Starting phenix.real_space_refine on Thu May 1 02:39:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5e_44209/05_2025/9b5e_44209.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5e_44209/05_2025/9b5e_44209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b5e_44209/05_2025/9b5e_44209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5e_44209/05_2025/9b5e_44209.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5e_44209/05_2025/9b5e_44209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5e_44209/05_2025/9b5e_44209.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.072 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 43 5.16 5 C 6449 2.51 5 N 1678 2.21 5 O 1953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 10128 Number of models: 1 Model: "" Number of chains: 6 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: "B" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 73} 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: 6.40, per 1000 atoms: 0.63 Number of scatterers: 10128 At special positions: 0 Unit cell: (92.568, 98.952, 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 43 16.00 P 3 15.00 Mg 2 11.99 O 1953 8.00 N 1678 7.00 C 6449 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=2.92 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: 3.19 Conformation dependent library (CDL) restraints added in 1.3 seconds 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2404 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 11 sheets defined 46.4% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.758A 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 73 through 79 removed outlier: 3.643A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.331A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 123 removed outlier: 3.646A pdb=" N LYS A 121 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN A 122 " --> pdb=" O TYR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.645A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 3.570A pdb=" N ASP A 223 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.388A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.647A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.617A 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 410 through 418 removed outlier: 4.356A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.549A 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: 3.644A 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: 3.776A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 528 removed outlier: 3.830A pdb=" N LYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.587A pdb=" N ARG A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.544A pdb=" N SER A 581 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER A 582 " --> pdb=" O TYR A 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 578 through 582' Processing helix chain 'A' and resid 591 through 597 Processing helix chain 'A' and resid 601 through 618 Processing helix chain 'A' and resid 618 through 628 Processing helix chain 'A' and resid 632 through 641 removed outlier: 3.571A pdb=" N THR A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) removed outlier: 3.794A 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: 3.711A pdb=" N CYS A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 689 removed outlier: 3.504A 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: 3.935A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 794 removed outlier: 3.795A 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 835 Processing helix chain 'A' and resid 840 through 849 Processing helix chain 'A' and resid 855 through 876 removed outlier: 3.518A pdb=" N THR A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.706A pdb=" N GLU A 882 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.787A 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 938 Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 969 through 979 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'C' and resid 98 through 112 Processing helix chain 'C' and resid 120 through 130 Processing helix chain 'C' and resid 130 through 146 Processing helix chain 'D' and resid 22 through 35 Processing helix chain 'D' and resid 37 through 41 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: 6.851A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.308A 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: 4.097A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL A 193 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 228 removed outlier: 4.097A 