Starting phenix.real_space_refine on Wed Sep 17 15:56:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5n_44218/09_2025/9b5n_44218.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5n_44218/09_2025/9b5n_44218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b5n_44218/09_2025/9b5n_44218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5n_44218/09_2025/9b5n_44218.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b5n_44218/09_2025/9b5n_44218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5n_44218/09_2025/9b5n_44218.map" } resolution = 3.12 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= 0.064 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 2 5.21 5 S 42 5.16 5 C 6074 2.51 5 N 1573 2.21 5 O 1833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9527 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7734 Classifications: {'peptide': 985} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 928} Chain breaks: 1 Chain: "C" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1158 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131} Chain: "D" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 596 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'A1AIV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.80, per 1000 atoms: 0.19 Number of scatterers: 9527 At special positions: 0 Unit cell: (100.016, 100.016, 119.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 3 15.00 Mg 2 11.99 O 1833 8.00 N 1573 7.00 C 6074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS C 85 " distance=2.91 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 266.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 10 sheets defined 47.3% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.909A pdb=" N TYR A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 36 Processing helix chain 'A' and resid 46 through 60 Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.709A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.886A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.342A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LYS A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 123 Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.781A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 3.521A pdb=" N ASP A 223 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.273A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.672A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN A 296 " --> pdb=" O HIS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 332 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 354 through 375 Processing helix chain 'A' and resid 389 through 392 Processing helix chain 'A' and resid 399 through 404 Processing helix chain 'A' and resid 410 through 418 removed outlier: 4.481A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.541A pdb=" N SER A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 450 Processing helix chain 'A' and resid 468 through 474 removed outlier: 3.648A pdb=" N ASN A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'A' and resid 486 through 499 Processing helix chain 'A' and resid 500 through 503 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.667A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 528 removed outlier: 3.901A pdb=" N LYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.519A pdb=" N ARG A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 Processing helix chain 'A' and resid 591 through 597 removed outlier: 3.506A pdb=" N ASN A 597 " --> pdb=" O CYS A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 618 Processing helix chain 'A' and resid 618 through 630 Processing helix chain 'A' and resid 632 through 641 removed outlier: 3.687A pdb=" N LYS A 639 " --> pdb=" O GLU A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 656 Processing helix chain 'A' and resid 662 through 679 removed outlier: 3.564A pdb=" N CYS A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 689 removed outlier: 3.574A pdb=" N GLN A 683 " --> pdb=" O ASN A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 737 Processing helix chain 'A' and resid 743 through 753 removed outlier: 4.016A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 794 removed outlier: 3.818A pdb=" N GLN A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 818 through 834 Processing helix chain 'A' and resid 840 through 849 Processing helix chain 'A' and resid 855 through 876 removed outlier: 3.529A pdb=" N THR A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.567A pdb=" N GLU A 882 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR A 883 " --> pdb=" O ILE A 880 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 879 through 883' Processing helix chain 'A' and resid 926 through 937 Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 969 through 979 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 98 through 112 removed outlier: 3.649A pdb=" N VAL C 102 