Starting phenix.real_space_refine on Wed Sep 17 17:44:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5e_44209/09_2025/9b5e_44209.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5e_44209/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9b5e_44209/09_2025/9b5e_44209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5e_44209/09_2025/9b5e_44209.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b5e_44209/09_2025/9b5e_44209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5e_44209/09_2025/9b5e_44209.map" } resolution = 2.81 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= 0.072 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): 0.01s 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: 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: 2.18, per 1000 atoms: 0.22 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: 1.02 Conformation dependent library (CDL) restraints added in 331.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.44 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: 2.05 Time building geometry restraints manager: 1.30 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: 3.810 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.780 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.890 ------------------------------------------------------------------------------- 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 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: 1.33 (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 ARG 0.002 0.000 ARG A 409 TYR 0.007 0.001 TYR A 732 PHE 0.011 0.001 PHE A 360 TRP 0.004 0.001 TRP A 669 HIS 0.002 0.000 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00264 (10344) covalent geometry : angle 0.44156 (14009) SS BOND : bond 0.88634 ( 1) SS BOND : angle 32.47940 ( 2) hydrogen bonds : bond 0.14235 ( 478) hydrogen bonds : angle 5.90132 ( 1323) 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 : 0.421 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: 0.7166 time to fit residues: 127.0044 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 : 0.293 ------------------------------------------------------------------------------- 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 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.0010 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.3980 overall best weight: 0.5586 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.138680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.096967 restraints weight = 12226.226| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.27 r_work: 0.2912 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 10347 Z= 0.140 Angle : 0.503 6.991 14011 Z= 0.263 Chirality : 0.043 0.152 1568 Planarity : 0.004 0.039 1812 Dihedral : 6.009 75.968 1411 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.04 % Allowed : 6.55 % 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 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: 1.54 (0.24), residues: 1273 helix: 1.78 (0.24), residues: 502 sheet: 1.00 (0.36), residues: 199 loop : 0.46 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 143 TYR 0.010 0.001 TYR A 736 PHE 0.011 0.001 PHE A 360 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00341 (10344) covalent geometry : angle 0.49906 (14009) SS BOND : bond 0.01841 ( 1) SS BOND : angle 4.94471 ( 2) hydrogen bonds : bond 0.04386 ( 478) hydrogen bonds : angle 4.84160 ( 1323) Misc. bond : bond 0.00160 ( 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 149 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7915 (mtp85) cc_final: 0.7378 (mtm-85) REVERT: A 184 MET cc_start: 0.8681 (mtp) cc_final: 0.8356 (mtt) REVERT: A 191 ASP cc_start: 0.8058 (m-30) cc_final: 0.7792 (p0) REVERT: A 465 ASP cc_start: 0.8890 (OUTLIER) cc_final: 0.8349 (t70) REVERT: A 516 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7143 (pm20) REVERT: A 668 MET cc_start: 0.8335 (mmm) cc_final: 0.8007 (mpp) REVERT: A 879 LYS cc_start: 0.8867 (mmmm) cc_final: 0.8396 (mtmt) REVERT: A 944 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7439 (tmt) REVERT: A 983 GLU cc_start: 0.8564 (mp0) cc_final: 0.8138 (mp0) REVERT: B 39 ASP cc_start: 0.8588 (m-30) cc_final: 0.8300 (p0) REVERT: C 92 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7853 (tm-30) outliers start: 23 outliers final: 8 residues processed: 138 average time/residue: 0.6555 time to fit residues: 96.9203 Evaluate side-chains 122 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 465 ASP Chi-restraints excluded: chain A residue 516 GLU 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 91 optimal weight: 1.9990 chunk 40 optimal weight: 0.0670 chunk 99 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 83 optimal weight: 0.0980 chunk 12 optimal weight: 0.7980 chunk 46 optimal weight: 0.0770 chunk 121 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 