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: 6.507A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.264A 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: 6.316A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N VAL A 990 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N SER A 947 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.757A 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: 6.670A pdb=" N CYS A 994 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.381A 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: 6.316A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N CYS A 995 " --> pdb=" O VAL A1003 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 12 through 16 removed outlier: 3.850A pdb=" N ARG B 42 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 24 through 26 removed outlier: 3.625A pdb=" N GLY C 24 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N HIS C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 12 through 16 removed outlier: 4.130A pdb=" N SER D 65 " --> pdb=" O GLN D 2 " (cutoff:3.500A) 491 hydrogen bonds defined for protein. 1323 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: 3.58 Time building geometry restraints manager: 3.00 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: 1723 1.27 - 1.40: 2410 1.40 - 1.54: 5989 1.54 - 1.67: 156 1.67 - 1.81: 66 Bond restraints: 10344 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 2.93e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.66e+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 8.97e-01 bond pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " ideal model delta sigma weight residual 1.531 1.520 0.011 1.20e-02 6.94e+03 8.42e-01 ... (remaining 10339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 13840 1.32 - 2.65: 89 2.65 - 3.97: 70 3.97 - 5.29: 6 5.29 - 6.61: 4 Bond angle restraints: 14009 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 121.70 128.18 -6.48 1.80e+00 3.09e-01 1.29e+01 angle pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 106.53 103.40 3.13 1.18e+00 7.24e-01 7.09e+00 angle pdb=" C3' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" C5' ATP A1103 " ideal model delta sigma weight residual 115.19 110.51 4.68 1.76e+00 3.23e-01 7.08e+00 angle pdb=" C2' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O3' ATP A1103 " ideal model delta sigma weight residual 111.83 105.26 6.57 2.67e+00 1.40e-01 6.06e+00 angle pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" O2' ATP A1103 " ideal model delta sigma weight residual 110.58 103.97 6.61 2.79e+00 1.28e-01 5.60e+00 ... (remaining 14004 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.31: 6043 16.31 - 32.63: 204 32.63 - 48.94: 46 48.94 - 65.26: 12 65.26 - 81.57: 3 Dihedral angle restraints: 6308 sinusoidal: 2587 harmonic: 3721 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 -138.95 52.95 1 1.00e+01 1.00e-02 3.82e+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 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" N GLN A 80 " pdb=" CA GLN A 80 " pdb=" CB GLN A 80 " pdb=" CG GLN A 80 " ideal model delta sinusoidal sigma weight residual -180.00 -122.88 -57.12 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 6305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1390 0.060 - 0.119: 154 0.119 - 0.179: 21 0.179 - 0.238: 1 0.238 - 0.298: 2 Chirality restraints: 1568 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 2.22e+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 -2.91 0.28 2.00e-01 2.50e+01 1.91e+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 1.35e+00 ... (remaining 1565 not shown) Planarity restraints: 1812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 94 " 0.026 5.00e-02 4.00e+02 3.91e-02 2.44e+00 pdb=" N PRO C 95 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 120 " -0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO C 121 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO C 121 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 121 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 17 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO C 18 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO C 18 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 18 " 0.016 5.00e-02 4.00e+02 ... (remaining 1809 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 76 2.61 - 3.18: 8766 3.18 - 3.75: 14660 3.75 - 4.33: 22165 4.33 - 4.90: 37204 Nonbonded interactions: 82871 Sorted by model distance: nonbonded pdb="MG MG A1101 " pdb=" O2B ATP A1103 " model vdw 2.037 2.170 nonbonded pdb=" OD2 ASP A 465 " pdb="MG MG A1102 " model vdw 2.043 2.170 nonbonded pdb=" OD2 ASP A 537 " pdb="MG MG A1101 " model vdw 2.078 2.170 nonbonded pdb=" O PRO C 18 " pdb=" OG SER C 19 " model vdw 2.171 3.040 nonbonded pdb=" OD2 ASP A 463 " pdb=" O3' ATP A1103 " model vdw 2.188 3.040 ... (remaining 82866 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 Found NCS groups: ncs_group { reference = (chain 'B' and resid 1 through 75) selection = (chain 'D' and resid 1 through 75) } 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: 3.140 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: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.440 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 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:13.