001 TRP A 328 HIS 0.003 0.001 HIS A1032 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8592) covalent geometry : angle 0.75457 (11835) hydrogen bonds : bond 0.17642 ( 344) hydrogen bonds : angle 6.84802 ( 983) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9628 (mmp) cc_final: 0.9366 (mmm) REVERT: A 389 MET cc_start: 0.8688 (pmm) cc_final: 0.8300 (pmm) REVERT: A 483 LEU cc_start: 0.9233 (tp) cc_final: 0.9002 (tp) REVERT: A 538 MET cc_start: 0.4037 (ttt) cc_final: 0.3357 (ttt) REVERT: A 670 MET cc_start: 0.9229 (mmp) cc_final: 0.8980 (mmm) REVERT: A 797 MET cc_start: 0.8448 (ppp) cc_final: 0.7691 (ppp) REVERT: A 872 MET cc_start: 0.9050 (mmp) cc_final: 0.8832 (mmm) REVERT: A 966 GLN cc_start: 0.9527 (tt0) cc_final: 0.9254 (mp10) REVERT: A 1001 LEU cc_start: 0.9395 (tt) cc_final: 0.9191 (pp) outliers start: 4 outliers final: 1 residues processed: 67 average time/residue: 0.0632 time to fit residues: 6.6405 Evaluate side-chains 53 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.0170 chunk 45 optimal weight: 6.9990 overall best weight: 2.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 GLN A 684 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.065009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.046923 restraints weight = 251361.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.048986 restraints weight = 117467.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.049921 restraints weight = 71440.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.050958 restraints weight = 49058.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.051426 restraints weight = 38195.761| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 8592 Z= 0.169 Angle : 0.739 8.074 11835 Z= 0.366 Chirality : 0.043 0.195 1391 Planarity : 0.004 0.044 1374 Dihedral : 18.662 179.377 1649 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.09 % Favored : 91.49 % Rotamer: Outliers : 0.36 % Allowed : 3.12 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.27), residues: 942 helix: -0.19 (0.24), residues: 424 sheet: -1.42 (0.52), residues: 98 loop : -1.37 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 198 TYR 0.017 0.002 TYR A 550 PHE 0.024 0.002 PHE A 200 TRP 0.022 0.001 TRP A 328 HIS 0.007 0.001 HIS A 503 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 8592) covalent geometry : angle 0.73856 (11835) hydrogen bonds : bond 0.05619 ( 344) hydrogen bonds : angle 5.38126 ( 983) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 358 MET cc_start: 0.9666 (mmp) cc_final: 0.9397 (mmm) REVERT: A 389 MET cc_start: 0.8547 (pmm) cc_final: 0.8126 (pmm) REVERT: A 440 GLN cc_start: 0.8882 (tt0) cc_final: 0.8629 (tt0) REVERT: A 483 LEU cc_start: 0.9390 (tp) cc_final: 0.9131 (tp) REVERT: A 538 MET cc_start: 0.4279 (ttt) cc_final: 0.4007 (ttt) REVERT: A 629 MET cc_start: 0.6967 (tmm) cc_final: 0.6715 (tpp) REVERT: A 807 LEU cc_start: 0.9569 (mt) cc_final: 0.9174 (tt) outliers start: 1 outliers final: 0 residues processed: 63 average time/residue: 0.0623 time to fit residues: 6.0987 Evaluate side-chains 43 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 89 optimal weight: 3.9990 chunk 38 optimal weight: 0.0370 chunk 29 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 40 optimal weight: 0.0000 overall best weight: 0.5064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN A 684 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.067877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.047880 restraints weight = 191403.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.049960 restraints weight = 98807.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.051737 restraints weight = 66033.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.052585 restraints weight = 49435.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.053061 restraints weight = 40744.734| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 8592 Z= 0.134 Angle : 0.721 8.169 11835 Z= 0.351 Chirality : 0.043 0.213 1391 Planarity : 0.004 0.044 1374 Dihedral : 18.474 178.925 1649 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.51 % Favored : 90.96 % Rotamer: Outliers : 0.36 % Allowed : 2.40 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.27), residues: 942 helix: -0.15 (0.24), residues: 427 sheet: -1.48 (0.51), residues: 98 loop : -1.43 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 198 TYR 0.010 0.001 TYR A 550 PHE 0.015 0.001 PHE A 200 TRP 0.017 0.001 TRP A 328 HIS 0.006 0.001 HIS A 503 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8592) covalent geometry : angle 0.72119 (11835) hydrogen