overall best weight: 0.3876 ------------------------------------------------------------------------------- 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 = 0.3826 r_free = 0.3826 target = 0.147492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.099159 restraints weight = 12609.438| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.42 r_work: 0.2944 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10347 Z= 0.109 Angle : 0.470 6.216 14011 Z= 0.244 Chirality : 0.042 0.151 1568 Planarity : 0.004 0.042 1812 Dihedral : 5.747 83.146 1408 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.68 % Allowed : 8.85 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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: 1.63 (0.24), residues: 1273 helix: 1.85 (0.24), residues: 502 sheet: 1.03 (0.35), residues: 207 loop : 0.52 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 143 TYR 0.009 0.001 TYR C 145 PHE 0.010 0.001 PHE A 360 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00257 (10344) covalent geometry : angle 0.46695 (14009) SS BOND : bond 0.00896 ( 1) SS BOND : angle 4.34151 ( 2) hydrogen bonds : bond 0.03716 ( 478) hydrogen bonds : angle 4.57740 ( 1323) Misc. bond : bond 0.00027 ( 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 135 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.8444 (mtp) cc_final: 0.8032 (mtt) REVERT: A 189 THR cc_start: 0.8268 (p) cc_final: 0.7601 (p) REVERT: A 191 ASP cc_start: 0.8221 (m-30) cc_final: 0.7720 (p0) REVERT: A 250 TYR cc_start: 0.7764 (m-80) cc_final: 0.7394 (m-80) REVERT: A 465 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8281 (t70) REVERT: A 668 MET cc_start: 0.8043 (mmm) cc_final: 0.7653 (mpp) REVERT: A 762 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8488 (pttt) REVERT: A 879 LYS cc_start: 0.8729 (mmmm) cc_final: 0.8139 (mtmt) REVERT: A 937 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7812 (mp0) REVERT: A 983 GLU cc_start: 0.8413 (mp0) cc_final: 0.7882 (mp0) REVERT: B 39 ASP cc_start: 0.8583 (m-30) cc_final: 0.8109 (p0) REVERT: C 92 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7570 (tm-30) REVERT: C 131 ARG cc_start: 0.7682 (mmm-85) cc_final: 0.7462 (mmm-85) outliers start: 19 outliers final: 10 residues processed: 128 average time/residue: 0.6001 time to fit residues: 82.4751 Evaluate side-chains 124 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 216 LYS 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 762 LYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 33 LYS 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 11 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 6 optimal weight: 0.0970 chunk 104 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 88 optimal weight: 0.7980 chunk 109 optimal weight: 0.3980 chunk 112 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.142833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.094359 restraints weight = 12556.525| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.52 r_work: 0.2935 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1460 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= 0.121 Angle : 0.466 6.648 14011 Z= 0.241 Chirality : 0.042 0.150 1568 Planarity : 0.004 0.044 1812 Dihedral : 5.708 82.458 1408 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.04 % Allowed : 9.91 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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: 1.67 (0.24), residues: 1273 helix: 1.87 (0.24), residues: 503 sheet: 1.03 (0.35), residues: 207 loop : 0.56 (0.27), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 5 TYR 0.012 0.001 TYR C 145 PHE 0.011 0.001 PHE A 360 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00294 (10344) covalent geometry : angle 0.46302 (14009) SS BOND : bond 0.00753 ( 1) SS BOND : angle 4.20668 ( 2) hydrogen bonds : bond 0.03652 ( 478) hydrogen bonds : angle 4.49693 ( 1323) Misc. bond : bond 0.00058 ( 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 141 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.8463 (mtp) cc_final: 0.8086 (mtt) REVERT: A 213 THR cc_start: 0.7415 (OUTLIER) cc_final: 0.7019 (t) REVERT: A 465 ASP cc_start: 0.8786 (OUTLIER) cc_final: 0.8312 (t70) REVERT: A 668 MET cc_start: 0.8084 (mmm) cc_final: 0.7684 (mpp) REVERT: A 762 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8497 (pttt) REVERT: A 879 LYS cc_start: 0.8736 (mmmm) cc_final: 0.8147 (mtmt) REVERT: A 937 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: A 983 GLU cc_start: 0.8359 (mp0) cc_final: 0.7815 (mp0) REVERT: B 39 ASP cc_start: 0.8465 (m-30) cc_final: 0.8042 (p0) REVERT: C 92 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7469 (tm-30) REVERT: C 131 ARG cc_start: 0.7701 (mmm-85) cc_final: 0.7468 (mmm-85) outliers start: 23 outliers final: 13 residues processed: 131 average time/residue: 0.5898 time to