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 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 : 0.009 0.886 10347 Z= 0.464 Angle : 0.588 43.917 14011 Z= 0.290 Chirality : 0.042 0.298 1568 Planarity : 0.003 0.039 1812 Dihedral : 9.403 81.569 3901 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.15 % Allowed : 1.77 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.24), residues: 1273 helix: 1.63 (0.24), residues: 501 sheet: 0.67 (0.34), residues: 207 loop : 0.42 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 669 HIS 0.002 0.000 HIS C 75 PHE 0.011 0.001 PHE A 360 TYR 0.007 0.001 TYR A 732 ARG 0.002 0.000 ARG A 409 Details of bonding type rmsd hydrogen bonds : bond 0.14235 ( 478) hydrogen bonds : angle 5.90132 ( 1323) SS BOND : bond 0.88634 ( 1) SS BOND : angle 32.47940 ( 2) covalent geometry : bond 0.00264 (10344) covalent geometry : angle 0.44156 (14009) Misc. bond : bond 0.08054 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 1.086 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.6708 (mtp85) cc_final: 0.6036 (mtm-85) REVERT: A 85 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7656 (mp0) REVERT: A 114 GLU cc_start: 0.8066 (pt0) cc_final: 0.7849 (pt0) REVERT: A 184 MET cc_start: 0.8244 (mtp) cc_final: 0.7836 (mtt) REVERT: A 191 ASP cc_start: 0.8097 (m-30) cc_final: 0.7717 (p0) REVERT: A 218 MET cc_start: 0.7520 (mtt) cc_final: 0.7300 (mtt) REVERT: A 235 TYR cc_start: 0.8284 (m-80) cc_final: 0.7971 (m-80) REVERT: A 274 ASP cc_start: 0.7507 (t70) cc_final: 0.6991 (p0) REVERT: A 353 ASP cc_start: 0.7930 (t0) cc_final: 0.7436 (t0) REVERT: A 442 MET cc_start: 0.8059 (tpp) cc_final: 0.7605 (mmm) REVERT: A 540 GLU cc_start: 0.7531 (tt0) cc_final: 0.7041 (mp0) REVERT: A 558 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7742 (tm-30) REVERT: A 601 ARG cc_start: 0.7457 (mtp85) cc_final: 0.6977 (mtp180) REVERT: A 668 MET cc_start: 0.7197 (mmm) cc_final: 0.6796 (mpp) REVERT: A 723 ASP cc_start: 0.7168 (m-30) cc_final: 0.6862 (m-30) REVERT: A 879 LYS cc_start: 0.8133 (mmmm) cc_final: 0.7398 (mtmt) REVERT: A 909 ASN cc_start: 0.7583 (t0) cc_final: 0.7189 (t0) REVERT: A 937 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: A 1011 LYS cc_start: 0.8274 (ttmm) cc_final: 0.8042 (ttmm) REVERT: B 39 ASP cc_start: 0.8348 (m-30) cc_final: 0.8031 (p0) REVERT: C 34 GLN cc_start: 0.8535 (tt0) cc_final: 0.8155 (tt0) REVERT: C 66 LYS cc_start: 0.8044 (mtmt) cc_final: 0.7840 (mttp) REVERT: C 72 ARG cc_start: 0.8280 (mmm-85) cc_final: 0.7625 (tpt170) REVERT: C 92 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7603 (tm-30) REVERT: C 117 ASP cc_start: 0.8409 (t0) cc_final: 0.8089 (t0) outliers start: 13 outliers final: 2 residues processed: 167 average time/residue: 1.5692 time to fit residues: 280.2394 Evaluate side-chains 121 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 118 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.0470 chunk 95 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 0.0010 chunk 60 optimal weight: 0.9990 chunk 73 optimal weight: 0.3980 chunk 114 optimal weight: 3.9990 overall best weight: 0.3084 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.139893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.098350 restraints weight = 12036.082| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.10 r_work: 0.2968 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10347 Z= 0.111 Angle : 0.485 7.265 14011 Z= 0.254 Chirality : 0.042 0.156 1568 Planarity : 0.004 0.039 1812 Dihedral : 6.072 78.009 1411 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.86 % Allowed : 6.73 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.24), residues: 1273 helix: 1.86 (0.24), residues: 503 sheet: 1.02 (0.36), residues: 193 loop : 0.49 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 669 HIS 0.002 0.001 HIS C 32 PHE 0.010 0.001 PHE A 360 TYR 0.010 0.001 TYR A 736 ARG 0.005 0.000 ARG C 143 