Starting phenix.real_space_refine on Tue Dec 31 04:37:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pjj_17711/12_2024/8pjj_17711.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pjj_17711/12_2024/8pjj_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_17711/12_2024/8pjj_17711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pjj_17711/12_2024/8pjj_17711.map" model { file = "/net/cci-nas-00/data/ceres_data/8pjj_17711/12_2024/8pjj_17711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pjj_17711/12_2024/8pjj_17711.cif" } resolution = 4.24 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= 0.010 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 8.43, per 1000 atoms: 1.01 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: 2.18 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 2.93 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: 3.74 Time building geometry restraints manager: 2.47 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 28.940 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.320 ------------------------------------------------------------------------------- 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= 0.181 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 : 19.23 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 (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: -1.14 (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 TRP 0.018 0.001 TRP A 328 HIS 0.003 0.001 HIS A1032 PHE 0.009 0.001 PHE A 518 TYR 0.009 0.001 TYR A 530 ARG 0.008 0.000 ARG A 375 *********************** 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 : 0.840 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: 0.8301 (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: 0.3358 (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: 0.8831 (mmm) REVERT: A 966 GLN cc_start: 0.9527 (tt0) cc_final: 0.9254 (mp10) outliers start: 4 outliers final: 1 residues processed: 67 average time/residue: 0.1732 time to fit residues: 17.9715 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 : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 88 optimal weight: 0.7980 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1156 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= 0.231 Angle : 0.736 8.225 11835 Z= 0.365 Chirality : 0.043 0.195 1391 Planarity : 0.004 0.045 1374 Dihedral : 18.668 179.857 1649 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.40 % Favored : 91.17 % Rotamer: Outliers : 0.24 % Allowed : 3.12 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.27), residues: 942 helix: -0.18 (0.24), residues: 423 sheet: -1.42 (0.52), residues: 98 loop : -1.33 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 328 HIS 0.007 0.001 HIS A 503 PHE 0.022 0.002 PHE A 200 TYR 0.016 0.002 TYR A 550 ARG 0.010 0.001 ARG A 198 *********************** 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 61 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 169 ASN cc_start: 0.8750 (p0) cc_final: 0.8542 (t0) REVERT: A 358 MET cc_start: 0.9637 (mmp) cc_final: 0.9354 (mmm) REVERT: A 389 MET cc_start: 0.8790 (pmm) cc_final: 0.8393 (pmm) REVERT: A 440 GLN cc_start: 0.8837 (tt0) cc_final: 0.8498 (tt0) REVERT: A 483 LEU cc_start: 0.9392 (tp) cc_final: 0.9141 (tp) REVERT: A 484 PHE cc_start: 0.9638 (m-10) cc_final: 0.9415 (m-10) REVERT: A 538 MET cc_start: 0.4016 (ttt) cc_final: 0.3762 (ttt) REVERT: A 629 MET cc_start: 0.7054 (tmm) cc_final: 0.6746 (tpp) REVERT: A 797 MET cc_start: 0.8662 (ppp) cc_final: 0.8024 (ppp) REVERT: A 1004 LEU cc_start: 0.8932 (mm) cc_final: 0.8723 (mm) REVERT: A 1076 LEU cc_start: 0.9415 (tp) cc_final: 0.9192 (mt) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1672 time to fit residues: 16.0242 Evaluate side-chains 46 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 8592 Z= 0.192 Angle : 0.701 7.929 11835 Z= 0.346 Chirality : 0.042 0.198 1391 Planarity : 0.004 0.048 1374 Dihedral : 18.543 179.211 1649 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.83 % Favored : 90.74 % Rotamer: Outliers : 0.48 % Allowed : 2.28 % 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 (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: -1.28 (0.27), residues: 942 helix: -0.05 (0.24), residues: 425 sheet: -1.49 (0.51), residues: 98 loop : -1.45 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 328 HIS 0.005 0.001 HIS A 503 PHE 0.019 0.001 PHE A 200 TYR 0.012 0.001 TYR A 550 ARG 0.007 0.000 ARG A 198 *********************** 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 65 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9647 (mmp) cc_final: 0.9370 (mmm) REVERT: A 389 MET cc_start: 0.8866 (pmm) cc_final: 0.8468 (pmm) REVERT: A 483 LEU cc_start: 0.9404 (tp) cc_final: 0.9144 (tp) REVERT: A 484 PHE cc_start: 0.9616 (m-10) cc_final: 0.9364 (m-10) REVERT: A 538 MET cc_start: 0.3728 (ttt) cc_final: 0.3528 (ttt) REVERT: A 670 MET cc_start: 0.9219 (mmp) cc_final: 0.8991 (mmm) REVERT: A 807 LEU cc_start: 0.9576 (mt) cc_final: 0.9172 (tt) REVERT: A 1001 LEU cc_start: 0.9403 (tt) cc_final: 0.9168 (pp) REVERT: A 1004 LEU cc_start: 0.8958 (mm) cc_final: 0.8708 (mm) REVERT: A 1076 LEU cc_start: 0.9381 (tp) cc_final: 0.9128 (mt) outliers start: 2 outliers final: 0 residues processed: 65 average time/residue: 0.1864 time to fit residues: 18.1507 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 : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 9 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 GLN A1032 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 8592 Z= 0.335 Angle : 0.813 8.017 11835 Z= 0.407 Chirality : 0.046 0.237 1391 Planarity : 0.006 0.086 1374 Dihedral : 18.787 178.662 1649 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 29.64 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.89 % Favored : 89.79 % Rotamer: Outliers : 0.24 % Allowed : 3.49 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -1.53 (0.27), residues: 942 helix: -0.35 (0.24), residues: 425 sheet: -1.60 (0.49), residues: 108 loop : -1.45 (0.33), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 328 HIS 0.008 0.002 HIS A1015 PHE 0.027 0.003 PHE A 200 TYR 0.018 0.003 TYR A 425 ARG 0.010 0.001 ARG A 867 *********************** 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 53 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 358 MET cc_start: 0.9602 (mmp) cc_final: 0.9289 (mmm) REVERT: A 389 MET cc_start: 0.8967 (pmm) cc_final: 0.8744 (pmm) REVERT: A 440 GLN cc_start: 0.8988 (tt0) cc_final: 0.8426 (tt0) REVERT: A 577 MET cc_start: 0.7791 (pmm) cc_final: 0.7262 (pmm) REVERT: A 629 MET cc_start: 0.7280 (tmm) cc_final: 0.6909 (tpp) REVERT: A 670 MET cc_start: 0.9237 (mmp) cc_final: 0.8997 (mmm) REVERT: A 1006 LEU cc_start: 0.9564 (tp) cc_final: 0.9315 (pp) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1887 time to fit residues: 15.0772 Evaluate side-chains 44 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 8592 Z= 0.250 Angle : 0.757 9.376 11835 Z= 0.375 Chirality : 0.045 0.226 1391 Planarity : 0.005 0.074 1374 Dihedral : 18.753 179.084 1649 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 23.21 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.57 % Favored : 90.11 % Rotamer: Outliers : 0.24 % Allowed : 1.80 % 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 (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: -1.46 (0.27), residues: 942 helix: -0.29 (0.24), residues: 424 sheet: -1.35 (0.51), residues: 101 loop : -1.52 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 328 HIS 0.005 0.001 HIS A 503 PHE 0.021 0.002 PHE A 200 TYR 0.027 0.002 TYR A 685 ARG 0.004 0.000 ARG A 867 *********************** 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 54 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: A 358 MET cc_start: 0.9595 (mmp) cc_final: 0.9289 (mmm) REVERT: A 389 MET cc_start: 0.9000 (pmm) cc_final: 0.8619 (pmm) REVERT: A 440 GLN cc_start: 0.9091 (tt0) cc_final: 0.8625 (tt0) REVERT: A 538 MET cc_start: 0.2334 (ttt) cc_final: 0.1553 (ttt) REVERT: A 577 MET cc_start: 0.8083 (pmm) cc_final: 0.7439 (pmm) REVERT: A 670 MET cc_start: 0.9228 (mmp) cc_final: 0.8960 (mmm) REVERT: A 1003 LEU cc_start: 0.9363 (tt) cc_final: 0.9104 (tt) REVERT: A 1006 LEU cc_start: 0.9552 (tp) cc_final: 0.9247 (pp) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1860 time to fit residues: 15.3825 Evaluate side-chains 46 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 7 optimal weight: 0.2980 chunk 31 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- 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 510 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3280 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= 0.262 Angle : 0.770 8.430 11835 Z= 0.381 Chirality : 0.045 0.241 1391 Planarity : 0.005 0.098 1374 Dihedral : 18.828 178.801 1649 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 25.04 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.79 % Favored : 89.89 % Rotamer: Outliers : 0.36 % Allowed : 1.32 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -1.55 (0.27), residues: 942 helix: -0.35 (0.24), residues: 419 sheet: -1.60 (0.48), residues: 108 loop : -1.48 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 328 HIS 0.005 0.002 HIS A 503 PHE 0.024 0.002 PHE