Starting phenix.real_space_refine on Fri Jun 13 07:37:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pjj_17711/06_2025/8pjj_17711.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pjj_17711/06_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_17711/06_2025/8pjj_17711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pjj_17711/06_2025/8pjj_17711.map" model { file = "/net/cci-nas-00/data/ceres_data/8pjj_17711/06_2025/8pjj_17711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pjj_17711/06_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): 0.57s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 10.39, per 1000 atoms: 1.24 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: 2.32 Conformation dependent library (CDL) restraints added in 2.0 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: 3.19 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: 3.23 Time building geometry restraints manager: 2.79 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: 6.750 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 33.140 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.070 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.760 ------------------------------------------------------------------------------- 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 : 1.115 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: 0.1904 time to fit residues: 19.6036 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 : 0.917 ------------------------------------------------------------------------------- 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 = 50)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.045187 restraints weight = 192529.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.047097 restraints weight = 101047.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.048661 restraints weight = 68328.065| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 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 : 0.819 Fit side-chains revert: symmetry clash REVERT: A 169 ASN cc_start: 0.9212 (p0) cc_final: 0.9009 (t0) REVERT: A 358 MET cc_start: 0.9671 (mmp) cc_final: 0.9409 (mmm) REVERT: A 389 MET cc_start: 0.8668 (pmm) cc_final: 0.8255 (pmm) REVERT: A 440 GLN cc_start: 0.8819 (tt0) cc_final: 0.8474 (tt0) REVERT: A 483 LEU cc_start: 0.9435 (tp) cc_final: 0.9162 (tp) REVERT: A 538 MET cc_start: 0.4229 (ttt) cc_final: 0.3952 (ttt) REVERT: A 629 MET cc_start: 0.6932 (tmm) cc_final: 0.6659 (tpp) REVERT: A 797 MET cc_start: 0.8825 (ppp) cc_final: 0.8220 (ppp) REVERT: A 1004 LEU cc_start: 0.8959 (mm) cc_final: 0.8741 (mm) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1526 time to fit residues: 14.7203 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 : 0.817 ------------------------------------------------------------------------------- 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: 2.9990 chunk 22 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 36 optimal weight: 0.0570 chunk 55 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 2 optimal weight: 30.0000 overall best weight: 1.5702 ------------------------------------------------------------------------------- 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 = 0.3747 r_free = 0.3747 target = 0.065872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.049049 restraints weight = 257864.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.050317 restraints weight = 122127.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.051683 restraints weight = 70364.298| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1495 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= 0.137 Angle : 0.703 7.706 11835 Z= 0.345 Chirality : 0.043 0.196 1391 Planarity : 0.004 0.046 1374 Dihedral : 18.534 179.112 1649 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.72 % Favored : 90.85 % Rotamer: Outliers : 0.36 % Allowed : 2.16 % Favored : 97.48 % 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: -1.27 (0.27), residues: 942 helix: -0.06 (0.24), residues: 425 sheet: -1.47 (0.51), residues: 98 loop : -1.44 (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 0.011 0.001 TYR A 550 ARG 0.007 0.001 ARG A 198 Details of bonding type rmsd hydrogen bonds : bond 0.04858 ( 344) hydrogen bonds : angle 5.09050 ( 983) covalent geometry : bond 0.00297 ( 8592) covalent geometry : angle 0.70253 (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 64 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.838 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: 0.9469 (mmm) REVERT: A 389 MET cc_start: 0.8770 (pmm) cc_final: 0.8363 (pmm) REVERT: A 483 LEU cc_start: 0.9408 (tp) cc_final: 0.9127 (tp) REVERT: A 538 MET cc_start: 0.4086 (ttt) cc_final: 0.3822 (ttt) REVERT: A 807 LEU cc_start: 0.9578 (mt) cc_final: 0.9218 (tt) REVERT: A 1004 LEU cc_start: 0.8976 (mm) cc_final: 0.8730 (mm) outliers start: 1 outliers final: 0 residues processed: 64 average time/residue: 0.2089 time to fit residues: 20.0076 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 : 0.975 ------------------------------------------------------------------------------- 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: 6.9990 chunk 32 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 = 0.3650 r_free = 0.3650 target = 0.061532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.043677 restraints weight = 229775.