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 478) hydrogen bonds : angle 4.77919 ( 1323) SS BOND : bond 0.01664 ( 1) SS BOND : angle 5.13821 ( 2) covalent geometry : bond 0.00253 (10344) covalent geometry : angle 0.48072 (14009) Misc. bond : bond 0.00089 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 1.244 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7728 (mtp85) cc_final: 0.7156 (mtm-85) REVERT: A 184 MET cc_start: 0.8490 (mtp) cc_final: 0.8150 (mtt) REVERT: A 191 ASP cc_start: 0.8108 (m-30) cc_final: 0.7782 (p0) REVERT: A 218 MET cc_start: 0.7809 (mtt) cc_final: 0.7556 (mtt) REVERT: A 235 TYR cc_start: 0.8854 (m-80) cc_final: 0.8634 (m-80) REVERT: A 353 ASP cc_start: 0.8098 (t0) cc_final: 0.7752 (t0) REVERT: A 442 MET cc_start: 0.8850 (tpp) cc_final: 0.8638 (mmm) REVERT: A 465 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8185 (t70) REVERT: A 540 GLU cc_start: 0.8439 (tt0) cc_final: 0.8205 (mp0) REVERT: A 668 MET cc_start: 0.8195 (mmm) cc_final: 0.7851 (mpp) REVERT: A 723 ASP cc_start: 0.8136 (m-30) cc_final: 0.7886 (m-30) REVERT: A 879 LYS cc_start: 0.8797 (mmmm) cc_final: 0.8279 (mtmt) REVERT: A 944 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.7287 (tmt) REVERT: A 983 GLU cc_start: 0.8498 (mp0) cc_final: 0.8053 (mp0) REVERT: B 39 ASP cc_start: 0.8564 (m-30) cc_final: 0.8245 (p0) REVERT: C 92 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7792 (tm-30) outliers start: 21 outliers final: 8 residues processed: 137 average time/residue: 1.3925 time to fit residues: 205.6457 Evaluate side-chains 120 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 4 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 13 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.142628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.095593 restraints weight = 12529.046| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.44 r_work: 0.2925 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10347 Z= 0.142 Angle : 0.489 6.652 14011 Z= 0.254 Chirality : 0.043 0.154 1568 Planarity : 0.004 0.043 1812 Dihedral : 5.804 81.670 1408 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.77 % Allowed : 8.67 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.24), residues: 1273 helix: 1.81 (0.24), residues: 502 sheet: 1.02 (0.35), residues: 207 loop : 0.50 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS C 125 PHE 0.012 0.001 PHE A 360 TYR 0.010 0.001 TYR C 145 ARG 0.007 0.000 ARG C 143 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 478) hydrogen bonds : angle 4.63971 ( 1323) SS BOND : bond 0.01008 ( 1) SS BOND : angle 4.82196 ( 2) covalent geometry : bond 0.00354 (10344) covalent geometry : angle 0.48566 (14009) Misc. bond : bond 0.00018 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7488 (mtp85) cc_final: 0.6737 (mtm-85) REVERT: A 184 MET cc_start: 0.8589 (mtp) cc_final: 0.8225 (mtt) REVERT: A 218 MET cc_start: 0.7698 (mtt) cc_final: 0.7395 (mtt) REVERT: A 235 TYR cc_start: 0.8753 (m-80) cc_final: 0.8538 (m-80) REVERT: A 353 ASP cc_start: 0.8232 (t0) cc_final: 0.7770 (t0) REVERT: A 465 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.8248 (t70) REVERT: A 540 GLU cc_start: 0.8440 (tt0) cc_final: 0.7896 (mp0) REVERT: A 668 MET cc_start: 0.8050 (mmm) cc_final: 0.7661 (mpp) REVERT: A 723 ASP cc_start: 0.8113 (m-30) cc_final: 0.7903 (m-30) REVERT: A 762 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8509 (pttt) REVERT: A 879 LYS cc_start: 0.8733 (mmmm) cc_final: 0.8150 (mtmt) REVERT: A 937 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: A 944 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.7213 (tmt) REVERT: A 983 GLU cc_start: 0.8408 (mp0) cc_final: 0.7871 (mp0) REVERT: B 39 ASP cc_start: 0.8543 (m-30) cc_final: 0.8095 (p0) REVERT: C 92 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7493 (tm-30) REVERT: D 27 LYS cc_start: 0.8779 (tppp) cc_final: 0.8577 (tppp) outliers start: 20 outliers final: 10 residues processed: 133 average time/residue: 1.4989 time to fit residues: 214.5815 Evaluate side-chains 126 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 20 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 88 optimal weight: 0.0670 chunk 50 optimal weight: 0.0980 chunk 70 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.143940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.095386 restraints weight = 12506.098| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.47 r_work: 0.2938 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10347 Z= 0.116 Angle : 0.467 6.749 14011 Z= 0.242 Chirality : 0.042 0.156 1568 Planarity : 0.004 0.045 1812 Dihedral : 5.786 82.732 1408 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.86 % Allowed : 10.27 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.24), residues: 1273 helix: 1.87 (0.24), residues: 501 sheet: 1.02 (0.35), residues: 207 loop : 0.52 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS C 125 PHE 0.011 0.001 PHE A 360 TYR 0.013 0.001 TYR C 145 ARG 0.005 0.000 ARG C 5 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 478) hydrogen bonds : angle 4.51313 ( 1323) SS BOND : bond 0.00474 ( 1) SS BOND : angle 4.27543 ( 2) covalent geometry : bond 0.00280 (10344) covalent geometry : angle 0.46393 (14009) Misc. bond : bond 0.00096 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.8461 (mtp) cc_final: 0.8098 (mtt) REVERT: A 235 TYR cc_start: 0.8756 (m-80) cc_final: 0.8536 (m-80) REVERT: A 353 ASP cc_start: 0.8218 (t0) cc_final: 0.7675 (m-30) REVERT: A 465 ASP cc_start: 0.8770 (OUTLIER) cc_final: 0.8262 (t70) REVERT: A 540 GLU cc_start: 0.8364 (tt0) cc_final: 0.7868 (mp0) REVERT: A 668 MET cc_start: 0.8079 (mmm) cc_final: 0.7682 (mpp) REVERT: A 723 ASP cc_start: 0.8089 (m-30) cc_final: 0.7873 (m-30) REVERT: A 762 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8495 (pttt) REVERT: A 879 LYS cc_start: 0.8730 (mmmm) cc_final: 0.8141 (mtmt) REVERT: A 937 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7810 (mp0) REVERT: A 983 GLU cc_start: 0.8352 (mp0) cc_final: 0.7816 (mp0) REVERT: B 39 ASP cc_start: 0.8464 (m-30) cc_final: 0.8043 (p0) REVERT: C 92 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7486 (tm-30) outliers start: 21 outliers final: 14 residues processed: 126 average time/residue: 1.3545 time to fit residues: 184.5314 Evaluate side-chains 127 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 111 optimal weight: 0.0670 chunk 96 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.143151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.094619 restraints weight = 12542.533| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.47 r_work: 0.2917 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10347 Z= 0.137 Angle : 0.479 6.972 14011 Z= 0.247 Chirality : 0.042 0.151 1568 Planarity : 0.004 0.048 1812 Dihedral : 5.786 83.423 1408 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.04 % Allowed : 10.62 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.24), residues: 1273 helix: 1.82 (0.24), residues: 501 sheet: 1.02 (0.35), residues: 206 loop : 0.54 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS C 125 PHE 0.012 0.001 PHE A 360 TYR 0.008 0.001 TYR A 736 ARG 0.011 0.000 ARG C 5 Details of bonding type rmsd hydrogen bonds : bond 0.03809 ( 478) hydrogen bonds : angle 4.51345 ( 1323) SS BOND : bond 0.00599 ( 1) SS BOND : angle 4.43854 ( 2) covalent geometry : bond 0.00340 (10344) covalent geometry : angle 0.47570 (14009) Misc. bond : bond 0.00058 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7494 (mtp85) cc_final: 0.6740 (mtm-85) REVERT: A 184 MET cc_start: 0.8617 (mtp) cc_final: 0.8256 (mtt) REVERT: A 213 THR cc_start: 0.7339 (OUTLIER) cc_final: 0.6942 (t) REVERT: A 235 TYR cc_start: 0.8757 (m-80) cc_final: 0.8526 (m-80) REVERT: A 250 TYR cc_start: 0.7746 (m-80) cc_final: 0.7427 (m-80) REVERT: A 353 ASP cc_start: 0.8228 (t0) cc_final: 0.7689 (m-30) REVERT: A 465 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8300 (t70) REVERT: A 540 GLU cc_start: 0.8358 (tt0) cc_final: 0.7853 (mp0) REVERT: A 668 MET cc_start: 0.8096 (mmm) cc_final: 0.7695 (mpp) REVERT: A 723 ASP cc_start: 0.8107 (m-30) cc_final: 0.7891 (m-30) REVERT: A 762 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8494 (pttt) REVERT: A 879 LYS cc_start: 0.8751 (mmmm) cc_final: 0.8154 (mtmt) REVERT: A 937 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7799 (mp0) REVERT: A 983 GLU cc_start: 0.8374 (mp0) cc_final: 0.7819 (mp0) REVERT: B 39 ASP cc_start: 0.8496 (m-30) cc_final: 0.8055 (p0) REVERT: C 92 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7450 (tm-30) REVERT: D 27 LYS cc_start: 0.8777 (tppp) cc_final: 0.8551 (tppp) outliers start: 23 outliers final: 13 residues processed: 130 average time/residue: 1.2757 time to fit residues: 178.8255 Evaluate side-chains 128 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 47 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.142991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.094502 restraints weight = 12610.490| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.47 r_work: 0.2906 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10347 Z= 0.149 Angle : 0.483 7.216 14011 Z= 0.250 Chirality : 0.043 0.150 1568 Planarity : 0.004 0.046 1812 