Starting phenix.real_space_refine on Fri May 16 19:42:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pjj_17711/05_2025/8pjj_17711.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pjj_17711/05_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_17711/05_2025/8pjj_17711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pjj_17711/05_2025/8pjj_17711.map" model { file = "/net/cci-nas-00/data/ceres_data/8pjj_17711/05_2025/8pjj_17711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pjj_17711/05_2025/8pjj_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): 0.38s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 8.62, per 1000 atoms: 1.03 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: 1.98 Conformation dependent library (CDL) restraints added in 1.7 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: 3.03 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: 2.82 Time building geometry restraints manager: 2.29 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 28.020 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.580 ------------------------------------------------------------------------------- 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 : 19.23 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 Details of bonding type rmsd hydrogen bonds : bond 0.17642 ( 344) hydrogen bonds : angle 6.84802 ( 983) covalent geometry : bond 0.00279 ( 8592) covalent geometry : angle 0.75457 (11835) *********************** 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 : 0.891 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: 0.1632 time to fit residues: 16.7263 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 : 0.912 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.064975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.045201 restraints weight = 192529.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.047068 restraints weight = 101395.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.048781 restraints weight = 68214.884| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 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 = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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= 0.172 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 Details of bonding type rmsd hydrogen bonds : bond 0.05885 ( 344) hydrogen bonds : angle 5.42784 ( 983) covalent geometry : bond 0.00359 ( 8592) covalent geometry : angle 0.73551 (11835) *********************** 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 : 0.827 Fit side-chains revert: symmetry clash REVERT: A 169 ASN cc_start: 0.9202 (p0) cc_final: 0.8996 (t0) REVERT: A 358 MET cc_start: 0.9664 (mmp) cc_final: 0.9396 (mmm) REVERT: A 389 MET cc_start: 0.8592 (pmm) cc_final: 0.8177 (pmm) REVERT: A 440 GLN cc_start: 0.8835 (tt0) cc_final: 0.8500 (tt0) REVERT: A 483 LEU cc_start: 0.9426 (tp) cc_final: 0.9152 (tp) REVERT: A 538 MET cc_start: 0.4263 (ttt) cc_final: 0.3989 (ttt) REVERT: A 629 MET cc_start: 0.6895 (tmm) cc_final: 0.6627 (tpp) REVERT: A 797 MET cc_start: 0.8805 (ppp) cc_final: 0.8198 (ppp) REVERT: A 1004 LEU cc_start: 0.8948 (mm) cc_final: 0.8728 (mm) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1558 time to fit residues: 15.0433 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 : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 16 optimal weight: 0.7980 chunk 36 optimal weight: 0.3980 chunk 55 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 2 optimal weight: 30.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.067361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.050286 restraints weight = 256104.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.051795 restraints weight = 120939.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.053236 restraints weight = 68046.128| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 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 = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 8592 Z= 0.130 Angle : 0.703 7.560 11835 Z= 0.343 Chirality : 0.043 0.189 1391 Planarity : 0.004 0.046 1374 Dihedral : 18.486 178.975 1649 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.40 % Favored : 91.06 % Rotamer: Outliers : 0.36 % Allowed : 1.92 % Favored : 97.72 % 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: -1.30 (0.27), residues: 942 helix: -0.12 (0.24), residues: 427 sheet: -1.44 (0.51), residues: 98 loop : -1.42 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 328 HIS 0.005 0.001 HIS A 503 PHE 0.017 0.001 PHE A 200 TYR 0.011 0.001 TYR A 550 ARG 0.009 0.001 ARG A 198 Details of bonding type rmsd