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU C 103 " --> pdb=" O ILE C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 130 Processing helix chain 'C' and resid 130 through 145 Processing helix chain 'D' and resid 22 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.841A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N THR A 129 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ILE A 43 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYR A 385 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 172 Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 228 removed outlier: 4.117A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL A 193 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 228 removed outlier: 4.117A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 506 through 509 removed outlier: 6.441A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER A 559 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 905 through 908 Processing sheet with id=AA7, first strand: chain 'A' and resid 920 through 922 removed outlier: 6.340A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL A 990 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N SER A 947 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU A 992 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU A 945 " --> pdb=" O GLU A 992 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N CYS A 994 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LEU A 951 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 920 through 922 removed outlier: 6.340A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N CYS A 995 " --> pdb=" O VAL A1003 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 25 through 26 removed outlier: 6.141A pdb=" N HIS C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS C 66 " --> pdb=" O HIS C 55 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 12 through 16 460 hydrogen bonds defined for protein. 1257 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.06 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1616 1.27 - 1.40: 2291 1.40 - 1.54: 5675 1.54 - 1.67: 92 1.67 - 1.81: 64 Bond restraints: 9738 Sorted by residual: bond pdb=" C04 A1AIV D 101 " pdb=" C05 A1AIV D 101 " ideal model delta sigma weight residual 1.453 1.526 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " ideal model delta sigma weight residual 1.531 1.518 0.013 1.20e-02 6.94e+03 1.20e+00 bond pdb=" C05 A1AIV D 101 " pdb=" N06 A1AIV D 101 " ideal model delta sigma weight residual 1.151 1.132 0.019 2.00e-02 2.50e+03 9.18e-01 bond pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 1.416 1.405 0.011 1.30e-02 5.92e+03 6.94e-01 ... (remaining 9733 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 13068 1.60 - 3.19: 73 3.19 - 4.79: 48 4.79 - 6.38: 1 6.38 - 7.98: 5 Bond angle restraints: 13195 Sorted by residual: angle pdb=" C LYS A 381 " pdb=" N GLN A 382 " pdb=" CA GLN A 382 " ideal model delta sigma weight residual 121.70 128.17 -6.47 1.80e+00 3.09e-01 1.29e+01 angle pdb=" C2' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O3' ATP A1103 " ideal model delta sigma weight residual 111.83 104.50 7.33 2.67e+00 1.40e-01 7.55e+00 angle pdb=" C3' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" C5' ATP A1103 " ideal model delta sigma weight residual 115.19 110.36 4.83 1.76e+00 3.23e-01 7.53e+00 angle pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 106.53 103.33 3.20 1.18e+00 7.24e-01 7.41e+00 angle pdb=" C03 A1AIV D 101 " pdb=" C02 A1AIV D 101 " pdb=" N01 A1AIV D 101 " ideal model delta sigma weight residual 111.06 103.08 7.98 3.00e+00 1.11e-01 7.07e+00 ... (remaining 13190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 5713 17.09 - 34.18: 166 34.18 - 51.27: 42 51.27 - 68.36: 6 68.36 - 85.45: 2 Dihedral angle restraints: 5929 sinusoidal: 2424 harmonic: 3505 Sorted by residual: dihedral pdb=" CB CYS A 593 " pdb=" SG CYS A 593 " pdb=" SG CYS C 85 " pdb=" CB CYS C 85 " ideal model delta sinusoidal sigma weight residual -86.00 -142.75 56.75 1 1.00e+01 1.00e-02 4.34e+01 dihedral pdb=" CA TYR C 60 " pdb=" C TYR C 60 " pdb=" N PRO C 61 " pdb=" CA PRO C 61 " ideal model delta harmonic sigma weight residual 0.00 28.00 -28.00 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA LYS A 884 " pdb=" C LYS A 884 " pdb=" N ASN A 885 " pdb=" CA ASN A 885 " ideal model delta harmonic sigma weight residual 180.00 163.77 16.23 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 5926 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1307 0.061 - 0.122: 145 0.122 - 0.183: 16 0.183 - 0.243: 1 0.243 - 0.304: 2 Chirality restraints: 1471 Sorted by residual: chirality pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O2' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C3' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" O3' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C4' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" C5' ATP A1103 " pdb=" O4' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.49 -2.73 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 1468 not shown) Planarity restraints: 1707 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 100 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" C SER C 100 " -0.036 2.00e-02 2.50e+03 pdb=" O SER C 100 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS C 101 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 103 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C LEU C 103 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU C 103 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU C 104 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 3 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C LEU C 3 " -0.030 2.00e-02 2.50e+03 pdb=" O LEU C 3 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS C 4 " 0.010 2.00e-02 2.50e+03 ... (remaining 1704 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 63 2.58 - 3.16: 8029 3.16 - 3.74: 13805 3.74 - 4.32: 20329 4.32 - 4.90: 34667 Nonbonded interactions: 76893 Sorted by model distance: nonbonded pdb=" OD2 ASP A 463 " pdb=" O3' ATP A1103 " model vdw 2.000 3.040 nonbonded pdb="MG MG A1102 " pdb=" O1B ATP A1103 " model vdw 2.033 2.170 nonbonded pdb=" OD2 ASP A 465 " pdb="MG MG A1102 " model vdw 2.039 2.170 nonbonded pdb="MG MG A1101 " pdb=" O2B ATP A1103 " model vdw 2.055 2.170 nonbonded pdb=" OD2 ASP A 537 " pdb="MG MG A1101 " model vdw 2.067 2.170 ... (remaining 76888 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 4.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.230 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:1.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 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 : 0.010 0.876 9741 Z= 0.479 Angle : 0.630 46.177 13197 Z= 0.313 Chirality : 0.042 0.304 1471 Planarity : 0.004 0.038 1707 Dihedral : 9.091 85.450 3662 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.50 % Favored : 97.25 % Rotamer: Outliers : 0.66 % Allowed : 3.68 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.25), residues: 1199 helix: 1.54 (0.25), residues: 482 sheet: 0.09 (0.36), residues: 211 loop : 0.32 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 409 TYR 0.011 0.001 TYR C 60 PHE 0.010 0.001 PHE A 842 TRP 0.005 0.001 TRP A 669 HIS 0.003 0.001 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9738) covalent geometry : angle 0.46590 (13195) SS BOND : bond 0.87569 ( 1) SS BOND : angle 34.50478 ( 2) hydrogen bonds : bond 0.14945 ( 447) hydrogen bonds : angle 5.85561 ( 1257) Misc. bond : bond 0.07573 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 181 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.8464 (mmp) cc_final: 0.8222 (mmm) REVERT: A 299 SER cc_start: 0.8395 (t) cc_final: 0.8161 (m) REVERT: A 368 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7985 (mm-30) REVERT: A 380 LEU cc_start: 0.8392 (mt) cc_final: 0.8039 (mp) REVERT: A 442 MET cc_start: 0.8989 (tpp) cc_final: 0.8658 (mmm) REVERT: A 723 ASP cc_start: 0.8116 (m-30) cc_final: 0.7791 (m-30) REVERT: A 869 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7853 (mm-30) REVERT: A 919 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8530 (ptp-170) REVERT: A 1011 LYS cc_start: 0.8423 (ttmm) cc_final: 0.8073 (tppt) REVERT: C 72 ARG cc_start: 0.8474 (mmm-85) cc_final: 0.8126 (mmm-85) outliers start: 7 outliers final: 3 residues processed: 185 average time/residue: 0.1275 time to fit residues: 30.1842 Evaluate side-chains 138 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 133 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.135218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.088826 restraints weight = 13484.471| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.98 r_work: 0.2996 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9741 Z= 0.157 Angle : 0.528 6.317 13197 Z= 0.278 Chirality : 0.043 0.185 1471 Planarity : 0.004 0.042 1707 Dihedral : 6.446 85.529 1339 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.50 % Favored : 97.41 % Rotamer: Outliers : 1.79 % Allowed : 7.07 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.25), residues: 1199 helix: 1.75 (0.24), residues: 489 sheet: 0.35 (0.37), residues: 211 loop : 0.22 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 201 TYR 0.009 0.001 TYR A 235 PHE 0.012 0.001 PHE A 842 TRP 0.009 0.001 TRP C 93 HIS 0.004 0.001 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 9738) covalent geometry : angle 0.52574 (13195) SS BOND : bond 0.00478 ( 1) SS BOND : angle 4.20486 ( 2) hydrogen bonds : bond 0.04330 ( 447) hydrogen bonds : angle 4.75991 ( 1257) Misc. bond : bond 0.00113 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.8816 (mtp) cc_final: 0.8543 (mmm) REVERT: A 51 GLU cc_start: 0.8443 (tp30) cc_final: 0.8202 (tp30) REVERT: A 80 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.7522 (tm-30) REVERT: A 196 MET cc_start: 0.8489 (mmp) cc_final: 0.8250 (mmm) REVERT: A 201 ARG cc_start: 