fit residues: 82.8264 Evaluate side-chains 126 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 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 33 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 81 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 78 optimal weight: 0.0670 chunk 41 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 75 optimal weight: 0.0060 chunk 35 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 overall best weight: 0.4134 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.144294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.095743 restraints weight = 12628.379| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.48 r_work: 0.2940 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10347 Z= 0.110 Angle : 0.466 6.941 14011 Z= 0.241 Chirality : 0.042 0.159 1568 Planarity : 0.004 0.045 1812 Dihedral : 5.712 83.721 1408 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.12 % Allowed : 10.53 % 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 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: 1.69 (0.24), residues: 1273 helix: 1.92 (0.24), residues: 502 sheet: 1.01 (0.35), residues: 207 loop : 0.57 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 143 TYR 0.007 0.001 TYR A 736 PHE 0.012 0.001 PHE C 62 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00262 (10344) covalent geometry : angle 0.46341 (14009) SS BOND : bond 0.00666 ( 1) SS BOND : angle 4.08546 ( 2) hydrogen bonds : bond 0.03520 ( 478) hydrogen bonds : angle 4.44831 ( 1323) Misc. bond : bond 0.00028 ( 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 135 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.8452 (mtp) cc_final: 0.8084 (mtt) REVERT: A 213 THR cc_start: 0.7413 (OUTLIER) cc_final: 0.7016 (t) REVERT: A 465 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8285 (t70) REVERT: A 668 MET cc_start: 0.8081 (mmm) cc_final: 0.7682 (mpp) REVERT: A 762 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8494 (pttt) REVERT: A 879 LYS cc_start: 0.8734 (mmmm) cc_final: 0.8139 (mtmt) REVERT: A 937 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: A 983 GLU cc_start: 0.8370 (mp0) cc_final: 0.7836 (mp0) REVERT: B 39 ASP cc_start: 0.8455 (m-30) cc_final: 0.8037 (p0) REVERT: C 92 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7464 (tm-30) REVERT: C 131 ARG cc_start: 0.7635 (mmm-85) cc_final: 0.7357 (mmm-85) outliers start: 24 outliers final: 15 residues processed: 125 average time/residue: 0.6246 time to fit residues: 83.8027 Evaluate side-chains 126 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 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 B residue 33 LYS 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 C residue 136 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 41 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 82 optimal weight: 0.2980 chunk 113 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 97 optimal weight: 0.0370 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.144230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.095553 restraints weight = 12668.765| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.49 r_work: 0.2943 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10347 Z= 0.118 Angle : 0.464 7.239 14011 Z= 0.240 Chirality : 0.042 0.163 1568 Planarity : 0.004 0.053 1812 Dihedral : 5.688 82.451 1408 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.12 % Allowed : 11.15 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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: 1.71 (0.24), residues: 1273 helix: 1.94 (0.24), residues: 501 sheet: 0.99 (0.35), residues: 207 loop : 0.58 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 5 TYR 0.007 0.001 TYR A 736 PHE 0.011 0.001 PHE A 360 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00287 (10344) covalent geometry : angle 0.46169 (14009) SS BOND : bond 0.00330 ( 1) SS BOND : angle 4.13774 ( 2) hydrogen bonds : bond 0.03542 ( 478) hydrogen bonds : angle 4.42140 ( 1323) Misc. bond : bond 0.00051 ( 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 138 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.8460 (mtp) cc_final: 0.8095 (mtt) REVERT: A 213 THR cc_start: 0.7355 (OUTLIER) cc_final: 0.6945 (t) REVERT: A 250 TYR cc_start: 0.7723 (m-80) cc_final: 0.7409 (m-80) REVERT: A 335 ASP cc_start: 0.7505 (m-30) cc_final: 0.7234 (p0) REVERT: A 465 ASP cc_start: 0.8776 (OUTLIER) cc_final: 0.8331 (t70) REVERT: A 668 MET cc_start: 0.8094 (mmm) cc_final: 0.7693 (mpp) REVERT: A 762 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8495 (pttt) REVERT: A 879 LYS cc_start: 0.8748 (mmmm) cc_final: 0.8153 (mtmt) REVERT: A 937 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: A 983 GLU cc_start: 0.8321 (mp0) cc_final: 0.7765 (mp0) REVERT: B 39 ASP cc_start: 0.8466 (m-30) cc_final: 0.8038 (p0) REVERT: C 92 