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.045824 restraints weight = 114242.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.046119 restraints weight = 74315.067| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2222 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= 0.201 Angle : 0.752 8.062 11835 Z= 0.373 Chirality : 0.044 0.222 1391 Planarity : 0.005 0.077 1374 Dihedral : 18.595 179.137 1649 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 23.64 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.26 % Favored : 90.43 % Rotamer: Outliers : 0.36 % Allowed : 2.88 % Favored : 96.75 % 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: -1.33 (0.27), residues: 942 helix: -0.12 (0.24), residues: 425 sheet: -1.54 (0.49), residues: 108 loop : -1.42 (0.33), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 328 HIS 0.006 0.002 HIS A 922 PHE 0.023 0.002 PHE A 200 TYR 0.010 0.002 TYR A1009 ARG 0.008 0.001 ARG A 867 Details of bonding type rmsd hydrogen bonds : bond 0.05179 ( 344) hydrogen bonds : angle 5.26654 ( 983) covalent geometry : bond 0.00420 ( 8592) covalent geometry : angle 0.75247 (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 59 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: A 358 MET cc_start: 0.9654 (mmp) cc_final: 0.9386 (mmm) REVERT: A 389 MET cc_start: 0.8799 (pmm) cc_final: 0.8377 (pmm) REVERT: A 440 GLN cc_start: 0.8877 (tt0) cc_final: 0.8433 (tt0) REVERT: A 483 LEU cc_start: 0.9449 (tp) cc_final: 0.9237 (tp) REVERT: A 629 MET cc_start: 0.7455 (tmm) cc_final: 0.7095 (tpp) REVERT: A 1003 LEU cc_start: 0.9422 (tt) cc_final: 0.9129 (tt) REVERT: A 1006 LEU cc_start: 0.9602 (tp) cc_final: 0.9339 (pp) outliers start: 1 outliers final: 0 residues processed: 59 average time/residue: 0.1713 time to fit residues: 15.5189 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 : 0.814 ------------------------------------------------------------------------------- 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: 0.9990 chunk 22 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 12 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 19 optimal weight: 0.0570 chunk 67 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 overall best weight: 0.7300 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.065613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.047768 restraints weight = 262076.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.050535 restraints weight = 129599.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.051442 restraints weight = 64881.410| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 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 = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2208 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 : 0.725 8.353 11835 Z= 0.354 Chirality : 0.044 0.208 1391 Planarity : 0.004 0.064 1374 Dihedral : 18.414 179.339 1649 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.26 % Favored : 90.43 % Rotamer: Outliers : 0.24 % Allowed : 2.16 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.23 (0.27), residues: 942 helix: -0.09 (0.24), residues: 426 sheet: -1.19 (0.55), residues: 89 loop : -1.42 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 328 HIS 0.006 0.001 HIS A 503 PHE 0.013 0.001 PHE A 200 TYR 0.008 0.001 TYR A 530 ARG 0.016 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.04474 ( 344) hydrogen bonds : angle 5.03980 ( 983) covalent geometry : bond 0.00286 ( 8592) covalent geometry : angle 0.72517 (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 60 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9690 (mmp) cc_final: 0.9425 (mmm) REVERT: A 389 MET cc_start: 0.8740 (pmm) cc_final: 0.8348 (pmm) REVERT: A 440 GLN cc_start: 0.9041 (tt0) cc_final: 0.8481 (tt0) REVERT: A 483 LEU cc_start: 0.9392 (tp) cc_final: 0.9135 (tp) REVERT: A 484 PHE cc_start: 0.9584 (m-80) cc_final: 0.9266 (m-10) REVERT: A 538 MET cc_start: 0.2512 (ttt) cc_final: 0.1739 (ttt) REVERT: A 807 LEU cc_start: 0.9604 (mt) cc_final: 0.9217 (tt) REVERT: A 1001 LEU cc_start: 0.9505 (tt) cc_final: 0.9277 (pp) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.2194 time to fit residues: 20.0853 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 : 0.917 ------------------------------------------------------------------------------- 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: 0.9990 chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 50.0000 chunk 39 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.065709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.045934 restraints weight = 198297.