0.6857 (mtp-110) cc_final: 0.6383 (mtp-110) REVERT: A 205 GLU cc_start: 0.7722 (tt0) cc_final: 0.7237 (pm20) REVERT: A 299 SER cc_start: 0.8257 (t) cc_final: 0.7901 (m) REVERT: A 368 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8079 (mm-30) REVERT: A 380 LEU cc_start: 0.8323 (mt) cc_final: 0.7959 (mp) REVERT: A 442 MET cc_start: 0.8570 (tpp) cc_final: 0.8022 (mmm) REVERT: A 626 MET cc_start: 0.7980 (ttm) cc_final: 0.7715 (ttm) REVERT: A 919 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8122 (ptp-170) REVERT: A 1011 LYS cc_start: 0.8564 (ttmm) cc_final: 0.7987 (tppt) REVERT: C 59 ASP cc_start: 0.8255 (m-30) cc_final: 0.7876 (t0) REVERT: C 72 ARG cc_start: 0.8803 (mmm-85) cc_final: 0.8413 (mmm-85) REVERT: C 97 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6775 (pt) REVERT: C 104 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7625 (pp) REVERT: C 135 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7456 (mm-30) REVERT: D 49 GLN cc_start: 0.7225 (mp10) cc_final: 0.6989 (mp10) outliers start: 19 outliers final: 8 residues processed: 142 average time/residue: 0.1130 time to fit residues: 21.3347 Evaluate side-chains 133 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain D residue 70 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 17 optimal weight: 10.0000 chunk 27 optimal weight: 0.0270 chunk 34 optimal weight: 0.5980 chunk 104 optimal weight: 0.6980 chunk 23 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 57 optimal weight: 0.0020 overall best weight: 0.3846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.135623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.088172 restraints weight = 13338.831| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.20 r_work: 0.2958 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9741 Z= 0.109 Angle : 0.477 6.887 13197 Z= 0.248 Chirality : 0.041 0.137 1471 Planarity : 0.003 0.044 1707 Dihedral : 6.150 88.418 1333 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.17 % Favored : 97.75 % Rotamer: Outliers : 1.60 % Allowed : 8.58 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.25), residues: 1199 helix: 1.83 (0.24), residues: 488 sheet: 0.36 (0.37), residues: 211 loop : 0.27 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 133 TYR 0.011 0.001 TYR A 119 PHE 0.009 0.001 PHE A 842 TRP 0.007 0.001 TRP C 93 HIS 0.002 0.001 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9738) covalent geometry : angle 0.47525 (13195) SS BOND : bond 0.00140 ( 1) SS BOND : angle 3.75593 ( 2) hydrogen bonds : bond 0.03610 ( 447) hydrogen bonds : angle 4.49069 ( 1257) Misc. bond : bond 0.00038 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8410 (tp30) cc_final: 0.8138 (tp30) REVERT: A 80 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.7265 (tm-30) REVERT: A 196 MET cc_start: 0.8466 (mmp) cc_final: 0.8241 (mmm) REVERT: A 201 ARG cc_start: 0.6757 (mtp-110) cc_final: 0.6244 (mtp-110) REVERT: A 218 MET cc_start: 0.6232 (mmm) cc_final: 0.5952 (mmm) REVERT: A 299 SER cc_start: 0.8190 (t) cc_final: 0.7839 (m) REVERT: A 368 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7987 (mm-30) REVERT: A 380 LEU cc_start: 0.8305 (mt) cc_final: 0.7886 (mp) REVERT: A 442 MET cc_start: 0.8451 (tpp) cc_final: 0.7888 (mmm) REVERT: A 626 MET cc_start: 0.7990 (ttm) cc_final: 0.7663 (ttt) REVERT: A 739 LYS cc_start: 0.8601 (tptp) cc_final: 0.7712 (ptpt) REVERT: A 869 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7600 (mm-30) REVERT: A 1011 LYS cc_start: 0.8521 (ttmm) cc_final: 0.7987 (tppt) REVERT: C 38 MET cc_start: 0.7831 (mmp) cc_final: 0.7062 (mmt) REVERT: C 59 ASP cc_start: 0.8274 (m-30) cc_final: 0.7814 (t0) REVERT: C 72 ARG cc_start: 0.8748 (mmm-85) cc_final: 0.8349 (mmm-85) REVERT: C 97 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6699 (pt) REVERT: C 104 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7564 (pp) REVERT: D 49 GLN cc_start: 0.7407 (mp10) cc_final: 0.7167 (mp10) outliers start: 17 outliers final: 9 residues processed: 133 average time/residue: 0.1210 time to fit residues: 21.3669 Evaluate side-chains 129 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 70 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 100 optimal weight: 0.3980 chunk 70 optimal weight: 0.4980 chunk 87 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 88 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.134771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.087191 restraints weight = 13573.141| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.28 r_work: 0.2945 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9741 Z= 0.127 Angle : 0.484 9.119 13197 Z= 0.252 Chirality : 0.042 0.170 1471 Planarity : 0.004 0.045 1707 Dihedral : 5.680 71.096 1328 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.42 % Favored : 97.50 % Rotamer: Outliers : 2.07 % Allowed : 9.05 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.25), residues: 1199 helix: 1.74 (0.24), residues: 495 