hydrogen bonds : bond 0.04924 ( 344) hydrogen bonds : angle 5.07804 ( 983) covalent geometry : bond 0.00281 ( 8592) covalent geometry : angle 0.70318 (11835) *********************** 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 : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9711 (mmp) cc_final: 0.9460 (mmm) REVERT: A 389 MET cc_start: 0.8745 (pmm) cc_final: 0.8322 (pmm) REVERT: A 483 LEU cc_start: 0.9385 (tp) cc_final: 0.9091 (tp) REVERT: A 484 PHE cc_start: 0.9627 (m-10) cc_final: 0.9403 (m-10) REVERT: A 538 MET cc_start: 0.3929 (ttt) cc_final: 0.3487 (ttt) REVERT: A 807 LEU cc_start: 0.9555 (mt) cc_final: 0.9192 (tt) REVERT: A 941 HIS cc_start: 0.9112 (t70) cc_final: 0.8910 (t70) REVERT: A 1004 LEU cc_start: 0.8949 (mm) cc_final: 0.8705 (mm) outliers start: 1 outliers final: 1 residues processed: 63 average time/residue: 0.1650 time to fit residues: 15.9850 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 : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 2 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 44 optimal weight: 0.0970 chunk 46 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 72 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 55 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.067369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.046724 restraints weight = 221804.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.049003 restraints weight = 107825.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.050415 restraints weight = 70119.301| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 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 = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1749 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= 0.125 Angle : 0.700 8.038 11835 Z= 0.341 Chirality : 0.042 0.194 1391 Planarity : 0.004 0.065 1374 Dihedral : 18.310 179.960 1649 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.87 % Favored : 91.70 % Rotamer: Outliers : 0.24 % Allowed : 2.76 % Favored : 97.00 % 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: -1.25 (0.27), residues: 942 helix: -0.07 (0.24), residues: 425 sheet: -1.49 (0.51), residues: 103 loop : -1.38 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 328 HIS 0.004 0.001 HIS A 503 PHE 0.015 0.001 PHE A 200 TYR 0.008 0.001 TYR A 550 ARG 0.003 0.000 ARG A 198 Details of bonding type rmsd hydrogen bonds : bond 0.04314 ( 344) hydrogen bonds : angle 4.95013 ( 983) covalent geometry : bond 0.00273 ( 8592) covalent geometry : angle 0.70026 (11835) *********************** 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 64 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9683 (mmp) cc_final: 0.9403 (mmm) REVERT: A 389 MET cc_start: 0.8708 (pmm) cc_final: 0.8332 (pmm) REVERT: A 440 GLN cc_start: 0.8829 (tt0) cc_final: 0.8432 (tt0) REVERT: A 483 LEU cc_start: 0.9445 (tp) cc_final: 0.9144 (tp) REVERT: A 538 MET cc_start: 0.3392 (ttt) cc_final: 0.2957 (ttt) REVERT: A 670 MET cc_start: 0.9218 (mmp) cc_final: 0.9018 (mmm) REVERT: A 797 MET cc_start: 0.8657 (ppp) cc_final: 0.7962 (ppp) REVERT: A 807 LEU cc_start: 0.9572 (mt) cc_final: 0.9261 (tt) REVERT: A 1004 LEU cc_start: 0.8955 (mm) cc_final: 0.8734 (mm) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1776 time to fit residues: 16.8489 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 : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 25 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 34 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.066382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.049667 restraints weight = 259884.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.051318 restraints weight = 118617.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.052091 restraints weight = 69852.065| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 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 = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 8592 Z= 0.129 Angle : 0.683 7.848 11835 Z= 0.336 Chirality : 0.042 0.202 1391 Planarity : 0.004 0.060 1374 Dihedral : 18.244 179.346 1649 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.83 % Favored : 90.85 % Rotamer: Outliers : 0.24 % Allowed : 1.68 % Favored : 98.08 % 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: -1.17 (0.28), residues: 942 helix: 0.03 (0.25), residues: 424 sheet: -1.34 (0.53), residues: 96 loop : -1.40 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 328 HIS 0.004 0.001 HIS A 503 PHE 0.014 0.001 PHE A 200 TYR 0.008 0.001 TYR A 550 ARG 0.005 0.000 ARG A1158 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 344) hydrogen bonds : angle 