bonds : bond 0.04863 ( 344) hydrogen bonds : angle 5.06063 ( 983) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9657 (mmp) cc_final: 0.9394 (mmm) REVERT: A 389 MET cc_start: 0.8671 (pmm) cc_final: 0.8237 (pmm) REVERT: A 483 LEU cc_start: 0.9381 (tp) cc_final: 0.9089 (tp) REVERT: A 538 MET cc_start: 0.3762 (ttt) cc_final: 0.3097 (ttt) REVERT: A 670 MET cc_start: 0.9180 (mmp) cc_final: 0.8973 (mmm) REVERT: A 740 MET cc_start: 0.9164 (mmp) cc_final: 0.8951 (mmm) REVERT: A 807 LEU cc_start: 0.9559 (mt) cc_final: 0.9225 (tt) REVERT: A 1004 LEU cc_start: 0.8854 (mm) cc_final: 0.8619 (mm) outliers start: 1 outliers final: 0 residues processed: 63 average time/residue: 0.0653 time to fit residues: 6.3820 Evaluate side-chains 50 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 94 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 684 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.062902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.042951 restraints weight = 220803.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.044937 restraints weight = 109883.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.046590 restraints weight = 72865.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.047852 restraints weight = 54634.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.048568 restraints weight = 44295.184| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 8592 Z= 0.196 Angle : 0.733 8.099 11835 Z= 0.363 Chirality : 0.043 0.213 1391 Planarity : 0.005 0.061 1374 Dihedral : 18.524 179.353 1649 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.62 % Favored : 90.96 % Rotamer: Outliers : 0.24 % Allowed : 2.52 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.27), residues: 942 helix: -0.08 (0.24), residues: 428 sheet: -1.73 (0.49), residues: 103 loop : -1.38 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 765 TYR 0.009 0.002 TYR A 890 PHE 0.021 0.002 PHE A 200 TRP 0.019 0.001 TRP A 328 HIS 0.006 0.001 HIS A 503 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 8592) covalent geometry : angle 0.73268 (11835) hydrogen bonds : bond 0.04971 ( 344) hydrogen bonds : angle 5.19555 ( 983) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9668 (mmp) cc_final: 0.9393 (mmm) REVERT: A 389 MET cc_start: 0.8738 (pmm) cc_final: 0.8333 (pmm) REVERT: A 440 GLN cc_start: 0.8892 (tt0) cc_final: 0.8402 (tt0) REVERT: A 483 LEU cc_start: 0.9427 (tp) cc_final: 0.9203 (tp) REVERT: A 670 MET cc_start: 0.9205 (mmp) cc_final: 0.8970 (mmm) REVERT: A 871 MET cc_start: 0.8806 (ptp) cc_final: 0.8384 (pmm) REVERT: A 1004 LEU cc_start: 0.8974 (mm) cc_final: 0.8741 (mm) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0610 time to fit residues: 5.5374 Evaluate side-chains 42 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 5 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 80 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 HIS A 684 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.063590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.044817 restraints weight = 246876.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.047683 restraints weight = 121203.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.048357 restraints weight = 70772.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.049265 restraints weight = 47665.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.049774 restraints weight = 40433.172| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 8592 Z= 0.152 Angle : 0.721 8.968 11835 Z= 0.355 Chirality : 0.043 0.217 1391 Planarity : 0.005 0.060 1374 Dihedral : 18.467 179.939 1649 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.26 % Favored : 90.43 % Rotamer: Outliers : 0.24 % Allowed : 2.16 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.27), residues: 942 helix: -0.04 (0.24), residues: 427 sheet: -1.49 (0.51), residues: 96 loop : -1.45 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1158 TYR 0.009 0.001 TYR A 550 PHE 0.018 0.002 PHE A 200 TRP 0.019 0.001 TRP A 328 HIS 0.005 0.001 HIS A 503 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8592) covalent geometry : angle 0.72090 (11835) hydrogen bonds : bond 0.04649 ( 344) hydrogen bonds : angle 5.14084 ( 983) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9655 (mmp) cc_final: 0.9376 (mmm) REVERT: A 389 MET cc_start: 0.8771 (pmm) cc_final: 0.8374 (pmm) REVERT: A 440 GLN cc_start: 0.9057 (tt0) cc_final: 0.8612 (tt0) REVERT: A 483 LEU cc_start: 0.9342 (tp) cc_final: 0.9106 (tp) REVERT: A 484 PHE cc_start: 0.9528 (m-80) cc_final: 0.9222 (m-10) REVERT: A 538 MET cc_start: 0.2376 (ttt) cc_final: 0.1490 (ttt) REVERT: A 577 MET cc_start: 0.7825 (pmm) cc_final: 0.7206 (pmm) REVERT: A 807 LEU cc_start: 0.9585 (mt) cc_final: 0.9245 (tt) REVERT: A 1004 LEU cc_start: 0.8893 (mm) cc_final: 0.8633 (mm) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0566 time to fit residues: 5.2558 Evaluate side-chains 41 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 2 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 GLN A 684 GLN A1032 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.062178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.042411 restraints weight = 238765.