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.047964 restraints weight = 99991.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.049645 restraints weight = 66787.448| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 8592 Z= 0.127 Angle : 0.707 9.338 11835 Z= 0.343 Chirality : 0.043 0.213 1391 Planarity : 0.005 0.087 1374 Dihedral : 18.299 179.221 1649 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.72 % Favored : 90.96 % Rotamer: Outliers : 0.24 % Allowed : 0.96 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.22 (0.28), residues: 942 helix: -0.08 (0.25), residues: 425 sheet: -1.46 (0.50), residues: 103 loop : -1.32 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 328 HIS 0.007 0.001 HIS A 510 PHE 0.014 0.001 PHE A 200 TYR 0.009 0.001 TYR A 550 ARG 0.005 0.000 ARG A 198 Details of bonding type rmsd hydrogen bonds : bond 0.04323 ( 344) hydrogen bonds : angle 4.94118 ( 983) covalent geometry : bond 0.00278 ( 8592) covalent geometry : angle 0.70733 (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 62 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9666 (mmp) cc_final: 0.9390 (mmm) REVERT: A 389 MET cc_start: 0.8790 (pmm) cc_final: 0.8398 (pmm) REVERT: A 440 GLN cc_start: 0.9011 (tt0) cc_final: 0.8432 (tt0) REVERT: A 483 LEU cc_start: 0.9421 (tp) cc_final: 0.9157 (tp) REVERT: A 484 PHE cc_start: 0.9572 (m-80) cc_final: 0.9278 (m-10) REVERT: A 538 MET cc_start: 0.1415 (ttt) cc_final: 0.1019 (ttt) REVERT: A 629 MET cc_start: 0.6546 (tmm) cc_final: 0.5802 (tpp) REVERT: A 797 MET cc_start: 0.8634 (ppp) cc_final: 0.7933 (ppp) REVERT: A 807 LEU cc_start: 0.9609 (mt) cc_final: 0.9296 (tt) REVERT: A 871 MET cc_start: 0.8716 (ptp) cc_final: 0.8509 (pmm) REVERT: A 872 MET cc_start: 0.8998 (mmp) cc_final: 0.8771 (mmm) REVERT: A 1001 LEU cc_start: 0.9477 (tt) cc_final: 0.9246 (pp) REVERT: A 1004 LEU cc_start: 0.8884 (mm) cc_final: 0.8652 (mm) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1674 time to fit residues: 15.8305 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 : 0.836 ------------------------------------------------------------------------------- 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: 7.9990 chunk 12 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 59 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 38 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 87 optimal weight: 0.4980 chunk 89 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 684 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.064952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.047658 restraints weight = 301864.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.050490 restraints weight = 116712.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.051706 restraints weight = 61097.728| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 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 = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2616 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= 0.134 Angle : 0.703 8.107 11835 Z= 0.343 Chirality : 0.043 0.216 1391 Planarity : 0.004 0.076 1374 Dihedral : 18.247 178.940 1649 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.15 % Favored : 90.43 % Rotamer: Outliers : 0.24 % Allowed : 0.72 % 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: -1.12 (0.28), residues: 942 helix: 0.03 (0.25), residues: 423 sheet: -1.46 (0.50), residues: 103 loop : -1.29 (0.32), residues: 416 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 0.014 0.001 PHE A 200 TYR 0.010 0.001 TYR A 263 ARG 0.007 0.001 ARG A1158 Details of bonding type rmsd hydrogen bonds : bond 0.04300 ( 344) hydrogen bonds : angle 4.92898 ( 983) covalent geometry : bond 0.00290 ( 8592) covalent geometry : angle 0.70324 (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 61 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9692 (mmp) cc_final: 0.9431 (mmm) REVERT: A 389 MET cc_start: 0.8877 (pmm) cc_final: 0.8497 (pmm) REVERT: A 440 GLN cc_start: 0.9007 (tt0) cc_final: 0.8386 (tt0) REVERT: A 483 LEU cc_start: 0.9356 (tp) cc_final: 0.9102 (tp) REVERT: A 484 PHE cc_start: 0.9611 (m-80) cc_final: 0.9328 (m-10) REVERT: A 538 MET cc_start: 0.1147 (ttt) cc_final: 0.0783 (ttt) REVERT: A 577 MET cc_start: 0.7837 (pmm) cc_final: 0.7485 (pmm) REVERT: A 797 MET cc_start: 0.8678 (ppp) cc_final: 0.7971 (ppp) REVERT: A 1001 LEU cc_start: 0.9514 (tt) cc_final: 0.9310 (pp) REVERT: A 1003 LEU cc_start: 0.9355 (tt) cc_final: 0.9108 (tt) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.2009 time to fit residues: 18.2064 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 : 0.879 ------------------------------------------------------------------------------- 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: 0.6980 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 49 optimal weight: 0.0050 chunk 38 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.066615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.046616 restraints weight = 223210.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.048788 restraints weight = 106475.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.050620 restraints weight = 68401.159| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- 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: 0.8386 moved from start: 0.2760 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= 0.122 Angle : 0.706 8.264 11835 Z= 0.341 Chirality : 0.043 0.209 1391 Planarity : 0.004 0.068 1374 Dihedral : 18.169 179.928 1649 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.04 % Favored : 90.64 % Rotamer: Outliers : 0.24 % Allowed : 0.72 % 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: -1.10 (0.28), residues: 942 helix: 0.05 (0.25), residues: 424 sheet: -1.35 (0.51), residues: 103 loop : -1.30 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 328 HIS 0.005 0.001 HIS A 510 PHE 0.013 0.001 PHE A 898 TYR 0.008 0.001 TYR A 177 ARG 0.006 0.000 ARG A1158 Details of bonding type rmsd hydrogen bonds : bond 0.04150 ( 344) hydrogen bonds : angle 4.81417 ( 983) covalent geometry : bond 0.00265 ( 8592) covalent geometry : angle 0.70591 (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 61 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9662 (mmp) cc_final: 0.9381 (mmm) REVERT: A 389 MET cc_start: 0.8773 (pmm) cc_final: 0.8391 (pmm) REVERT: A 440 GLN cc_start: 0.9029 (tt0) cc_final: 0.8477 (tt0) REVERT: A 483 LEU cc_start: 0.9401 (tp) cc_final: 0.9133 (tp) REVERT: A 484 PHE cc_start: 0.9577 (m-80) cc_final: 0.9286 (m-10) REVERT: A 577 MET cc_start: 0.7964 (pmm) cc_final: 0.7537 (pmm) REVERT: A 797 MET cc_start: 0.8615 (ppp) cc_final: 0.7894 (ppp) REVERT: A 957 MET cc_start: 0.9502 (ppp) cc_final: 0.9295 (ppp) REVERT: A 1004 LEU cc_start: 0.8823 (mm) cc_final: 0.8612 (mm) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1887 time to fit residues: 17.1375 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 : 0.892 ------------------------------------------------------------------------------- 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: 5.9990 chunk 33 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 chunk 72 optimal weight: 0.6980 chunk 40 optimal weight: 0.1980 chunk 68 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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 = 0.3744 r_free = 0.3744 target = 0.065372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.047853 restraints weight = 256314.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.050228 restraints weight = 124621.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.051128 restraints weight = 66339.099| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 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 = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2891 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= 0.127 Angle : 0.691 7.804 11835 Z= 0.335 Chirality : 0.042 0.213 1391 Planarity : 0.004 0.067 1374 Dihedral : 18.113 179.884 1649 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.83 % Favored : 90.85 % 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: -1.06 (0.28), residues: 942 helix: 0.09 (0.25), residues: 424 sheet: -1.40 (0.51), residues: 103 loop : -1.27 (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 0.013 0.001 PHE A 200 TYR 0.008 0.001 TYR A 550 ARG 0.008 0.000 ARG A1158 Details of bonding type rmsd hydrogen bonds : bond 0.04209 ( 344) hydrogen bonds : angle 4.79544 ( 983) covalent geometry : bond 0.00278 ( 8592) covalent geometry : angle 0.69076 (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 62 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 2.