Starting phenix.real_space_refine on Fri Jul 3 15:25:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8pjj_17711/07_2026/8pjj_17711.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pjj_17711/07_2026/8pjj_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8pjj_17711/07_2026/8pjj_17711.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8pjj_17711/07_2026/8pjj_17711.cif" model { file = "/net/cci-nas-00/data/ceres_data/8pjj_17711/07_2026/8pjj_17711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pjj_17711/07_2026/8pjj_17711.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pjj_17711/07_2026/8pjj_17711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pjj_17711/07_2026/8pjj_17711.map" } resolution = 4.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7392 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 42 5.49 5 S 47 5.16 5 C 5137 2.51 5 N 1438 2.21 5 O 1684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.14s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8348 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7474 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 946, 7463 Classifications: {'peptide': 946} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 898} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 946, 7463 Classifications: {'peptide': 946} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 898} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 7593 Chain: "B" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 847 Classifications: {'RNA': 40} Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 19, 'rna3p_pyr': 18} Link IDs: {'rna2p': 2, 'rna3p': 37} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.19, per 1000 atoms: 0.38 Number of scatterers: 8348 At special positions: 0 Unit cell: (74.56, 102.52, 137.004, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 47 16.00 P 42 15.00 O 1684 8.00 N 1438 7.00 C 5137 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 502.3 milliseconds 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: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 171 through 181 Processing helix chain 'A' and resid 223 through 242 Processing helix chain 'A' and resid 268 through 283 Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 352 through 371 Processing helix chain 'A' and resid 371 through 384 Processing helix chain 'A' and resid 385 through 388 Processing helix chain 'A' and resid 389 through 400 removed outlier: 3.741A pdb=" N ASN A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 415 removed outlier: 3.601A pdb=" N THR A 415 " --> pdb=" O GLY A 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 416 through 428 removed outlier: 3.564A pdb=" N SER A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 458 Processing helix chain 'A' and resid 486 through 494 Processing helix chain 'A' and resid 513 through 530 removed outlier: 3.585A pdb=" N ASP A 525 " --> pdb=" O VAL A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 551 Processing helix chain 'A' and resid 570 through 578 Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 636 through 651 removed outlier: 3.737A pdb=" N LEU A 640 " --> pdb=" O SER A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 676 Processing helix chain 'A' and resid 695 through 703 removed outlier: 3.785A pdb=" N GLN A 699 " --> pdb=" O PRO A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 722 removed outlier: 3.554A pdb=" N GLU A 721 " --> pdb=" O THR A 717 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR A 722 " --> pdb=" O ASN A 718 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 717 through 722' Processing helix chain 'A' and resid 758 through 767 Processing helix chain 'A' and resid 782 through 789 removed outlier: 3.584A pdb=" N LEU A 789 " --> pdb=" O ARG A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 812 Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 829 through 842 removed outlier: 3.620A pdb=" N VAL A 833 " --> pdb=" O PRO A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 862 removed outlier: 3.739A pdb=" N ARG A 861 " --> pdb=" O ARG A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 878 removed outlier: 5.040A pdb=" N MET A 871 " --> pdb=" O ARG A 867 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU A 874 " --> pdb=" O LYS A 870 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 876 " --> pdb=" O MET A 872 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 877 " --> pdb=" O VAL A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 893 Processing helix chain 'A' and resid 908 through 914 Processing helix chain 'A' and resid 920 through 937 Processing helix chain 'A' and resid 940 through 950 removed outlier: 3.923A pdb=" N ARG A 945 " --> pdb=" O