Dihedral : 5.846 83.571 1408 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.30 % Allowed : 11.06 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.24), residues: 1273 helix: 1.80 (0.24), residues: 502 sheet: 0.97 (0.35), residues: 207 loop : 0.56 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS A 29 PHE 0.012 0.001 PHE C 62 TYR 0.008 0.001 TYR C 74 ARG 0.012 0.000 ARG C 5 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 478) hydrogen bonds : angle 4.51011 ( 1323) SS BOND : bond 0.00723 ( 1) SS BOND : angle 4.35227 ( 2) covalent geometry : bond 0.00371 (10344) covalent geometry : angle 0.47977 (14009) Misc. bond : bond 0.00084 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7530 (mtp85) cc_final: 0.6793 (mtm-85) REVERT: A 184 MET cc_start: 0.8638 (mtp) cc_final: 0.8284 (mtt) REVERT: A 213 THR cc_start: 0.7404 (OUTLIER) cc_final: 0.7006 (t) REVERT: A 235 TYR cc_start: 0.8764 (m-80) cc_final: 0.8526 (m-80) REVERT: A 250 TYR cc_start: 0.7762 (m-80) cc_final: 0.7447 (m-80) REVERT: A 335 ASP cc_start: 0.7514 (m-30) cc_final: 0.7240 (p0) REVERT: A 353 ASP cc_start: 0.8246 (t0) cc_final: 0.7698 (m-30) REVERT: A 465 ASP cc_start: 0.8794 (OUTLIER) cc_final: 0.8356 (t70) REVERT: A 540 GLU cc_start: 0.8355 (tt0) cc_final: 0.7849 (mp0) REVERT: A 668 MET cc_start: 0.8104 (mmm) cc_final: 0.7700 (mpp) REVERT: A 723 ASP cc_start: 0.8121 (m-30) cc_final: 0.7884 (m-30) REVERT: A 762 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8492 (pttt) REVERT: A 879 LYS cc_start: 0.8762 (mmmm) cc_final: 0.8176 (mtmt) REVERT: A 937 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: A 983 GLU cc_start: 0.8324 (mp0) cc_final: 0.7741 (mp0) REVERT: B 39 ASP cc_start: 0.8510 (m-30) cc_final: 0.8061 (p0) REVERT: C 92 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7472 (tm-30) outliers start: 26 outliers final: 18 residues processed: 130 average time/residue: 1.2102 time to fit residues: 170.4104 Evaluate side-chains 132 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 14 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 53 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.142364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.095590 restraints weight = 12484.700| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.45 r_work: 0.2913 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10347 Z= 0.137 Angle : 0.481 7.368 14011 Z= 0.249 Chirality : 0.042 0.211 1568 Planarity : 0.004 0.048 1812 Dihedral : 5.872 85.136 1408 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.21 % Allowed : 11.50 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.24), residues: 1273 helix: 1.82 (0.24), residues: 501 sheet: 0.94 (0.35), residues: 207 loop : 0.55 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.000 HIS A 29 PHE 0.014 0.001 PHE C 62 TYR 0.008 0.001 TYR A 736 ARG 0.009 0.000 ARG C 5 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 478) hydrogen bonds : angle 4.48288 ( 1323) SS BOND : bond 0.00707 ( 1) SS BOND : angle 4.48511 ( 2) covalent geometry : bond 0.00337 (10344) covalent geometry : angle 0.47794 (14009) Misc. bond : bond 0.00095 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7525 (mtp85) cc_final: 0.6785 (mtm-85) REVERT: A 184 MET cc_start: 0.8613 (mtp) cc_final: 0.8260 (mtt) REVERT: A 213 THR cc_start: 0.7395 (OUTLIER) cc_final: 0.6998 (t) REVERT: A 235 TYR cc_start: 0.8764 (m-80) cc_final: 0.8522 (m-80) REVERT: A 250 TYR cc_start: 0.7704 (m-80) cc_final: 0.7380 (m-80) REVERT: A 335 ASP cc_start: 0.7527 (m-30) cc_final: 0.7242 (p0) REVERT: A 353 ASP cc_start: 0.8247 (t0) cc_final: 0.7705 (m-30) REVERT: A 540 GLU cc_start: 0.8354 (tt0) cc_final: 0.7866 (mp0) REVERT: A 668 MET cc_start: 0.8100 (mmm) cc_final: 0.7701 (mpp) REVERT: A 723 ASP cc_start: 0.8123 (m-30) cc_final: 0.7878 (m-30) REVERT: A 762 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8492 (pttt) REVERT: A 879 LYS cc_start: 0.8761 (mmmm) cc_final: 0.8177 (mtmt) REVERT: A 937 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: A 983 GLU cc_start: 0.8323 (mp0) cc_final: 0.7757 (mp0) REVERT: B 39 ASP cc_start: 0.8509 (m-30) cc_final: 0.8057 (p0) REVERT: C 92 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7485 (tm-30) REVERT: D 27 LYS cc_start: 0.8763 (tppp) cc_final: 0.8547 (tppp) outliers start: 25 outliers final: 17 residues processed: 131 average time/residue: 1.1742 time to fit residues: 166.0637 Evaluate side-chains 131 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 44 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 79 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 42 optimal weight: 0.2980 