sheet: 0.38 (0.37), residues: 215 loop : 0.31 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 133 TYR 0.009 0.001 TYR C 60 PHE 0.009 0.001 PHE A 842 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9738) covalent geometry : angle 0.48360 (13195) SS BOND : bond 0.01854 ( 1) SS BOND : angle 2.11771 ( 2) hydrogen bonds : bond 0.03564 ( 447) hydrogen bonds : angle 4.41706 ( 1257) Misc. bond : bond 0.00005 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8451 (tp30) cc_final: 0.8155 (tp30) REVERT: A 80 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.7473 (tm-30) REVERT: A 196 MET cc_start: 0.8482 (mmp) cc_final: 0.8275 (mmm) REVERT: A 201 ARG cc_start: 0.6775 (mtp-110) cc_final: 0.6269 (mtp-110) REVERT: A 218 MET cc_start: 0.6149 (mmm) cc_final: 0.5787 (mmm) REVERT: A 299 SER cc_start: 0.8194 (t) cc_final: 0.7825 (m) REVERT: A 380 LEU cc_start: 0.8394 (mt) cc_final: 0.8074 (mp) REVERT: A 442 MET cc_start: 0.8479 (tpp) cc_final: 0.7917 (mmm) REVERT: A 626 MET cc_start: 0.7998 (ttm) cc_final: 0.7645 (ttt) REVERT: A 723 ASP cc_start: 0.8260 (m-30) cc_final: 0.7800 (m-30) REVERT: A 739 LYS cc_start: 0.8603 (tptp) cc_final: 0.7717 (ptpt) REVERT: A 869 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7599 (mm-30) REVERT: A 1011 LYS cc_start: 0.8558 (ttmm) cc_final: 0.7985 (tppt) REVERT: C 38 MET cc_start: 0.7949 (mmp) cc_final: 0.7180 (mmt) REVERT: C 59 ASP cc_start: 0.8234 (m-30) cc_final: 0.7799 (t0) REVERT: C 72 ARG cc_start: 0.8767 (mmm-85) cc_final: 0.8377 (mmm-85) REVERT: C 97 LEU cc_start: 0.7241 (pt) cc_final: 0.6738 (pt) REVERT: C 104 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7567 (pp) REVERT: C 131 ARG cc_start: 0.8455 (mmm-85) cc_final: 0.8098 (mmm160) REVERT: D 49 GLN cc_start: 0.7618 (mp10) cc_final: 0.7384 (mp10) outliers start: 22 outliers final: 14 residues processed: 137 average time/residue: 0.1235 time to fit residues: 22.3734 Evaluate side-chains 132 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 70 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 21 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 118 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.133655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.086093 restraints weight = 13503.697| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.98 r_work: 0.2962 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9741 Z= 0.148 Angle : 0.493 8.936 13197 Z= 0.256 Chirality : 0.042 0.165 1471 Planarity : 0.004 0.046 1707 Dihedral : 5.743 74.642 1328 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.09 % Favored : 97.83 % Rotamer: Outliers : 2.07 % Allowed : 9.43 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.25), residues: 1199 helix: 1.61 (0.24), residues: 501 sheet: 0.32 (0.37), residues: 214 loop : 0.34 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 8 TYR 0.010 0.001 TYR D 59 PHE 0.010 0.001 PHE A 842 TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 9738) covalent geometry : angle 0.49283 (13195) SS BOND : bond 0.01168 ( 1) SS BOND : angle 1.59537 ( 2) hydrogen bonds : bond 0.03731 ( 447) hydrogen bonds : angle 4.37239 ( 1257) Misc. bond : bond 0.00074 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.7523 (tm-30) REVERT: A 201 ARG cc_start: 0.6833 (mtp-110) cc_final: 0.6359 (mtp-110) REVERT: A 218 MET cc_start: 0.5982 (mmm) cc_final: 0.5635 (mmm) REVERT: A 299 SER cc_start: 0.8270 (t) cc_final: 0.7899 (m) REVERT: A 380 LEU cc_start: 0.8439 (mt) cc_final: 0.8130 (mp) REVERT: A 442 MET cc_start: 0.8577 (tpp) cc_final: 0.7996 (mmm) REVERT: A 526 PHE cc_start: 0.9188 (OUTLIER) cc_final: 0.8955 (m-80) REVERT: A 626 MET cc_start: 0.8103 (ttm) cc_final: 0.7754 (ttt) REVERT: A 646 GLU cc_start: 0.8197 (mp0) cc_final: 0.7979 (mp0) REVERT: A 668 MET cc_start: 0.7973 (mmm) cc_final: 0.7759 (mmm) REVERT: A 739 LYS cc_start: 0.8609 (tptp) cc_final: 0.7750 (ptpt) REVERT: A 869 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7607 (mp0) REVERT: A 937 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7562 (mp0) REVERT: A 1011 LYS cc_start: 0.8612 (ttmm) cc_final: 0.8041 (tppt) REVERT: C 8 ARG cc_start: 0.7845 (ttm110) cc_final: 0.7530 (mtm180) REVERT: C 59 ASP cc_start: 0.8232 (m-30) cc_final: 0.7772 (t0) REVERT: C 131 ARG cc_start: 0.8463 (mmm-85) cc_final: 0.8207 (mmm-85) REVERT: D 49 GLN cc_start: 0.7780 (mp10) cc_final: 0.7544 (mp10) outliers start: 22 outliers final: 16 residues processed: 134 average time/residue: 0.1127 time to fit residues: 20.0298 Evaluate side-chains 132 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.133081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.085379 restraints weight = 13501.053| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.97 r_work: 0.2932 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9741 Z= 0.164 Angle : 0.500 8.196 13197 Z= 0.259 Chirality : 0.042 0.161 1471 Planarity : 0.004 0.046 1707 Dihedral : 5.863 74.410 1328 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.17 % Favored : 97.75 % Rotamer: Outliers : 2.36 % Allowed : 9.05 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.25), residues: 1199 helix: 1.56 (0.24), residues: 501 sheet: 0.19 (0.35), residues: 221 loop : 0.24 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 54 TYR 0.016 0.001 TYR D 59 PHE 0.010 0.001 PHE A 842 TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 9738) covalent geometry : angle 0.49953 (13195) SS BOND : bond 0.00563 ( 1) SS BOND : angle 1.29955 ( 2) hydrogen bonds : bond 0.03863 ( 447) hydrogen bonds : angle 4.37396 ( 1257) Misc. bond : bond 0.00106 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.7271 (tm-30) REVERT: A 201 ARG cc_start: 0.6898 (mtp-110) cc_final: 0.6431 (mtp-110) REVERT: A 299 SER cc_start: 0.8257 (t) cc_final: 0.7902 (m) REVERT: A 442 MET cc_start: 0.8545 (tpp) cc_final: 0.7883 (mpp) REVERT: A 526 PHE cc_start: 0.9156 (OUTLIER) cc_final: 0.8927 (m-80) REVERT: A 626 MET cc_start: 0.8073 (ttm) cc_final: 0.7788 (ttm) REVERT: A 646 GLU cc_start: 0.8255 (mp0) cc_final: 0.7965 (mp0) REVERT: A 668 MET cc_start: 0.7913 (mmm) cc_final: 0.7697 (mmm) REVERT: A 739 LYS cc_start: 0.8603 (tptp) cc_final: 0.7739 (ptpt) REVERT: A 869 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: A 1011 LYS cc_start: 0.8585 (ttmm) cc_final: 0.7995 (tppt) REVERT: C 8 ARG cc_start: 0.7785 (ttm110) cc_final: 0.7437 (mtm180) REVERT: C 38 MET cc_start: 0.7913 (mmp) cc_final: 0.7052 (mmt) REVERT: C 59 ASP cc_start: 0.8152 (m-30) cc_final: 0.7703 (t0) REVERT: C 131 ARG cc_start: 0.8455 (mmm-85) cc_final: 0.8234 (mmm-85) REVERT: D 3 ILE cc_start: 0.9186 (pt) cc_final: 0.8976 (mp) REVERT: D 48 LYS cc_start: 0.8869 (tppt) cc_final: 0.8656 (tppt) REVERT: D 49 GLN cc_start: 0.7734 (mp10) cc_final: 0.7434 (mp10) outliers start: 25 outliers final: 17 residues processed: 139 average time/residue: 0.1082 time to fit residues: 20.2779 Evaluate side-chains 134 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 57 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 25 optimal weight: 0.0870 chunk 79 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.133784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.086108 restraints weight = 13446.774| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.97 r_work: 0.2947 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9741 Z= 0.130 Angle : 0.499 10.948 13197 Z= 0.258 Chirality : 0.041 0.148 1471 Planarity : 0.004 0.045 1707 Dihedral : 5.740 66.903 1328 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.17 % Favored : 97.75 % Rotamer: Outliers : 2.26 % Allowed : 9.80 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.25), residues: 1199 helix: 1.72 (0.24), residues: 495 sheet: 0.21 (0.35), residues: 221 loop : 0.21 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 54 TYR 0.023 0.001 TYR D 59 PHE 0.009 0.001 PHE A 842 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9738) covalent geometry : angle 0.49908 (13195) SS BOND : bond 0.00923 ( 1) SS BOND : angle 0.97371 ( 2) hydrogen bonds : bond 0.03568 ( 447) hydrogen bonds : angle 4.29834 ( 1257) Misc. bond : bond 0.00082 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.7272 (tm-30) REVERT: A 201 ARG cc_start: 0.6902 (mtp-110) cc_final: 0.6429 (mtp-110) REVERT: A 218 MET cc_start: 0.6061 (mmm) cc_final: 0.5558 (mmm) REVERT: A 299 SER cc_start: 0.8252 (t) cc_final: 0.7890 (m) REVERT: A 306 GLU cc_start: 0.8997 (mp0) cc_final: 0.8745 (mp0) REVERT: A 333 GLN cc_start: 0.8393 (mp10) cc_final: 0.7923 (tm-30) REVERT: A 442 MET cc_start: 0.8498 (tpp) cc_final: 0.7932 (mmm) REVERT: A 526 PHE cc_start: 0.9133 (OUTLIER) cc_final: 0.8899 (m-80) REVERT: A 626 MET cc_start: 0.8065 (ttm) cc_final: 0.7779 (ttm) REVERT: A 646 GLU cc_start: 0.8335 (mp0) cc_final: 0.8087 (mp0) REVERT: A 668 MET cc_start: 0.7879 (mmm) cc_final: 0.7673 (mmm) REVERT: A 739 LYS cc_start: 0.8596 (tptp) cc_final: 0.7735 (ptpt) REVERT: A 869 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7615 (mp0) REVERT: A 937 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7562 (mp0) REVERT: A 944 MET cc_start: 0.8146 (ttp) cc_final: 0.7607 (ttp) REVERT: A 1011 LYS cc_start: 0.8562 (ttmm) cc_final: 0.7976 (tppt) REVERT: C 8 ARG cc_start: 0.7749 (ttm110) cc_final: 0.7410 (mtm180) REVERT: C 38 MET cc_start: 0.7853 (mmp) cc_final: 0.7052 (mmt) REVERT: C 59 ASP cc_start: 0.8193 (m-30) cc_final: 0.7681 (t0) REVERT: D 3 ILE cc_start: 0.9181 (pt) cc_final: 0.8956 (mp) REVERT: D 48 LYS cc_start: 0.8887 (tppt) cc_final: 0.8562 (tppt) REVERT: D 49 GLN cc_start: 0.7838 (mp10) cc_final: 0.7533 (mp10) REVERT: D 59 TYR cc_start: 0.7174 (m-80) cc_final: 0.6583 (m-10) outliers start: 24 outliers final: 18 residues processed: 137 average time/residue: 0.1024 time to fit residues: 19.1244 Evaluate side-chains 137 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 63 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 68 optimal weight: 0.0870 chunk 39 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 