4.95668 ( 983) covalent geometry : bond 0.00282 ( 8592) covalent geometry : angle 0.68266 (11835) *********************** 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 65 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9716 (mmp) cc_final: 0.9464 (mmm) REVERT: A 389 MET cc_start: 0.8785 (pmm) cc_final: 0.8410 (pmm) REVERT: A 440 GLN cc_start: 0.8820 (tt0) cc_final: 0.8389 (tt0) REVERT: A 483 LEU cc_start: 0.9419 (tp) cc_final: 0.9138 (tp) REVERT: A 670 MET cc_start: 0.9185 (mmp) cc_final: 0.8972 (mmm) REVERT: A 1004 LEU cc_start: 0.8969 (mm) cc_final: 0.8757 (mm) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1856 time to fit residues: 17.8606 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 : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 19 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 39 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 81 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.064747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.044934 restraints weight = 199188.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.046834 restraints weight = 103249.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.048540 restraints weight = 69237.992| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 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 = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2263 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= 0.142 Angle : 0.693 7.909 11835 Z= 0.339 Chirality : 0.043 0.213 1391 Planarity : 0.004 0.054 1374 Dihedral : 18.255 178.546 1649 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.04 % Favored : 90.64 % 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 (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: -1.16 (0.28), residues: 942 helix: 0.04 (0.25), residues: 423 sheet: -1.35 (0.52), residues: 96 loop : -1.40 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 328 HIS 0.008 0.001 HIS A 510 PHE 0.015 0.001 PHE A 200 TYR 0.008 0.001 TYR A 550 ARG 0.004 0.000 ARG A 867 Details of bonding type rmsd hydrogen bonds : bond 0.04378 ( 344) hydrogen bonds : angle 4.96863 ( 983) covalent geometry : bond 0.00308 ( 8592) covalent geometry : angle 0.69347 (11835) *********************** 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 64 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9674 (mmp) cc_final: 0.9401 (mmm) REVERT: A 389 MET cc_start: 0.8777 (pmm) cc_final: 0.8387 (pmm) REVERT: A 440 GLN cc_start: 0.8940 (tt0) cc_final: 0.8520 (tt0) REVERT: A 483 LEU cc_start: 0.9414 (tp) cc_final: 0.9138 (tp) REVERT: A 577 MET cc_start: 0.7780 (pmm) cc_final: 0.6988 (pmm) REVERT: A 670 MET cc_start: 0.9180 (mmp) cc_final: 0.8944 (mmm) REVERT: A 797 MET cc_start: 0.8700 (ppp) cc_final: 0.7979 (ppp) REVERT: A 872 MET cc_start: 0.8984 (mmp) cc_final: 0.8781 (mmm) REVERT: A 1003 LEU cc_start: 0.9399 (tt) cc_final: 0.9140 (tt) REVERT: A 1004 LEU cc_start: 0.8929 (mm) cc_final: 0.8703 (mm) outliers start: 1 outliers final: 0 residues processed: 64 average time/residue: 0.1783 time to fit residues: 16.9868 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 : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 45 optimal weight: 1.9990 chunk 12 optimal weight: 0.0670 chunk 83 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 38 optimal weight: 30.0000 chunk 22 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.067122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.050187 restraints weight = 298586.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.052304 restraints weight = 126309.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.053619 restraints weight = 68472.627| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 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 = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2387 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= 0.123 Angle : 0.704 9.369 11835 Z= 0.342 Chirality : 0.043 0.206 1391 Planarity : 0.004 0.084 1374 Dihedral : 18.150 179.119 1649 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.72 % Favored : 90.85 % Rotamer: Outliers : 0.24 % Allowed : 1.32 % Favored : 98.44 % 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: -1.03 (0.28), residues: 942 helix: 0.09 (0.25), residues: 424 sheet: -1.13 (0.54), residues: 96 loop : -1.30 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 328 HIS 0.005 0.001 HIS A 503 PHE 0.012 0.001 PHE A1052 TYR 0.009 0.001 TYR A 177 ARG 0.004 0.000 ARG A 198 Details of bonding type rmsd hydrogen bonds : bond 0.04205 ( 344) hydrogen bonds : angle 4.84979 ( 983) covalent geometry : bond 0.00268 ( 8592) covalent