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.044447 restraints weight = 112937.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.046117 restraints weight = 72990.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.047331 restraints weight = 54369.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.048182 restraints weight = 43979.760| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 8592 Z= 0.173 Angle : 0.740 9.003 11835 Z= 0.363 Chirality : 0.044 0.230 1391 Planarity : 0.005 0.061 1374 Dihedral : 18.519 179.177 1649 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 21.25 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.57 % Favored : 90.11 % Rotamer: Outliers : 0.36 % Allowed : 1.68 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.27), residues: 942 helix: -0.09 (0.24), residues: 427 sheet: -1.31 (0.51), residues: 101 loop : -1.42 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1158 TYR 0.011 0.002 TYR A1009 PHE 0.020 0.002 PHE A 200 TRP 0.021 0.001 TRP A 328 HIS 0.010 0.002 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 8592) covalent geometry : angle 0.74020 (11835) hydrogen bonds : bond 0.04892 ( 344) hydrogen bonds : angle 5.14842 ( 983) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9634 (mmp) cc_final: 0.9358 (mmm) REVERT: A 389 MET cc_start: 0.8810 (pmm) cc_final: 0.8409 (pmm) REVERT: A 440 GLN cc_start: 0.9102 (tt0) cc_final: 0.8656 (tt0) REVERT: A 483 LEU cc_start: 0.9415 (tp) cc_final: 0.9197 (tp) REVERT: A 484 PHE cc_start: 0.9579 (m-80) cc_final: 0.9274 (m-10) REVERT: A 538 MET cc_start: 0.1759 (ttt) cc_final: 0.1342 (ttt) REVERT: A 670 MET cc_start: 0.9167 (mmm) cc_final: 0.8897 (mmm) REVERT: A 797 MET cc_start: 0.8769 (ppp) cc_final: 0.8050 (ppp) REVERT: A 1004 LEU cc_start: 0.8903 (mm) cc_final: 0.8687 (mm) outliers start: 1 outliers final: 0 residues processed: 58 average time/residue: 0.0723 time to fit residues: 6.4310 Evaluate side-chains 42 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 33 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 95 optimal weight: 10.0000 chunk 10 optimal weight: 0.1980 chunk 63 optimal weight: 0.0030 chunk 69 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 684 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.065149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.044706 restraints weight = 248108.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.047061 restraints weight = 113951.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.048936 restraints weight = 72837.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.050351 restraints weight = 53165.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.051036 restraints weight = 42214.719| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 8592 Z= 0.129 Angle : 0.721 8.194 11835 Z= 0.351 Chirality : 0.044 0.218 1391 Planarity : 0.005 0.100 1374 Dihedral : 18.348 179.675 1649 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.04 % Favored : 90.64 % Rotamer: Outliers : 0.24 % Allowed : 0.84 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.27), residues: 942 helix: -0.08 (0.24), residues: 428 sheet: -1.49 (0.50), residues: 103 loop : -1.34 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1158 TYR 0.008 0.001 TYR A 550 PHE 0.014 0.001 PHE A 200 TRP 0.017 0.001 TRP A 328 HIS 0.005 0.001 HIS A 503 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8592) covalent geometry : angle 0.72053 (11835) hydrogen bonds : bond 0.04458 ( 344) hydrogen bonds : angle 4.96257 ( 983) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9634 (mmp) cc_final: 0.9351 (mmm) REVERT: A 389 MET cc_start: 0.8830 (pmm) cc_final: 0.8443 (pmm) REVERT: A 440 GLN cc_start: 0.9098 (tt0) cc_final: 0.8564 (tt0) REVERT: A 483 LEU cc_start: 0.9355 (tp) cc_final: 0.9091 (tp) REVERT: A 484 PHE cc_start: 0.9547 (m-80) cc_final: 0.9267 (m-10) REVERT: A 538 MET cc_start: 0.1178 (ttt) cc_final: 0.0781 (ttt) REVERT: A 577 MET cc_start: 0.7768 (pmm) cc_final: 0.7421 (pmm) REVERT: A 629 MET cc_start: 0.6063 (tmm) cc_final: 0.5354 (tpp) REVERT: A 807 LEU cc_start: 0.9596 (mt) cc_final: 0.9243 (tt) REVERT: A 1004 LEU cc_start: 0.8836 (mm) cc_final: 0.8571 (mm) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0696 time to fit residues: 6.4364 Evaluate side-chains 43 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 97 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.061216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.042882 restraints weight = 158986.