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7459 (tm-30) REVERT: D 1 MET cc_start: 0.5169 (tpt) cc_final: 0.4904 (tmm) outliers start: 24 outliers final: 16 residues processed: 127 average time/residue: 0.6344 time to fit residues: 86.6716 Evaluate side-chains 127 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 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 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 33 LYS Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 78 optimal weight: 0.0870 chunk 6 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 74 optimal weight: 0.0010 overall best weight: 0.4966 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.144108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.095620 restraints weight = 12546.402| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.48 r_work: 0.2931 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10347 Z= 0.119 Angle : 0.465 7.480 14011 Z= 0.241 Chirality : 0.042 0.204 1568 Planarity : 0.004 0.045 1812 Dihedral : 5.715 83.217 1408 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.21 % Allowed : 11.42 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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: 1.70 (0.24), residues: 1273 helix: 1.94 (0.24), residues: 502 sheet: 0.96 (0.35), residues: 207 loop : 0.58 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 143 TYR 0.007 0.001 TYR A 736 PHE 0.011 0.001 PHE A 360 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00290 (10344) covalent geometry : angle 0.46220 (14009) SS BOND : bond 0.01039 ( 1) SS BOND : angle 4.05637 ( 2) hydrogen bonds : bond 0.03515 ( 478) hydrogen bonds : angle 4.39133 ( 1323) Misc. bond : bond 0.00017 ( 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 135 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 THR cc_start: 0.9069 (t) cc_final: 0.8806 (m) REVERT: A 184 MET cc_start: 0.8403 (mtp) cc_final: 0.8031 (mtt) REVERT: A 213 THR cc_start: 0.7322 (OUTLIER) cc_final: 0.6922 (t) REVERT: A 250 TYR cc_start: 0.7715 (m-80) cc_final: 0.7398 (m-80) REVERT: A 335 ASP cc_start: 0.7466 (m-30) cc_final: 0.7210 (p0) REVERT: A 465 ASP cc_start: 0.8840 (OUTLIER) cc_final: 0.8436 (t70) REVERT: A 668 MET cc_start: 0.8081 (mmm) cc_final: 0.7681 (mpp) REVERT: A 762 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8482 (pttt) REVERT: A 879 LYS cc_start: 0.8753 (mmmm) cc_final: 0.8152 (mtmt) REVERT: A 937 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: A 983 GLU cc_start: 0.8330 (mp0) cc_final: 0.7738 (mp0) REVERT: B 39 ASP cc_start: 0.8469 (m-30) cc_final: 0.8034 (p0) REVERT: C 92 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7441 (tm-30) REVERT: D 1 MET cc_start: 0.5139 (tpt) cc_final: 0.4886 (tmm) outliers start: 25 outliers final: 18 residues processed: 125 average time/residue: 0.5978 time to fit residues: 80.6339 Evaluate side-chains 131 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 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 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 33 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 9 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 1 optimal weight: 0.2980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.142634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.094237 restraints weight = 12690.330| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.48 r_work: 0.2912 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1681 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= 0.162 Angle : 0.484 7.478 14011 Z= 0.251 Chirality : 0.043 0.147 1568 Planarity : 0.004 0.045 1812 Dihedral : 5.805 83.668 1408 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.21 % Allowed : 11.59 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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: 1.62 (0.24), residues: 1273 helix: 1.87 (0.24), residues: 501 sheet: 0.91 (0.35), residues: 207 loop : 0.54 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 5 TYR 0.008 0.001 TYR A 81 PHE 0.013 0.001 PHE A 360 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00405 (10344) covalent geometry : angle 0.48117 (14009) SS BOND : bond 0.01078 ( 1) SS BOND : angle 4.41913 ( 2) hydrogen bonds : bond 0.03913 ( 478) hydrogen bonds : angle 4.44145 ( 1323) 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 134 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7555 (mtp85) cc_final: 0.6788 (mtm-85) REVERT: A 184 MET cc_start: 0.8507 (mtp) cc_final: 0.8151 (mtt) REVERT: A 213 THR cc_start: 0.7377 (OUTLIER) cc_final: 0.6978 (t) REVERT: A 250 TYR cc_start: 0.7730 (m-80) cc_final: 0.7406 (m-80) REVERT: A 335 ASP cc_start: 0.7497 (m-30) cc_final: 0.7208 (p0) REVERT: A 668 MET cc_start: 0.8097 (mmm) cc_final: 0.7748 (mpp) REVERT: A 762 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8485 (pttt) REVERT: A 879 LYS cc_start: 0.8773 (mmmm) cc_final: 