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9690 (mmp) cc_final: 0.9425 (mmm) REVERT: A 389 MET cc_start: 0.8919 (pmm) cc_final: 0.8538 (pmm) REVERT: A 440 GLN cc_start: 0.9020 (tt0) cc_final: 0.8495 (tt0) REVERT: A 483 LEU cc_start: 0.9352 (tp) cc_final: 0.9090 (tp) REVERT: A 484 PHE cc_start: 0.9629 (m-80) cc_final: 0.9303 (m-10) REVERT: A 577 MET cc_start: 0.8183 (pmm) cc_final: 0.7789 (pmm) REVERT: A 637 PHE cc_start: 0.8727 (m-80) cc_final: 0.8455 (m-80) REVERT: A 797 MET cc_start: 0.8661 (ppp) cc_final: 0.7950 (ppp) REVERT: A 1001 LEU cc_start: 0.9485 (tt) cc_final: 0.9250 (pp) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2014 time to fit residues: 19.3160 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 : 0.821 ------------------------------------------------------------------------------- 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: 0.7980 chunk 60 optimal weight: 0.2980 chunk 25 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 74 optimal weight: 0.3980 chunk 85 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 51 optimal weight: 40.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.066088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.046621 restraints weight = 202702.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.048682 restraints weight = 100460.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.050143 restraints weight = 66176.080| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 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 = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3004 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= 0.123 Angle : 0.705 8.984 11835 Z= 0.340 Chirality : 0.042 0.210 1391 Planarity : 0.004 0.067 1374 Dihedral : 18.074 179.371 1649 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.51 % Favored : 91.17 % Rotamer: Outliers : 0.24 % Allowed : 0.60 % Favored : 99.16 % 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: -1.07 (0.28), residues: 942 helix: 0.07 (0.25), residues: 424 sheet: -1.37 (0.51), residues: 103 loop : -1.29 (0.32), residues: 415 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 0.009 0.000 ARG A 844 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 344) hydrogen bonds : angle 4.79713 ( 983) covalent geometry : bond 0.00270 ( 8592) covalent geometry : angle 0.70472 (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 63 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9652 (mmp) cc_final: 0.9372 (mmm) REVERT: A 389 MET cc_start: 0.8812 (pmm) cc_final: 0.8440 (pmm) REVERT: A 440 GLN cc_start: 0.9016 (tt0) cc_final: 0.8577 (tt0) REVERT: A 483 LEU cc_start: 0.9379 (tp) cc_final: 0.9106 (tp) REVERT: A 484 PHE cc_start: 0.9576 (m-80) cc_final: 0.9290 (m-10) REVERT: A 577 MET cc_start: 0.8172 (pmm) cc_final: 0.7756 (pmm) REVERT: A 637 PHE cc_start: 0.8725 (m-80) cc_final: 0.8481 (m-80) REVERT: A 797 MET cc_start: 0.8667 (ppp) cc_final: 0.7962 (ppp) REVERT: A 807 LEU cc_start: 0.9620 (mt) cc_final: 0.9277 (tt) REVERT: A 896 GLU cc_start: 0.8658 (pp20) cc_final: 0.8227 (pp20) REVERT: A 1004 LEU cc_start: 0.8829 (mm) cc_final: 0.8611 (mm) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.2332 time to fit residues: 21.5980 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 : 0.860 ------------------------------------------------------------------------------- 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: 0.0270 chunk 15 optimal weight: 6.9990 chunk 42 optimal weight: 0.4980 chunk 9 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 16 optimal weight: 0.2980 chunk 69 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 overall best weight: 1.5642 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.065087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.046912 restraints weight = 263179.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.048677 restraints weight = 115604.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.049816 restraints weight = 78659.637| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 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 = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3132 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= 0.129 Angle : 0.698 8.521 11835 Z= 0.338 Chirality : 0.042 0.214 1391 Planarity : 0.004 0.068 1374 Dihedral : 18.092 179.356 1649 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.15 % 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: -1.02 (0.28), residues: 942 helix: 0.12 (0.25), residues: 426 sheet: -1.38 (0.51), residues: 103 loop : -1.26 (0.32), residues: 413 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 0.013 0.001 PHE A 200 TYR 0.008 0.001 TYR A 420 ARG 0.004 0.000 ARG A1158 Details of bonding type rmsd hydrogen bonds : bond 0.04202 ( 344) hydrogen bonds : angle 4.80685 ( 983) covalent geometry : bond 0.00283 ( 8592) covalent geometry : angle 0.69807 (11835) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4041.49 seconds wall clock time: 73 minutes 6.55 seconds (4386.55 seconds total)