geometry : angle 0.70406 (11835) *********************** 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 64 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9706 (mmp) cc_final: 0.9439 (mmm) REVERT: A 389 MET cc_start: 0.8925 (pmm) cc_final: 0.8545 (pmm) REVERT: A 440 GLN cc_start: 0.8825 (tt0) cc_final: 0.8367 (tt0) REVERT: A 483 LEU cc_start: 0.9395 (tp) cc_final: 0.9100 (tp) REVERT: A 670 MET cc_start: 0.9146 (mmp) cc_final: 0.8921 (mmm) REVERT: A 807 LEU cc_start: 0.9594 (mt) cc_final: 0.9281 (tt) REVERT: A 1004 LEU cc_start: 0.8940 (mm) cc_final: 0.8707 (mm) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1722 time to fit residues: 16.4520 Evaluate side-chains 49 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 12 optimal weight: 0.0870 chunk 18 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 50.0000 chunk 49 optimal weight: 0.0060 chunk 38 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 chunk 93 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.5974 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.067331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.047440 restraints weight = 221727.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.049573 restraints weight = 104805.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.050927 restraints weight = 67685.257| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 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 = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2578 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= 0.119 Angle : 0.695 8.774 11835 Z= 0.337 Chirality : 0.042 0.204 1391 Planarity : 0.004 0.074 1374 Dihedral : 18.080 178.740 1649 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 14.57 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.28), residues: 942 helix: 0.05 (0.25), residues: 424 sheet: -1.21 (0.52), residues: 103 loop : -1.32 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 328 HIS 0.004 0.001 HIS A 503 PHE 0.011 0.001 PHE A 518 TYR 0.010 0.001 TYR A 467 ARG 0.006 0.000 ARG A1158 Details of bonding type rmsd hydrogen bonds : bond 0.04090 ( 344) hydrogen bonds : angle 4.76331 ( 983) covalent geometry : bond 0.00258 ( 8592) covalent geometry : angle 0.69479 (11835) *********************** 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 65 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9671 (mmp) cc_final: 0.9379 (mmm) REVERT: A 389 MET cc_start: 0.8726 (pmm) cc_final: 0.8340 (pmm) REVERT: A 440 GLN cc_start: 0.8872 (tt0) cc_final: 0.8486 (tt0) REVERT: A 483 LEU cc_start: 0.9384 (tp) cc_final: 0.9074 (tp) REVERT: A 577 MET cc_start: 0.7672 (pmm) cc_final: 0.7288 (pmm) REVERT: A 637 PHE cc_start: 0.8671 (m-80) cc_final: 0.8442 (m-80) REVERT: A 670 MET cc_start: 0.9145 (mmp) cc_final: 0.8935 (mmm) REVERT: A 797 MET cc_start: 0.8632 (ppp) cc_final: 0.7925 (ppp) REVERT: A 1003 LEU cc_start: 0.9364 (tt) cc_final: 0.9141 (tt) REVERT: A 1004 LEU cc_start: 0.8886 (mm) cc_final: 0.8646 (mm) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1822 time to fit residues: 17.6163 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 : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 40 optimal weight: 0.0060 chunk 68 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.066616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.048473 restraints weight = 254069.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.050671 restraints weight = 123370.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.051608 restraints weight = 72491.169| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 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 = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 8592 Z= 0.126 Angle : 0.702 8.622 11835 Z= 0.341 Chirality : 0.042 0.207 1391 Planarity : 0.004 0.070 1374 Dihedral : 18.103 178.557 1649 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.36 % Favored : 90.32 % Rotamer: Outliers : 0.24 % Allowed : 0.36 % Favored : 99.40 % 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: -0.99 (0.28), residues: 942 helix: 0.13 (0.25), residues: 425 sheet: -1.26 (0.52), residues: 103 loop : -1.25 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 328 HIS 0.004 0.001 HIS A 503 PHE 0.012 0.001 PHE A 200 TYR 0.008 0.001 TYR A 467 ARG 0.006 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 344) hydrogen bonds : angle 4.77117 ( 983) covalent geometry : bond 0.00276 ( 8592) covalent geometry : angle 0.70228 (11835) *********************** 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 64 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9686 (mmp) cc_final: 