chunk 68 optimal weight: 0.9980 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 = 0.3735 r_free = 0.3735 target = 0.142566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.094214 restraints weight = 12693.140| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.47 r_work: 0.2902 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10347 Z= 0.158 Angle : 0.497 7.747 14011 Z= 0.257 Chirality : 0.043 0.165 1568 Planarity : 0.004 0.048 1812 Dihedral : 5.933 84.325 1408 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.30 % Allowed : 11.77 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.24), residues: 1273 helix: 1.77 (0.24), residues: 502 sheet: 0.87 (0.35), residues: 207 loop : 0.53 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS A 29 PHE 0.014 0.001 PHE C 62 TYR 0.008 0.001 TYR A 81 ARG 0.010 0.000 ARG C 143 Details of bonding type rmsd hydrogen bonds : bond 0.03948 ( 478) hydrogen bonds : angle 4.50915 ( 1323) SS BOND : bond 0.00888 ( 1) SS BOND : angle 4.60315 ( 2) covalent geometry : bond 0.00395 (10344) covalent geometry : angle 0.49373 (14009) Misc. bond : bond 0.00040 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7556 (mtp85) cc_final: 0.6832 (mtm-85) REVERT: A 184 MET cc_start: 0.8633 (mtp) cc_final: 0.8269 (mtt) REVERT: A 213 THR cc_start: 0.7396 (OUTLIER) cc_final: 0.7002 (t) REVERT: A 235 TYR cc_start: 0.8763 (m-80) cc_final: 0.8512 (m-80) REVERT: A 250 TYR cc_start: 0.7685 (m-80) cc_final: 0.7358 (m-80) REVERT: A 335 ASP cc_start: 0.7524 (m-30) cc_final: 0.7253 (p0) REVERT: A 353 ASP cc_start: 0.8280 (t0) cc_final: 0.7714 (m-30) REVERT: A 540 GLU cc_start: 0.8363 (tt0) cc_final: 0.7887 (mp0) REVERT: A 668 MET cc_start: 0.8115 (mmm) cc_final: 0.7770 (mpp) REVERT: A 723 ASP cc_start: 0.8140 (m-30) cc_final: 0.7904 (m-30) REVERT: A 762 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8494 (pttt) REVERT: A 879 LYS cc_start: 0.8771 (mmmm) cc_final: 0.8181 (mtmt) REVERT: A 937 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: A 983 GLU cc_start: 0.8333 (mp0) cc_final: 0.7768 (mp0) REVERT: B 39 ASP cc_start: 0.8518 (m-30) cc_final: 0.8058 (p0) REVERT: C 92 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7488 (tm-30) REVERT: D 27 LYS cc_start: 0.8851 (tppp) cc_final: 0.8559 (tppp) outliers start: 26 outliers final: 20 residues processed: 129 average time/residue: 1.2103 time to fit residues: 168.8255 Evaluate side-chains 131 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 44 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 44 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.141997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.095189 restraints weight = 12490.971| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.45 r_work: 0.2909 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10347 Z= 0.153 Angle : 0.496 7.806 14011 Z= 0.256 Chirality : 0.043 0.161 1568 Planarity : 0.004 0.047 1812 Dihedral : 5.950 83.716 1408 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.30 % Allowed : 11.68 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.24), residues: 1273 helix: 1.77 (0.24), residues: 502 sheet: 0.85 (0.35), residues: 207 loop : 0.51 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS A 29 PHE 0.015 0.001 PHE C 62 TYR 0.012 0.001 TYR A 81 ARG 0.010 0.000 ARG C 143 Details of bonding type rmsd hydrogen bonds : bond 0.03927 ( 478) hydrogen bonds : angle 4.49642 ( 1323) SS BOND : bond 0.00837 ( 1) SS BOND : angle 4.60126 ( 2) covalent geometry : bond 0.00379 (10344) covalent geometry : angle 0.49314 (14009) Misc. bond : bond 0.00048 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7534 (mtp85) cc_final: 0.6884 (mtm-85) REVERT: A 184 MET cc_start: 0.8632 (mtp) cc_final: 0.8274 (mtt) REVERT: A 213 THR cc_start: 0.7398 (OUTLIER) cc_final: 0.7005 (t) REVERT: A 250 TYR cc_start: 0.7703 (m-80) cc_final: 0.7400 (m-80) REVERT: A 335 ASP cc_start: 0.7511 (m-30) cc_final: 0.7249 (p0) REVERT: A 353 ASP cc_start: 0.8296 (t0) cc_final: 0.7893 (t0) REVERT: A 540 GLU cc_start: 0.8353 (tt0) cc_final: 0.7886 (mp0) REVERT: A 668 MET cc_start: 0.8119 (mmm) cc_final: 0.7720 (mpp) REVERT: A 699 GLN cc_start: 0.8305 (mp10) cc_final: 0.8089 (mp10) REVERT: A 723 ASP cc_start: 0.8135 (m-30) cc_final: 0.7897 (m-30) REVERT: A 762 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8489 (pttt) REVERT: A 879 LYS cc_start: 0.8767 (mmmm) cc_final: 0.8178 (mtmt) REVERT: A 937 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7944 (mp0) REVERT: A 983 GLU cc_start: 0.8332 (mp0) cc_final: 0.7764 (mp0) REVERT: B 39 ASP cc_start: 0.8532 (m-30) cc_final: 0.8058 (p0) REVERT: C 92 