78 optimal weight: 0.0040 chunk 73 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.5370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.133932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.086759 restraints weight = 13333.268| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.16 r_work: 0.2942 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9741 Z= 0.120 Angle : 0.487 9.470 13197 Z= 0.252 Chirality : 0.041 0.149 1471 Planarity : 0.004 0.041 1707 Dihedral : 5.645 63.132 1328 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.25 % Favored : 97.66 % Rotamer: Outliers : 2.17 % Allowed : 9.80 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.25), residues: 1199 helix: 1.76 (0.24), residues: 494 sheet: 0.22 (0.35), residues: 221 loop : 0.22 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 133 TYR 0.017 0.001 TYR A 119 PHE 0.009 0.001 PHE A 842 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9738) covalent geometry : angle 0.48726 (13195) SS BOND : bond 0.00888 ( 1) SS BOND : angle 0.69256 ( 2) hydrogen bonds : bond 0.03458 ( 447) hydrogen bonds : angle 4.25475 ( 1257) Misc. bond : bond 0.00014 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.7233 (tm-30) REVERT: A 201 ARG cc_start: 0.6878 (mtp-110) cc_final: 0.6397 (mtp-110) REVERT: A 218 MET cc_start: 0.6180 (mmm) cc_final: 0.5688 (mmm) REVERT: A 299 SER cc_start: 0.8253 (t) cc_final: 0.7885 (m) REVERT: A 306 GLU cc_start: 0.9008 (mp0) cc_final: 0.8753 (mp0) REVERT: A 442 MET cc_start: 0.8539 (tpp) cc_final: 0.8005 (mmm) REVERT: A 526 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8901 (m-80) REVERT: A 626 MET cc_start: 0.8060 (ttm) cc_final: 0.7771 (ttm) REVERT: A 646 GLU cc_start: 0.8362 (mp0) cc_final: 0.8064 (mp0) REVERT: A 739 LYS cc_start: 0.8602 (tptp) cc_final: 0.7738 (ptpt) REVERT: A 869 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7598 (mm-30) REVERT: A 937 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: A 944 MET cc_start: 0.8146 (ttp) cc_final: 0.7622 (ttp) REVERT: A 1011 LYS cc_start: 0.8564 (ttmm) cc_final: 0.7976 (tppt) REVERT: C 8 ARG cc_start: 0.7766 (ttm110) cc_final: 0.7367 (mtm180) REVERT: C 38 MET cc_start: 0.7843 (mmp) cc_final: 0.7045 (mmt) REVERT: C 59 ASP cc_start: 0.8185 (m-30) cc_final: 0.7672 (t0) REVERT: C 83 SER cc_start: 0.8652 (m) cc_final: 0.8119 (p) REVERT: C 135 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7074 (mm-30) REVERT: D 3 ILE cc_start: 0.9165 (pt) cc_final: 0.8936 (mp) REVERT: D 48 LYS cc_start: 0.8914 (tppt) cc_final: 0.8655 (tppt) REVERT: D 49 GLN cc_start: 0.7991 (mp10) cc_final: 0.7782 (mp10) outliers start: 23 outliers final: 18 residues processed: 137 average time/residue: 0.1123 time to fit residues: 20.7215 Evaluate side-chains 137 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 95 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 9 optimal weight: 0.3980 chunk 62 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 76 optimal weight: 0.1980 chunk 26 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 118 optimal weight: 0.0670 chunk 52 optimal weight: 0.7980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.134452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.086857 restraints weight = 13388.875| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.97 r_work: 0.2957 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9741 Z= 0.108 Angle : 0.488 9.031 13197 Z= 0.252 Chirality : 0.041 0.146 1471 Planarity : 0.004 0.041 1707 Dihedral : 5.574 62.708 1328 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.34 % Favored : 97.58 % Rotamer: Outliers : 1.98 % Allowed : 9.90 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.25), residues: 1199 helix: 1.81 (0.24), residues: 494 sheet: 0.29 (0.35), residues: 220 loop : 0.23 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 133 TYR 0.016 0.001 TYR A 119 PHE 0.008 0.001 PHE A 842 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9738) covalent geometry : angle 0.48765 (13195) SS BOND : bond 0.01039 ( 1) SS BOND : angle 0.75795 ( 2) hydrogen bonds : bond 0.03286 ( 447) hydrogen bonds : angle 4.20362 ( 1257) Misc. bond : bond 0.00070 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7177 (tm-30) REVERT: A 201 ARG cc_start: 0.6873 (mtp-110) cc_final: 0.6492 (mtp-110) REVERT: A 218 MET cc_start: 0.6130 (mmm) cc_final: 0.5605 (mmm) REVERT: A 299 SER cc_start: 0.8250 (t) cc_final: 0.7881 (m) REVERT: A 333 GLN cc_start: 0.8420 (mp10) cc_final: 0.7944 (tm-30) REVERT: A 442 MET cc_start: 0.8521 (tpp) cc_final: 0.7990 (mmm) REVERT: A 526 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.8894 (m-80) REVERT: A 626 MET cc_start: 0.8050 (ttm) cc_final: 0.7712 (ttt) REVERT: A 646 GLU cc_start: 0.8353 (mp0) cc_final: 0.8047 (mp0) REVERT: A 739 LYS cc_start: 0.8514 (tptp) cc_final: 0.7574 (ptpt) REVERT: A 869 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7575 (mm-30) REVERT: A 944 MET cc_start: 0.8140 (ttp) cc_final: 0.7651 (ttp) REVERT: A 1011 LYS cc_start: 0.8554 (ttmm) cc_final: 0.7968 (tppt) REVERT: C 8 ARG cc_start: 0.7765 (ttm110) cc_final: 0.7387 (mtm180) REVERT: C 38 MET cc_start: 0.7825 (mmp) cc_final: 0.7037 (mmt) REVERT: C 59 ASP cc_start: 0.8196 (m-30) cc_final: 0.7700 (t0) REVERT: C 83 SER cc_start: 0.8668 (m) cc_final: 0.8256 (p) REVERT: C 104 LEU cc_start: 0.8109 (mm) cc_final: 0.7467 (pp) REVERT: D 3 ILE cc_start: 0.9158 (pt) cc_final: 0.8930 (mp) REVERT: D 40 GLN cc_start: 0.7071 (tt0) cc_final: 0.6221 (tp40) REVERT: D 49 GLN cc_start: 0.7900 (mp10) cc_final: 0.7695 (mp10) outliers start: 21 outliers final: 18 residues processed: 133 average time/residue: 0.1136 time to fit residues: 20.2075 Evaluate side-chains 136 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 1 optimal weight: 0.9990 chunk 102 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 78 optimal weight: 0.0570 chunk 72 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 82 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.134060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.086472 restraints weight = 13406.224| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.98 r_work: 0.2953 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9741 Z= 0.126 Angle : 0.503 8.785 13197 Z= 0.259 Chirality : 0.041 0.144 1471 Planarity : 0.004 0.042 1707 Dihedral : 5.558 57.501 1328 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.25 % Favored : 97.66 % Rotamer: Outliers : 1.98 % Allowed : 9.99 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.25), residues: 1199 helix: 1.78 (0.24), residues: 494 sheet: 0.29 (0.35), residues: 220 loop : 0.23 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 74 TYR 0.022 0.001 TYR A 235 PHE 0.009 0.001 PHE A 842 TRP 0.005 0.001 TRP A 669 HIS 0.003 0.001 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9738) covalent geometry : angle 0.50307 (13195) SS BOND : bond 0.00683 ( 1) SS BOND : angle 0.75388 ( 2) hydrogen bonds : bond 0.03404 ( 447) hydrogen bonds : angle 4.20588 ( 1257) Misc. bond : bond 0.00010 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.7190 (tm-30) REVERT: A 201 ARG cc_start: 0.6904 (mtp-110) cc_final: 0.6531 (mtp-110) REVERT: A 218 MET cc_start: 0.6141 (mmm) cc_final: 0.5620 (mmm) REVERT: A 299 SER cc_start: 0.8264 (t) cc_final: 0.7891 (m) REVERT: A 333 GLN cc_start: 0.8375 (mp10) cc_final: 0.7950 (tm-30) REVERT: A 442 MET cc_start: 0.8528 (tpp) cc_final: 0.7990 (mmm) REVERT: A 526 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.8891 (m-80) REVERT: A 626 MET cc_start: 0.8053 (ttm) cc_final: 0.7712 (ttt) REVERT: A 646 GLU cc_start: 0.8356 (mp0) cc_final: 0.8041 (mp0) REVERT: A 739 LYS cc_start: 0.8507 (tptp) cc_final: 0.7570 (ptpt) REVERT: A 869 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7586 (mm-30) REVERT: A 944 MET cc_start: 0.8170 (ttp) cc_final: 0.7646 (ttp) REVERT: A 1011 LYS cc_start: 0.8583 (ttmm) cc_final: 0.7985 (tppt) REVERT: C 8 ARG cc_start: 0.7749 (ttm110) cc_final: 0.7353 (mtm180) REVERT: C 38 MET cc_start: 0.7799 (mmp) cc_final: 0.6982 (mmt) REVERT: C 59 ASP cc_start: 0.8190 (m-30) cc_final: 0.7681 (t0) REVERT: C 83 SER cc_start: 0.8666 (m) cc_final: 0.8269 (p) REVERT: C 104 LEU cc_start: 0.8118 (mm) cc_final: 0.7469 (pp) REVERT: C 135 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7209 (mm-30) REVERT: D 3 ILE cc_start: 0.9163 (pt) cc_final: 0.8930 (mp) outliers start: 21 outliers final: 17 residues processed: 132 average time/residue: 0.1159 time to fit residues: 20.5786 Evaluate side-chains 135 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 66 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 116 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 64 optimal weight: 0.0270 chunk 16 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.132450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.083616 restraints weight = 13678.983| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.99 r_work: 0.2942 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9741 Z= 0.150 Angle : 0.521 10.467 13197 Z= 0.266 Chirality : 0.042 0.148 1471 Planarity : 0.004 0.043 1707 Dihedral : 5.597 57.215 1328 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.17 % Favored : 97.75 % Rotamer: Outliers : 2.07 % Allowed : 10.18 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.25), residues: 1199 helix: 1.72 (0.24), residues: 495 sheet: 0.23 (0.35), residues: 220 loop : 0.20 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 133 TYR 0.019 0.001 TYR A 235 PHE 0.009 0.001 PHE A 842 TRP 0.007 0.001 TRP A 669 HIS 0.002 0.001 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 9738) covalent geometry : angle 0.52072 (13195) SS BOND : bond 0.00650 ( 1) SS BOND : angle 0.89928 ( 2) hydrogen bonds : bond 0.03649 ( 447) hydrogen bonds : angle 4.24965 ( 1257) Misc. bond : bond 0.00068 ( 2) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2227.14 seconds wall clock time: 38 minutes 38.30 seconds (2318.30 seconds total)