A 200 TYR 0.025 0.002 TYR A 685 ARG 0.006 0.001 ARG A 867 *********************** 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 52 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9575 (mmp) cc_final: 0.9278 (mmm) REVERT: A 389 MET cc_start: 0.9002 (pmm) cc_final: 0.8649 (pmm) REVERT: A 440 GLN cc_start: 0.9076 (tt0) cc_final: 0.8643 (tt0) REVERT: A 483 LEU cc_start: 0.9430 (tp) cc_final: 0.9222 (tp) REVERT: A 538 MET cc_start: 0.2429 (ttt) cc_final: 0.1744 (ttt) REVERT: A 872 MET cc_start: 0.8780 (mmp) cc_final: 0.8541 (mmm) REVERT: A 1001 LEU cc_start: 0.9456 (tt) cc_final: 0.9214 (pp) outliers start: 1 outliers final: 0 residues processed: 52 average time/residue: 0.1904 time to fit residues: 15.1930 Evaluate side-chains 44 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 58 optimal weight: 30.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 510 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3477 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= 0.239 Angle : 0.757 8.201 11835 Z= 0.374 Chirality : 0.044 0.234 1391 Planarity : 0.005 0.101 1374 Dihedral : 18.790 177.030 1649 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 23.21 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.57 % Favored : 90.00 % Rotamer: Outliers : 0.48 % Allowed : 0.96 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -1.56 (0.27), residues: 942 helix: -0.34 (0.24), residues: 419 sheet: -1.64 (0.48), residues: 108 loop : -1.50 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 328 HIS 0.005 0.001 HIS A 503 PHE 0.021 0.002 PHE A 200 TYR 0.015 0.002 TYR A 685 ARG 0.004 0.000 ARG A 867 *********************** 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 56 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: A 358 MET cc_start: 0.9564 (mmp) cc_final: 0.9270 (mmm) REVERT: A 389 MET cc_start: 0.9002 (pmm) cc_final: 0.8651 (pmm) REVERT: A 440 GLN cc_start: 0.9113 (tt0) cc_final: 0.8688 (tt0) REVERT: A 483 LEU cc_start: 0.9407 (tp) cc_final: 0.9184 (tp) REVERT: A 538 MET cc_start: 0.1959 (ttt) cc_final: 0.1544 (ttt) REVERT: A 577 MET cc_start: 0.8346 (pmm) cc_final: 0.8028 (pmm) REVERT: A 629 MET cc_start: 0.7035 (tmm) cc_final: 0.6308 (tpp) REVERT: A 807 LEU cc_start: 0.9683 (mt) cc_final: 0.9284 (tt) REVERT: A 1001 LEU cc_start: 0.9477 (tt) cc_final: 0.9244 (pp) outliers start: 2 outliers final: 0 residues processed: 56 average time/residue: 0.1817 time to fit residues: 15.6461 Evaluate side-chains 46 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 0.0970 chunk 8 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 chunk 85 optimal weight: 9.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 8592 Z= 0.184 Angle : 0.741 8.630 11835 Z= 0.361 Chirality : 0.045 0.224 1391 Planarity : 0.005 0.088 1374 Dihedral : 18.610 175.499 1649 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.26 % Favored : 90.32 % 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 (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: -1.46 (0.27), residues: 942 helix: -0.28 (0.24), residues: 425 sheet: -1.42 (0.51), residues: 96 loop : -1.50 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 328 HIS 0.006 0.001 HIS A 503 PHE 0.015 0.001 PHE A 200 TYR 0.009 0.001 TYR A 611 ARG 0.016 0.001 ARG A 844 *********************** 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 61 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9572 (mmp) cc_final: 0.9281 (mmm) REVERT: A 389 MET cc_start: 0.8995 (pmm) cc_final: 0.8619 (pmm) REVERT: A 440 GLN cc_start: 0.9100 (tt0) cc_final: 0.8617 (tt0) REVERT: A 483 LEU cc_start: 0.9386 (tp) cc_final: 0.9157 (tp) REVERT: A 538 MET cc_start: 0.1627 (ttt) cc_final: 0.1062 (ttt) REVERT: A 577 MET cc_start: 0.8348 (pmm) cc_final: 0.7965 (pmm) REVERT: A 629 MET cc_start: 0.6989 (tmm) cc_final: 0.6286 (tpp) REVERT: A 670 MET cc_start: 0.9052 (mmm) cc_final: 0.8775 (mmm) REVERT: A 807 LEU cc_start: 0.9644 (mt) cc_final: 0.9223 (tt) REVERT: A 1001 LEU cc_start: 0.9472 (tt) cc_final: 0.9230 (pp) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1932 time to fit residues: 17.9166 Evaluate side-chains 45 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.0980 chunk 88 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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: 0.8303 moved from start: 0.3490 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= 0.179 Angle : 0.737 8.993 11835 Z= 0.358 Chirality : 0.044 0.225 1391 Planarity : 0.005 0.080 1374 Dihedral : 18.491 175.795 1649 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.04 % Favored : 90.53 % 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 (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: -1.39 (0.27), residues: 942 helix: -0.22 (0.24), residues: 426 sheet: -1.39 (0.51), residues: 96 loop : -1.47 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 328 HIS 0.006 0.001 HIS A 503 PHE 0.015 0.001 PHE A 200 TYR 0.009 0.001 TYR A 550 ARG 0.002 0.000 ARG A 938 *********************** 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 58 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9577 (mmp) cc_final: 0.9279 (mmm) REVERT: A 389 MET cc_start: 0.8999 (pmm) cc_final: 0.8628 (pmm) REVERT: A 440 GLN cc_start: 0.9066 (tt0) cc_final: 0.8686 (tt0) REVERT: A 483 LEU cc_start: 0.9364 (tp) cc_final: 0.9138 (tp) REVERT: A 538 MET cc_start: 0.1209 (ttt) cc_final: 0.0641 (ttt) REVERT: A 577 MET cc_start: 0.8421 (pmm) cc_final: 0.8019 (pmm) REVERT: A 629 MET cc_start: 0.7022 (tmm) cc_final: 0.6295 (tpp) REVERT: A 797 MET cc_start: 0.8589 (ppp) cc_final: 0.7919 (ppp) REVERT: A 807 LEU cc_start: 0.9649 (mt) cc_final: 0.9210 (tt) REVERT: A 1001 LEU cc_start: 0.9469 (tt) cc_final: 0.9218 (pp) REVERT: A 1004 LEU cc_start: 0.8958 (mm) cc_final: 0.8749 (mm) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1935 time to fit residues: 16.8832 Evaluate side-chains 46 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 64 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 60 optimal weight: 0.0170 chunk 47 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.0220 ------------------------------------------------------------------------------- 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: 0.8278 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 8592 Z= 0.177 Angle : 0.725 8.822 11835 Z= 0.351 Chirality : 0.044 0.224 1391 Planarity : 0.004 0.075 1374 Dihedral : 18.313 176.130 1649 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.40 % Favored : 91.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.27), residues: 942 helix: -0.15 (0.24), residues: 426 sheet: -0.93 (0.46), residues: 129 loop : -1.53 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 328 HIS 0.005 0.001 HIS A 503 PHE 0.012 0.001 PHE A 200 TYR 0.009 0.001 TYR A 550 ARG 0.003 0.000 ARG A 938 ********************** 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 61 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: A 358 MET cc_start: 0.9576 (mmp) cc_final: 0.9275 (mmm) REVERT: A 389 MET cc_start: 0.9000 (pmm) cc_final: 0.8628 (pmm) REVERT: A 440 GLN cc_start: 0.9047 (tt0) cc_final: 0.8631 (tt0) REVERT: A 483 LEU cc_start: 0.9362 (tp) cc_final: 0.9119 (tp) REVERT: A 538 MET cc_start: 0.1072 (ttt) cc_final: 0.0726 (ttt) REVERT: A 577 MET cc_start: 0.8521 (pmm) cc_final: 0.8136 (pmm) REVERT: A 637 PHE cc_start: 0.8767 (m-10) cc_final: 0.8485 (m-80) REVERT: A 734 ASP cc_start: 0.9329 (p0) cc_final: 0.8954 (p0) REVERT: A 797 MET cc_start: 0.8544 (ppp) cc_final: 0.7847 (ppp) REVERT: A 807 LEU cc_start: 0.9644 (mt) cc_final: 0.9198 (tt) REVERT: A 1001 LEU cc_start: 0.9458 (tt) cc_final: 0.9190 (pp) REVERT: A 1004 LEU cc_start: 0.8931 (mm) cc_final: 0.8713 (mm) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.2003 time to fit residues: 17.9259 Evaluate side-chains 47 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 77 optimal weight: 0.0670 chunk 32 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 14 optimal weight: 0.0000 chunk 68 optimal weight: 0.0000 overall best weight: 0.8130 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.064172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.047901 restraints weight = 243832.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.049410 restraints weight = 108778.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.050783 restraints weight = 62694.436| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 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 = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 8592 Z= 0.173 Angle : 0.713 8.599 11835 Z= 0.345 Chirality : 0.043 0.223 1391 Planarity : 0.005 0.071 1374 Dihedral : 18.227 176.641 1649 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.83 % Favored : 90.64 % 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 (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: -1.21 (0.28), residues: 942 helix: -0.08 (0.24), residues: 426 sheet: -1.03 (0.49), residues: 117 loop : -1.43 (0.33), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 328 HIS 0.005 0.001 HIS A 503 PHE 0.011 0.001 PHE A 200 TYR 0.008 0.001 TYR A 177 ARG 0.009 0.000 ARG A1158 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1627.82 seconds wall clock time: 31 minutes 12.51 seconds (1872.51 seconds total)