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7492 (tm-30) REVERT: D 27 LYS cc_start: 0.8871 (tppp) cc_final: 0.8561 (tppp) outliers start: 26 outliers final: 20 residues processed: 130 average time/residue: 1.2624 time to fit residues: 176.7471 Evaluate side-chains 134 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 44 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 17 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 83 optimal weight: 0.3980 chunk 117 optimal weight: 0.1980 chunk 42 optimal weight: 0.1980 chunk 112 optimal weight: 0.9980 chunk 64 optimal weight: 0.2980 chunk 34 optimal weight: 0.5980 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.144392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.096001 restraints weight = 12616.885| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.50 r_work: 0.2946 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10347 Z= 0.104 Angle : 0.466 7.965 14011 Z= 0.241 Chirality : 0.041 0.160 1568 Planarity : 0.004 0.050 1812 Dihedral : 5.808 85.293 1408 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.68 % Allowed : 12.48 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.24), residues: 1273 helix: 1.92 (0.24), residues: 502 sheet: 0.92 (0.35), residues: 207 loop : 0.58 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.000 HIS C 125 PHE 0.012 0.001 PHE C 62 TYR 0.007 0.001 TYR A 736 ARG 0.010 0.000 ARG C 143 Details of bonding type rmsd hydrogen bonds : bond 0.03379 ( 478) hydrogen bonds : angle 4.36596 ( 1323) SS BOND : bond 0.00683 ( 1) SS BOND : angle 4.10336 ( 2) covalent geometry : bond 0.00242 (10344) covalent geometry : angle 0.46387 (14009) Misc. bond : bond 0.00013 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 THR cc_start: 0.9081 (t) cc_final: 0.8836 (m) REVERT: A 184 MET cc_start: 0.8434 (mtp) cc_final: 0.8057 (mtt) REVERT: A 213 THR cc_start: 0.7406 (OUTLIER) cc_final: 0.7009 (t) REVERT: A 250 TYR cc_start: 0.7718 (m-80) cc_final: 0.7397 (m-80) REVERT: A 335 ASP cc_start: 0.7556 (m-30) cc_final: 0.7229 (p0) REVERT: A 353 ASP cc_start: 0.8251 (t0) cc_final: 0.7904 (t0) REVERT: A 540 GLU cc_start: 0.8324 (tt0) cc_final: 0.7869 (mp0) REVERT: A 668 MET cc_start: 0.8092 (mmm) cc_final: 0.7701 (mpp) REVERT: A 723 ASP cc_start: 0.8164 (m-30) cc_final: 0.7926 (m-30) REVERT: A 762 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8479 (pttt) REVERT: A 879 LYS cc_start: 0.8743 (mmmm) cc_final: 0.8147 (mtmt) REVERT: A 937 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7965 (mp0) REVERT: A 983 GLU cc_start: 0.8303 (mp0) cc_final: 0.7707 (mp0) REVERT: B 39 ASP cc_start: 0.8508 (m-30) cc_final: 0.8056 (p0) REVERT: C 5 ARG cc_start: 0.6897 (tpt-90) cc_final: 0.6672 (ttt180) REVERT: C 92 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7472 (tm-30) REVERT: D 27 LYS cc_start: 0.8811 (tppp) cc_final: 0.8507 (tppp) outliers start: 19 outliers final: 14 residues processed: 123 average time/residue: 1.3803 time to fit residues: 183.9998 Evaluate side-chains 125 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 762 LYS 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 B residue 7 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 44 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 6 optimal weight: 0.0670 chunk 50 optimal weight: 0.4980 chunk 123 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 0.3980 chunk 52 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.3747 r_free = 0.3747 target = 0.143768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.095432 restraints weight = 12573.741| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.48 r_work: 0.2934 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10347 Z= 0.125 Angle : 0.482 8.852 14011 Z= 0.248 Chirality : 0.042 0.172 1568 Planarity : 0.004 0.052 1812 Dihedral : 5.737 83.906 1408 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.68 % Allowed : 12.65 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.24), residues: 1273 helix: 1.93 (0.24), residues: 501 sheet: 0.90 (0.35), residues: 207 loop : 0.56 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.000 HIS A 144 PHE 0.013 0.001 PHE C 62 TYR 0.008 0.001 TYR A 81 ARG 0.006 0.000 ARG C 5 Details of bonding type rmsd hydrogen bonds : bond 0.03572 ( 478) hydrogen bonds : angle 4.38672 ( 1323) SS BOND : bond 0.00822 ( 1) SS BOND : angle 4.29731 ( 2) covalent geometry : bond 0.00307 (10344) covalent geometry : angle 0.47913 (14009) Misc. bond : bond 0.00051 ( 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: 8166.06 seconds wall clock time: 142 minutes 26.12 seconds (8546.12 seconds total)