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.044509 restraints weight = 89386.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.046015 restraints weight = 62825.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.046955 restraints weight = 48854.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.047550 restraints weight = 40877.643| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 8592 Z= 0.189 Angle : 0.748 7.769 11835 Z= 0.369 Chirality : 0.044 0.238 1391 Planarity : 0.005 0.091 1374 Dihedral : 18.488 179.714 1649 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 22.23 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.04 % Favored : 90.64 % Rotamer: Outliers : 0.24 % Allowed : 0.96 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.27), residues: 942 helix: -0.10 (0.24), residues: 425 sheet: -1.50 (0.49), residues: 108 loop : -1.36 (0.33), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 198 TYR 0.011 0.002 TYR A 420 PHE 0.021 0.002 PHE A 200 TRP 0.020 0.001 TRP A 328 HIS 0.006 0.002 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 8592) covalent geometry : angle 0.74773 (11835) hydrogen bonds : bond 0.04984 ( 344) hydrogen bonds : angle 5.07318 ( 983) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9631 (mmp) cc_final: 0.9347 (mmm) REVERT: A 389 MET cc_start: 0.8825 (pmm) cc_final: 0.8439 (pmm) REVERT: A 440 GLN cc_start: 0.9117 (tt0) cc_final: 0.8569 (tt0) REVERT: A 484 PHE cc_start: 0.9563 (m-80) cc_final: 0.9300 (m-10) REVERT: A 538 MET cc_start: 0.1342 (ttt) cc_final: 0.0946 (ttt) REVERT: A 577 MET cc_start: 0.8036 (pmm) cc_final: 0.7624 (pmm) REVERT: A 629 MET cc_start: 0.6443 (tmm) cc_final: 0.5759 (tpp) REVERT: A 797 MET cc_start: 0.8757 (ppp) cc_final: 0.8080 (ppp) REVERT: A 843 MET cc_start: 0.9557 (ppp) cc_final: 0.9282 (ppp) REVERT: A 1004 LEU cc_start: 0.8898 (mm) cc_final: 0.8675 (mm) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0646 time to fit residues: 5.0173 Evaluate side-chains 42 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 48 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 chunk 62 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 684 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.064224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.044346 restraints weight = 230921.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.046654 restraints weight = 107822.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.048552 restraints weight = 69243.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.049455 restraints weight = 50953.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.049871 restraints weight = 41562.071| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 8592 Z= 0.132 Angle : 0.736 7.921 11835 Z= 0.358 Chirality : 0.044 0.223 1391 Planarity : 0.005 0.090 1374 Dihedral : 18.377 177.731 1649 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.57 % Favored : 90.11 % Rotamer: Outliers : 0.24 % Allowed : 0.24 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.27), residues: 942 helix: -0.08 (0.24), residues: 426 sheet: -1.56 (0.50), residues: 103 loop : -1.33 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 198 TYR 0.008 0.001 TYR A 550 PHE 0.015 0.001 PHE A 200 TRP 0.017 0.001 TRP A 328 HIS 0.005 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8592) covalent geometry : angle 0.73562 (11835) hydrogen bonds : bond 0.04509 ( 344) hydrogen bonds : angle 4.91924 ( 983) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: A 358 MET cc_start: 0.9623 (mmp) cc_final: 0.9336 (mmm) REVERT: A 389 MET cc_start: 0.8811 (pmm) cc_final: 0.8424 (pmm) REVERT: A 440 GLN cc_start: 0.9110 (tt0) cc_final: 0.8663 (tt0) REVERT: A 483 LEU cc_start: 0.9355 (tp) cc_final: 0.9116 (tp) REVERT: A 484 PHE cc_start: 0.9560 (m-80) cc_final: 0.9242 (m-10) REVERT: A 538 MET cc_start: 0.0851 (ttt) cc_final: 0.0503 (ttt) REVERT: A 577 MET cc_start: 0.8119 (pmm) cc_final: 0.7705 (pmm) REVERT: A 629 MET cc_start: 0.6375 (tmm) cc_final: 0.5681 (tpp) REVERT: A 637 PHE cc_start: 0.8685 (m-80) cc_final: 0.8437 (m-80) REVERT: A 797 MET cc_start: 0.8761 (ppp) cc_final: 0.8117 (ppp) REVERT: A 807 LEU cc_start: 0.9633 (mt) cc_final: 0.9271 (tt) REVERT: A 843 MET cc_start: 0.9548 (ppp) cc_final: 0.9271 (ppp) REVERT: A 1004 LEU cc_start: 0.8841 (mm) cc_final: 0.8568 (mm) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.0634 time to fit residues: 5.5970 Evaluate side-chains 43 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 58 optimal weight: 0.0270 chunk 42 optimal weight: 0.2980 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 39 optimal weight: 0.0870 chunk 38 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 684 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.054607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.033590 restraints weight = 234173.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.035570 restraints weight = 117916.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.036885 restraints weight = 79733.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.037828 restraints weight = 61491.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.038440 restraints weight = 51220.171| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 8592 Z= 0.127 Angle : 0.723 7.948 11835 Z= 0.350 Chirality : 0.043 0.219 1391 Planarity : 0.005 0.082 1374 Dihedral : 18.171 177.348 1649 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.51 % Favored : 91.17 % Rotamer: Outliers : 0.24 % Allowed : 0.24 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.27), residues: 942 helix: -0.03 (0.24), residues: 426 sheet: -1.52 (0.50), residues: 103 loop : -1.37 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 173 TYR 0.011 0.001 TYR A 890 PHE 0.022 0.001 PHE A 898 TRP 0.016 0.001 TRP A 328 HIS 0.004 0.001 HIS A1032 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8592) covalent geometry : angle 0.72282 (11835) hydrogen bonds : bond 0.04282 ( 344) hydrogen bonds : angle 4.81453 ( 983) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9691 (mmp) cc_final: 0.9474 (mmm) REVERT: A 389 MET cc_start: 0.9307 (pmm) cc_final: 0.9037 (pmm) REVERT: A 440 GLN cc_start: 0.8755 (tt0) cc_final: 0.8270 (tt0) REVERT: A 483 LEU cc_start: 0.9403 (tp) cc_final: 0.9115 (tp) REVERT: A 538 MET cc_start: 0.0395 (ttt) cc_final: 0.0139 (ttt) REVERT: A 577 MET cc_start: 0.8397 (pmm) cc_final: 0.8053 (pmm) REVERT: A 629 MET cc_start: 0.6868 (tmm) cc_final: 0.6280 (tpp) REVERT: A 797 MET cc_start: 0.8877 (ppp) cc_final: 0.8263 (ppp) REVERT: A 807 LEU cc_start: 0.9646 (mt) cc_final: 0.9204 (tt) REVERT: A 896 GLU cc_start: 0.8901 (pp20) cc_final: 0.8535 (pp20) REVERT: A 1004 LEU cc_start: 0.8926 (mm) cc_final: 0.8722 (mm) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0779 time to fit residues: 7.1650 Evaluate side-chains 48 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 71 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 63 optimal weight: 0.0070 chunk 73 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 83 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 39 optimal weight: 0.3980 chunk 18 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 684 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.055945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.035731 restraints weight = 190757.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.037464 restraints weight = 108907.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.038632 restraints weight = 77512.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.039470 restraints weight = 61665.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.040027 restraints weight = 52341.799| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 8592 Z= 0.126 Angle : 0.732 10.671 11835 Z= 0.352 Chirality : 0.044 0.275 1391 Planarity : 0.004 0.077 1374 Dihedral : 18.086 178.141 1649 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.36 % Favored : 90.32 % Rotamer: Outliers : 0.24 % Allowed : 0.12 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.27), residues: 942 helix: 0.00 (0.25), residues: 426 sheet: -1.42 (0.51), residues: 103 loop : -1.36 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 861 TYR 0.008 0.001 TYR A 550 PHE 0.011 0.001 PHE A 518 TRP 0.015 0.001 TRP A 328 HIS 0.004 0.001 HIS A1032 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8592) covalent geometry : angle 0.73240 (11835) hydrogen bonds : bond 0.04268 ( 344) hydrogen bonds : angle 4.75684 ( 983) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1881.62 seconds wall clock time: 32 minutes 57.13 seconds (1977.13 seconds total)