0.9403 (mmm) REVERT: A 389 MET cc_start: 0.8809 (pmm) cc_final: 0.8410 (pmm) REVERT: A 440 GLN cc_start: 0.8905 (tt0) cc_final: 0.8448 (tt0) REVERT: A 483 LEU cc_start: 0.9389 (tp) cc_final: 0.9105 (tp) REVERT: A 577 MET cc_start: 0.7833 (pmm) cc_final: 0.7378 (pmm) REVERT: A 637 PHE cc_start: 0.8624 (m-80) cc_final: 0.8398 (m-80) REVERT: A 670 MET cc_start: 0.9114 (mmp) cc_final: 0.8914 (mmm) REVERT: A 797 MET cc_start: 0.8676 (ppp) cc_final: 0.7948 (ppp) REVERT: A 871 MET cc_start: 0.8660 (ptp) cc_final: 0.8417 (pmm) REVERT: A 1004 LEU cc_start: 0.8868 (mm) cc_final: 0.8633 (mm) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1614 time to fit residues: 15.9080 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 : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 59 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 85 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.3772 r_free = 0.3772 target = 0.067031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.049322 restraints weight = 200848.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.051927 restraints weight = 102321.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.052433 restraints weight = 58628.532| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 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 = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2836 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= 0.120 Angle : 0.694 8.565 11835 Z= 0.337 Chirality : 0.042 0.205 1391 Planarity : 0.004 0.071 1374 Dihedral : 18.015 179.476 1649 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.51 % Favored : 91.17 % Rotamer: Outliers : 0.24 % Allowed : 0.36 % Favored : 99.40 % 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: -1.02 (0.28), residues: 942 helix: 0.11 (0.25), residues: 426 sheet: -1.22 (0.52), residues: 103 loop : -1.29 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 328 HIS 0.003 0.001 HIS A 510 PHE 0.012 0.001 PHE A 200 TYR 0.008 0.001 TYR A 177 ARG 0.006 0.000 ARG A1158 Details of bonding type rmsd hydrogen bonds : bond 0.04124 ( 344) hydrogen bonds : angle 4.73403 ( 983) covalent geometry : bond 0.00264 ( 8592) covalent geometry : angle 0.69414 (11835) ********************** 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 67 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9688 (mmp) cc_final: 0.9403 (mmm) REVERT: A 389 MET cc_start: 0.8877 (pmm) cc_final: 0.8490 (pmm) REVERT: A 440 GLN cc_start: 0.8917 (tt0) cc_final: 0.8429 (tt0) REVERT: A 483 LEU cc_start: 0.9353 (tp) cc_final: 0.9074 (tp) REVERT: A 577 MET cc_start: 0.8021 (pmm) cc_final: 0.7578 (pmm) REVERT: A 637 PHE cc_start: 0.8750 (m-80) cc_final: 0.8492 (m-80) REVERT: A 670 MET cc_start: 0.9118 (mmp) cc_final: 0.8913 (mmm) REVERT: A 797 MET cc_start: 0.8698 (ppp) cc_final: 0.7978 (ppp) REVERT: A 934 ARG cc_start: 0.9601 (ptt-90) cc_final: 0.9373 (ptt90) REVERT: A 1004 LEU cc_start: 0.8791 (mm) cc_final: 0.8545 (mm) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1766 time to fit residues: 17.5144 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 : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 50 optimal weight: 20.0000 chunk 73 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 91 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.067686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.050121 restraints weight = 259167.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.052193 restraints weight = 121062.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.052848 restraints weight = 79004.522| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 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 = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2979 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= 0.118 Angle : 0.699 8.546 11835 Z= 0.339 Chirality : 0.042 0.202 1391 Planarity : 0.004 0.069 1374 Dihedral : 17.947 179.902 1649 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.83 % Favored : 90.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.28), residues: 942 helix: 0.18 (0.25), residues: 426 sheet: -0.86 (0.51), residues: 117 loop : -1.36 (0.33), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 328 HIS 0.003 0.001 HIS A 503 PHE 0.011 0.001 PHE A 518 TYR 0.008 0.001 TYR A 177 ARG 0.006 0.000 ARG A1158 Details of bonding type rmsd hydrogen bonds : bond 0.04046 ( 344) hydrogen bonds : angle 4.70031 ( 983) covalent geometry : bond 0.00260 ( 8592) covalent geometry : angle 0.69949 (11835) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3454.42 seconds wall clock time: 61 minutes 7.02 seconds (3667.02 seconds total)