HIS A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 975 Processing helix chain 'A' and resid 977 through 981 removed outlier: 3.821A pdb=" N CYS A 980 " --> pdb=" O PRO A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1008 Processing helix chain 'A' and resid 1101 through 1110 removed outlier: 3.573A pdb=" N ALA A1105 " --> pdb=" O GLU A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1125 Processing helix chain 'A' and resid 1126 through 1129 removed outlier: 3.678A pdb=" N ILE A1129 " --> pdb=" O PRO A1126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1126 through 1129' Processing helix chain 'A' and resid 1133 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 192 removed outlier: 3.689A pdb=" N LEU A 204 " --> pdb=" O ALA A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 188 through 192 Processing sheet with id=AA3, first strand: chain 'A' and resid 465 through 468 removed outlier: 7.478A pdb=" N ILE A 436 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N CYS A 485 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A 504 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N MET A 538 " --> pdb=" O ILE A 504 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A 403 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N SER A 539 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE A 405 " --> pdb=" O SER A 539 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU A 557 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE A 404 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL A 559 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ARG A 406 " --> pdb=" O VAL A 559 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 568 through 569 removed outlier: 5.252A pdb=" N PHE A 569 " --> pdb=" O THR A 779 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A 730 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N PHE A 778 " --> pdb=" O VAL A 730 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL A 732 " --> pdb=" O PHE A 778 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ALA A 655 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE A 656 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N SER A 716 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL A 658 " --> pdb=" O SER A 716 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLN A 686 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU A 715 " --> pdb=" O GLN A 686 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU A 688 " --> pdb=" O LEU A 715 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 737 through 744 removed outlier: 3.861A pdb=" N ALA A 738 " --> pdb=" O VAL A 755 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL A 755 " --> pdb=" O ALA A 738 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A 753 " --> pdb=" O MET A 740 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1055 through 1056 removed outlier: 3.880A pdb=" N SER A1062 " --> pdb=" O ILE A1056 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N CYS A1063 " --> pdb=" O ALA A1028 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU A1030 " --> pdb=" O CYS A1063 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS A1027 " --> pdb=" O THR A1023 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LYS A1020 " --> pdb=" O LYS A1016 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1090 through 1092 325 hydrogen bonds defined for protein. 933 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 1.67 Time building geometry restraints manager: 0.96 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: 5053 35.95 - 71.89: 99 71.89 - 107.84: 13 107.84 - 143.79: 3 143.79 - 179.73: 2 Dihedral angle restraints: 5170 sinusoidal: 2390 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 5167 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.270 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 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 : 15.677 179.735 3360 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.57 % Favored : 90.11 % Rotamer: Outliers : 0.72 % Allowed : 0.24 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.28), residues: 942 helix: -0.09 (0.26), residues: 415 sheet: -1.24 (0.51), residues: 113 loop : -1.20 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 375 TYR 0.009 0.001 TYR A 530 PHE 0.009 0.001 PHE A 518 TRP 0.018 0.001 TRP A 328 HIS 0.003 0.001 HIS A1032 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.15 ( 8592) covalent geometry : angle 0.75457 / 0.38 (11835) hydrogen bonds : bond 0.17642 / 12.32 ( 344) hydrogen bonds : angle 6.84802 / 4.68 ( 983) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9628 (mmp) cc_final: 0.9366 (mmm) REVERT: A 389 MET cc_start: 0.8688 (pmm) cc_final: 0.8300 (pmm) REVERT: A 483 LEU cc_start: 0.9233 (tp) cc_final: 0.9002 (tp) REVERT: A 538 MET cc_start: 0.4037 (ttt) cc_final: 0.3357 (ttt) REVERT: A 670 MET cc_start: 0.9229 (mmp) cc_final: 0.8980 (mmm) REVERT: A 797 MET cc_start: 0.8448 (ppp) cc_final: 0.7691 (ppp) REVERT: A 872 MET cc_start: 0.9050 (mmp) cc_final: 0.8832 (mmm) REVERT: A 966 GLN cc_start: 0.9527 (tt0) cc_final: 0.9254 (mp10) REVERT: A 1001 LEU cc_start: 0.9395 (tt) cc_final: 0.9191 (pp) outliers start: 4 outliers final: 1 residues processed: 67 average time/residue: 0.0619 time to fit residues: 6.5250 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 : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.0170 chunk 45 optimal weight: 6.9990 overall best weight: 2.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 684 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.065451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.047336 restraints weight = 251203.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.048793 restraints weight = 124777.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.050005 restraints weight = 77779.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.051121 restraints weight = 51368.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.051369 restraints weight = 38270.980| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 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 = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 8592 Z= 0.168 Angle : 0.734 8.495 11835 Z= 0.364 Chirality : 0.043 0.190 1391 Planarity : 0.004 0.046 1374 Dihedral : 14.985 179.207 1511 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.30 % Favored : 91.28 % Rotamer: Outliers : 0.24 % Allowed : 2.88 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.27), residues: 942 helix: -0.17 (0.24), residues: 422 sheet: -1.42 (0.52), residues: 98 loop : -1.33 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 198 TYR 0.015 0.002 TYR A 550 PHE 0.020 0.002 PHE A 200 TRP 0.020 0.001 TRP A 328 HIS 0.007 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 ( 8592) covalent geometry : angle 0.73442 / 0.36 (11835) hydrogen bonds : bond 0.05961 / 4.13 ( 344) hydrogen bonds : angle 5.44325 / 3.72 ( 983) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9659 (mmp) cc_final: 0.9403 (mmm) REVERT: A 389 MET cc_start: 0.8594 (pmm) cc_final: 0.8136 (pmm) REVERT: A 440 GLN cc_start: 0.8851 (tt0) cc_final: 0.8532 (tt0) REVERT: A 483 LEU cc_start: 0.9383 (tp) cc_final: 0.9112 (tp) REVERT: A 538 MET cc_start: 0.4211 (ttt) cc_final: 0.3952 (ttt) REVERT: A 629 MET cc_start: 0.6998 (tmm) cc_final: 0.6675 (tpp) REVERT: A 797 MET cc_start: 0.8689 (ppp) cc_final: 0.8035 (ppp) REVERT: A 1004 LEU cc_start: 0.8893 (mm) cc_final: 0.8680 (mm) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0609 time to fit residues: 6.0368 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 : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 89 optimal weight: 4.9990 chunk 38 optimal weight: 50.0000 chunk 29 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 684 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.066760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.047147 restraints weight = 192377.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.049120 restraints weight = 98197.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.050461 restraints weight = 65593.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.051746 restraints weight = 49999.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.052473 restraints weight = 40728.906| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1547 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= 0.134 Angle : 0.708 7.240 11835 Z= 0.347 Chirality : 0.043 0.190 1391 Planarity : 0.004 0.058 1374 Dihedral : 14.948 179.686 1511 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.40 % Favored : 91.17 % Rotamer: Outliers : 0.36 % Allowed : 2.64 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.27), residues: 942 helix: -0.01 (0.25), residues: 419 sheet: -1.43 (0.51), residues: 98 loop : -1.47 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 198 TYR 0.011 0.001 TYR A 550 PHE 0.018 0.001 PHE A 200 TRP 0.018 0.001 TRP A 328 HIS 0.005 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 8592) covalent geometry : angle 0.70771 / 0.35 (11835) hydrogen bonds : bond 0.04701 / 3.29 ( 344) hydrogen bonds : angle 5.00201 / 3.45 ( 983) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9667 (mmp) cc_final: 0.9391 (mmm) REVERT: A 389 MET cc_start: 0.8651 (pmm) cc_final: 0.8256 (pmm) REVERT: A 483 LEU cc_start: 0.9394 (tp) cc_final: 0.9098 (tp) REVERT: A 484 PHE cc_start: 0.9564 (m-10) cc_final: 0.9358 (m-10) REVERT: A 538 MET cc_start: 0.3745 (ttt) cc_final: 0.3330 (ttt) REVERT: A 807 LEU cc_start: 0.9566 (mt) cc_final: 0.9215 (tt) REVERT: A 871 MET cc_start: 0.8784 (ptp) cc_final: 0.8531 (pmm) REVERT: A 1001 LEU cc_start: 0.9440 (tt) cc_final: 0.9216 (pp) REVERT: A 1004 LEU cc_start: 0.8926 (mm) cc_final: 0.8689 (mm) outliers start: 1 outliers final: 0 residues processed: 64 average time/residue: 0.0730 time to fit residues: 7.0696 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 : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 94 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 81 optimal weight: 20.0000 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 GLN ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 GLN A1032 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.061297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.041961 restraints weight = 223405.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.043823 restraints weight = 110962.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.045033 restraints weight = 72551.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.046346 restraints weight = 55047.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.047096 restraints weight = 44922.151| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 8592 Z= 0.211 Angle : 0.767 9.849 11835 Z= 0.380 Chirality : 0.044 0.220 1391 Planarity : 0.005 0.079 1374 Dihedral : 15.136 179.048 1511 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 24.13 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.94 % Favored : 90.74 % Rotamer: Outliers : 0.36 % Allowed : 3.12 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.28), residues: 942 helix: -0.14 (0.24), residues: 425 sheet: -1.51 (0.49), residues: 110 loop : -1.38 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1158 TYR 0.011 0.002 TYR A 420 PHE 0.026 0.002 PHE A 200 TRP 0.024 0.002 TRP A 328 HIS 0.007 0.002 HIS A 922 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.21 ( 8592) covalent geometry : angle 0.76707 / 0.38 (11835) hydrogen bonds : bond 0.05336 / 3.74 ( 344) hydrogen bonds : angle 5.24777 / 3.62 ( 983) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9628 (mmp) cc_final: 0.9351 (mmm) REVERT: A 389 MET cc_start: 0.8778 (pmm) cc_final: 0.8372 (pmm) REVERT: A 440 GLN cc_start: 0.8942 (tt0) cc_final: 0.8456 (tt0) REVERT: A 483 LEU cc_start: 0.9393 (tp) cc_final: 0.9191 (tp) REVERT: A 871 MET cc_start: 0.8580 (ptp) cc_final: 0.8374 (pmm) REVERT: A 1004 LEU cc_start: 0.9039 (mm) cc_final: 0.8795 (mm) outliers start: 1 outliers final: 0 residues processed: 58 average time/residue: 0.0620 time to fit residues: 5.6869 Evaluate side-chains 43 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 5 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 73 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 9 optimal weight: 20.0000 chunk 80 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 ASN A 510 HIS A 684 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.065417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.046466 restraints weight = 244478.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.049345 restraints weight = 117897.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.050158 restraints weight = 69044.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.051214 restraints weight = 45705.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.051434 restraints weight = 37554.006| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 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 = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2238 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= 0.133 Angle : 0.727 8.386 11835 Z= 0.355 Chirality : 0.044 0.205 1391 Planarity : 0.004 0.066 1374 Dihedral : 14.930 178.868 1511 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.83 % Favored : 90.74 % Rotamer: Outliers : 0.24 % Allowed : 2.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.27), residues: 942 helix: -0.12 (0.24), residues: 428 sheet: -1.12 (0.55), residues: 89 loop : -1.40 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 173 TYR 0.008 0.001 TYR A 425 PHE 0.014 0.001 PHE A 200 TRP 0.017 0.001 TRP A 328 HIS 0.005 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 8592) covalent geometry : angle 0.72710 / 0.35 (11835) hydrogen bonds : bond 0.04515 / 3.14 ( 344) hydrogen bonds : angle 5.03094 / 3.49 ( 983) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9647 (mmp) cc_final: 0.9358 (mmm) REVERT: A 389 MET cc_start: 0.8722 (pmm) cc_final: 0.8341 (pmm) REVERT: A 440 GLN cc_start: 0.8973 (tt0) cc_final: 0.8607 (tt0) REVERT: A 483 LEU cc_start: 0.9398 (tp) cc_final: 0.9130 (tp) REVERT: A 538 MET cc_start: 0.2419 (ttt) cc_final: 0.1687 (ttt) REVERT: A 807 LEU cc_start: 0.9586 (mt) cc_final: 0.9232 (tt) REVERT: A 1004 LEU cc_start: 0.8919 (mm) cc_final: 0.8633 (mm) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0620 time to fit residues: 5.9132 Evaluate side-chains 42 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 2 optimal weight: 50.0000 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 38 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 684 GLN A 965 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.060508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.040954 restraints weight = 239413.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.042847 restraints weight = 114551.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.044541 restraints weight = 74730.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.045402 restraints weight = 55842.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.046431 restraints weight = 46078.295| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2857 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= 0.211 Angle : 0.761 8.649 11835 Z= 0.378 Chirality : 0.044 0.235 1391 Planarity : 0.005 0.062 1374 Dihedral : 15.221 178.972 1511 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 25.35 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.57 % Favored : 90.11 % Rotamer: Outliers : 0.24 % Allowed : 1.08 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.27), residues: 942 helix: -0.24 (0.24), residues: 425 sheet: -1.49 (0.48), residues: 110 loop : -1.35 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 867 TYR 0.013 0.002 TYR A 420 PHE 0.023 0.002 PHE A 200 TRP 0.022 0.002 TRP A 328 HIS 0.009 0.002 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.21 ( 8592) covalent geometry : angle 0.76104 / 0.38 (11835) hydrogen bonds : bond 0.05239 / 3.69 ( 344) hydrogen bonds : angle 5.25424 / 3.63 ( 983) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 358 MET cc_start: 0.9692 (mmp) cc_final: 0.9461 (mmm) REVERT: A 389 MET cc_start: 0.9046 (pmm) cc_final: 0.8761 (pmm) REVERT: A 440 GLN cc_start: 0.8896 (tt0) cc_final: 0.8356 (tt0) REVERT: A 483 LEU cc_start: 0.9425 (tp) cc_final: 0.9218 (tp) REVERT: A 538 MET cc_start: 0.1385 (ttt) cc_final: 0.1036 (ttt) REVERT: A 797 MET cc_start: 0.8901 (ppp) cc_final: 0.8244 (ppp) REVERT: A 843 MET cc_start: 0.9412 (ttp) cc_final: 0.9042 (ptm) REVERT: A 872 MET cc_start: 0.8749 (mmp) cc_final: 0.8537 (mmm) REVERT: A 1004 LEU cc_start: 0.9064 (mm) cc_final: 0.8816 (mm) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0614 time to fit residues: 5.4611 Evaluate side-chains 38 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 33 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 63 optimal weight: 0.0980 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 684 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.064007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.046668 restraints weight = 251159.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.048335 restraints weight = 106097.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.049376 restraints weight = 74096.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.050452 restraints weight = 46441.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.050697 restraints weight = 35825.379| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 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 = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2794 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= 0.133 Angle : 0.726 8.270 11835 Z= 0.355 Chirality : 0.044 0.214 1391 Planarity : 0.005 0.100 1374 Dihedral : 15.005 178.821 1511 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.36 % Favored : 90.32 % Rotamer: Outliers : 0.24 % Allowed : 0.96 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.27), residues: 942 helix: -0.16 (0.24), residues: 426 sheet: -1.45 (0.50), residues: 103 loop : -1.34 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 198 TYR 0.008 0.001 TYR A 263 PHE 0.014 0.001 PHE A 200 TRP 0.017 0.001 TRP A 328 HIS 0.004 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 8592) covalent geometry : angle 0.72557 / 0.36 (11835) hydrogen bonds : bond 0.04443 / 3.13 ( 344) hydrogen bonds : angle 5.01952 / 3.48 ( 983) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 358 MET cc_start: 0.9623 (mmp) cc_final: 0.9338 (mmm) REVERT: A 389 MET cc_start: 0.8823 (pmm) cc_final: 0.8448 (pmm) REVERT: A 440 GLN cc_start: 0.9059 (tt0) cc_final: 0.8666 (tt0) REVERT: A 483 LEU cc_start: 0.9358 (tp) cc_final: 0.9107 (tp) REVERT: A 538 MET cc_start: 0.1281 (ttt) cc_final: 0.0713 (ttt) REVERT: A 577 MET cc_start: 0.7904 (pmm) cc_final: 0.7527 (pmm) REVERT: A 797 MET cc_start: 0.8724 (ppp) cc_final: 0.8024 (ppp) REVERT: A 807 LEU cc_start: 0.9626 (mt) cc_final: 0.9286 (pp) REVERT: A 1004 LEU cc_start: 0.8972 (mm) cc_final: 0.8695 (mm) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0737 time to fit residues: 6.8021 Evaluate side-chains 43 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 97 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 18 optimal weight: 0.3980 chunk 77 optimal weight: 0.4980 chunk 50 optimal weight: 20.0000 chunk 79 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 12 optimal weight: 0.0970 chunk 71 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 684 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.063562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.044751 restraints weight = 158522.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.046600 restraints weight = 88150.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.048235 restraints weight = 61139.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.048970 restraints weight = 47162.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.049825 restraints weight = 39702.917| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 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 = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 8592 Z= 0.136 Angle : 0.721 8.029 11835 Z= 0.352 Chirality : 0.043 0.222 1391 Planarity : 0.005 0.094 1374 Dihedral : 14.885 179.553 1511 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.94 % Favored : 90.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.27), residues: 942 helix: -0.07 (0.25), residues: 425 sheet: -1.44 (0.49), residues: 103 loop : -1.39 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 173 TYR 0.011 0.001 TYR A 611 PHE 0.015 0.001 PHE A 200 TRP 0.017 0.001 TRP A 328 HIS 0.005 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 8592) covalent geometry : angle 0.72142 / 0.35 (11835) hydrogen bonds : bond 0.04453 / 3.14 ( 344) hydrogen bonds : angle 4.95057 / 3.43 ( 983) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.9621 (mmp) cc_final: 0.9339 (mmm) REVERT: A 389 MET cc_start: 0.8841 (pmm) cc_final: 0.8464 (pmm) REVERT: A 440 GLN cc_start: 0.9022 (tt0) cc_final: 0.8608 (tt0) REVERT: A 483 LEU cc_start: 0.9395 (tp) cc_final: 0.9145 (tp) REVERT: A 538 MET cc_start: 0.1107 (ttt) cc_final: 0.0754 (ttt) REVERT: A 577 MET cc_start: 0.8047 (pmm) cc_final: 0.7656 (pmm) REVERT: A 797 MET cc_start: 0.8762 (ppp) cc_final: 0.8136 (ppp) REVERT: A 807 LEU cc_start: 0.9634 (mt) cc_final: 0.9295 (tt) REVERT: A 1004 LEU cc_start: 0.8999 (mm) cc_final: 0.8756 (mm) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0780 time to fit residues: 7.0784 Evaluate side-chains 43 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 48 optimal weight: 0.0970 chunk 46 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 overall best weight: 3.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 684 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.060928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.043634 restraints weight = 236757.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.045864 restraints weight = 111708.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.046641 restraints weight = 67977.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.047401 restraints weight = 45802.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.047720 restraints weight = 39146.493| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3246 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= 0.189 Angle : 0.750 9.665 11835 Z= 0.370 Chirality : 0.044 0.234 1391 Planarity : 0.005 0.092 1374 Dihedral : 14.998 179.073 1511 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 22.17 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.36 % Favored : 90.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.27), residues: 942 helix: -0.11 (0.24), residues: 425 sheet: -1.47 (0.48), residues: 110 loop : -1.43 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 173 TYR 0.010 0.002 TYR A 420 PHE 0.021 0.002 PHE A 200 TRP 0.019 0.001 TRP A 328 HIS 0.005 0.002 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 ( 8592) covalent geometry : angle 0.74951 / 0.37 (11835) hydrogen bonds : bond 0.04960 / 3.50 ( 344) hydrogen bonds : angle 5.09173 / 3.52 ( 983) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.298 Fit side-chains REVERT: A 358 MET cc_start: 0.9611 (mmp) cc_final: 0.9323 (mmm) REVERT: A 389 MET cc_start: 0.8801 (pmm) cc_final: 0.8404 (pmm) REVERT: A 440 GLN cc_start: 0.9098 (tt0) cc_final: 0.8707 (tt0) REVERT: A 483 LEU cc_start: 0.9388 (tp) cc_final: 0.9187 (tp) REVERT: A 538 MET cc_start: 0.1308 (ttt) cc_final: 0.0946 (ttt) REVERT: A 577 MET cc_start: 0.8303 (pmm) cc_final: 0.7933 (pmm) REVERT: A 637 PHE cc_start: 0.8677 (m-80) cc_final: 0.8426 (m-80) REVERT: A 797 MET cc_start: 0.8855 (ppp) cc_final: 0.8265 (ppp) REVERT: A 1004 LEU cc_start: 0.9024 (mm) cc_final: 0.8735 (mm) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0633 time to fit residues: 5.3642 Evaluate side-chains 40 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 66 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 58 optimal weight: 0.2980 chunk 42 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 0.0060 chunk 28 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 overall best weight: 1.2602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 684 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.063637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.047058 restraints weight = 264019.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.049539 restraints weight = 105963.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.051023 restraints weight = 56213.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.050907 restraints weight = 38785.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.051102 restraints weight = 36273.263| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 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 = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3265 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= 0.134 Angle : 0.734 7.815 11835 Z= 0.359 Chirality : 0.044 0.222 1391 Planarity : 0.005 0.093 1374 Dihedral : 14.840 176.622 1511 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.15 % Favored : 90.43 % Rotamer: Outliers : 0.24 % Allowed : 0.12 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.27), residues: 942 helix: -0.11 (0.24), residues: 426 sheet: -1.53 (0.49), residues: 103 loop : -1.39 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 173 TYR 0.008 0.001 TYR A 611 PHE 0.015 0.001 PHE A 200 TRP 0.017 0.001 TRP A 328 HIS 0.004 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 8592) covalent geometry : angle 0.73441 / 0.36 (11835) hydrogen bonds : bond 0.04483 / 3.16 ( 344) hydrogen bonds : angle 4.96169 / 3.43 ( 983) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 358 MET cc_start: 0.9636 (mmp) cc_final: 0.9364 (mmm) REVERT: A 389 MET cc_start: 0.8818 (pmm) cc_final: 0.8434 (pmm) REVERT: A 440 GLN cc_start: 0.9078 (tt0) cc_final: 0.8735 (tt0) REVERT: A 483 LEU cc_start: 0.9349 (tp) cc_final: 0.9107 (tp) REVERT: A 577 MET cc_start: 0.8292 (pmm) cc_final: 0.7905 (pmm) REVERT: A 637 PHE cc_start: 0.8709 (m-80) cc_final: 0.8448 (m-80) REVERT: A 797 MET cc_start: 0.8841 (ppp) cc_final: 0.8242 (ppp) REVERT: A 1004 LEU cc_start: 0.8988 (mm) cc_final: 0.8745 (mm) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0687 time to fit residues: 6.2726 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 : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 71 optimal weight: 4.9990 chunk 60 optimal weight: 0.0010 chunk 63 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 3 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 overall best weight: 2.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 684 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.062193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.042921 restraints weight = 212755.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.044824 restraints weight = 104097.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.046207 restraints weight = 69133.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.047535 restraints weight = 52717.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.048152 restraints weight = 42763.977| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 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 = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 8592 Z= 0.149 Angle : 0.727 7.687 11835 Z= 0.357 Chirality : 0.043 0.228 1391 Planarity : 0.005 0.091 1374 Dihedral : 14.877 176.962 1511 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 19.53 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.83 % Favored : 90.74 % Rotamer: Outliers : 0.24 % Allowed : 0.12 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.27), residues: 942 helix: -0.04 (0.25), residues: 426 sheet: -1.57 (0.49), residues: 103 loop : -1.41 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 173 TYR 0.009 0.001 TYR A 550 PHE 0.017 0.002 PHE A 200 TRP 0.017 0.001 TRP A 328 HIS 0.004 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 8592) covalent geometry : angle 0.72678 / 0.36 (11835) hydrogen bonds : bond 0.04597 / 3.25 ( 344) hydrogen bonds : angle 4.96113 / 3.43 ( 983) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1842.04 seconds wall clock time: 32 minutes 31.74 seconds (1951.74 seconds total)