0.8174 (mtmt) REVERT: A 937 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7949 (mp0) REVERT: A 983 GLU cc_start: 0.8336 (mp0) cc_final: 0.7770 (mp0) REVERT: B 39 ASP cc_start: 0.8511 (m-30) cc_final: 0.8052 (p0) REVERT: C 92 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7469 (tm-30) REVERT: D 27 LYS cc_start: 0.8805 (tppp) cc_final: 0.8541 (tppt) outliers start: 25 outliers final: 17 residues processed: 125 average time/residue: 0.5904 time to fit residues: 79.3324 Evaluate side-chains 126 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 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 14 optimal weight: 0.6980 chunk 120 optimal weight: 20.0000 chunk 103 optimal weight: 0.9980 chunk 82 optimal weight: 0.0570 chunk 96 optimal weight: 0.2980 chunk 56 optimal weight: 0.0030 chunk 94 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.3308 ------------------------------------------------------------------------------- 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 = 0.143514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.095366 restraints weight = 12500.446| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.52 r_work: 0.2953 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10347 Z= 0.097 Angle : 0.453 7.721 14011 Z= 0.234 Chirality : 0.041 0.144 1568 Planarity : 0.004 0.054 1812 Dihedral : 5.722 84.992 1408 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.68 % Allowed : 12.39 % 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 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: 1.73 (0.24), residues: 1273 helix: 1.97 (0.24), residues: 503 sheet: 0.95 (0.35), residues: 207 loop : 0.61 (0.27), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 5 TYR 0.007 0.001 TYR A 736 PHE 0.011 0.001 PHE C 62 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00226 (10344) covalent geometry : angle 0.45099 (14009) SS BOND : bond 0.00421 ( 1) SS BOND : angle 3.81280 ( 2) hydrogen bonds : bond 0.03298 ( 478) hydrogen bonds : angle 4.30648 ( 1323) Misc. bond : bond 0.00080 ( 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 128 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.8371 (mtp) cc_final: 0.8010 (mmm) REVERT: A 182 THR cc_start: 0.9085 (t) cc_final: 0.8846 (m) REVERT: A 184 MET cc_start: 0.8359 (mtp) cc_final: 0.7979 (mtt) REVERT: A 213 THR cc_start: 0.7398 (OUTLIER) cc_final: 0.6972 (t) REVERT: A 250 TYR cc_start: 0.7735 (m-80) cc_final: 0.7378 (m-80) REVERT: A 335 ASP cc_start: 0.7534 (m-30) cc_final: 0.7212 (p0) REVERT: A 668 MET cc_start: 0.8087 (mmm) cc_final: 0.7702 (mpp) REVERT: A 762 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8477 (pttt) REVERT: A 879 LYS cc_start: 0.8765 (mmmm) cc_final: 0.8161 (mtmt) REVERT: A 937 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7856 (mp0) REVERT: B 39 ASP cc_start: 0.8509 (m-30) cc_final: 0.8057 (p0) REVERT: C 92 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7461 (tm-30) REVERT: D 1 MET cc_start: 0.5374 (tpt) cc_final: 0.4929 (tmm) outliers start: 19 outliers final: 14 residues processed: 122 average time/residue: 0.5987 time to fit residues: 78.6198 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 : 0.313 ------------------------------------------------------------------------------- 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 461 VAL 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 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 33 LYS 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 79 optimal weight: 0.0970 chunk 92 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.3745 r_free = 0.3745 target = 0.142801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.094605 restraints weight = 12333.441| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.50 r_work: 0.2936 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10347 Z= 0.125 Angle : 0.467 7.506 14011 Z= 0.242 Chirality : 0.042 0.151 1568 Planarity : 0.004 0.045 1812 Dihedral : 5.707 83.380 1408 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.59 % Allowed : 12.57 % 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 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: 1.69 (0.24), residues: 1273 helix: 1.91 (0.24), residues: 502 sheet: 0.94 (0.35), residues: 207 loop : 0.59 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 5 TYR 0.007 0.001 TYR A 736 PHE 0.014 0.001 PHE C 62 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00307 (10344) covalent geometry : angle 0.46457 (14009) SS BOND : bond 0.00805 ( 1) SS BOND : angle 4.05091 ( 2) hydrogen bonds : bond 0.03559 ( 478) hydrogen bonds : angle 4.35224 ( 1323) Misc. bond : bond 0.00017 ( 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 126 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.8422 (mtp) cc_final: 0.8044 (mmm) REVERT: A 182 THR cc_start: 0.9092 (t) cc_final: 0.8859 (m) REVERT: A 184 MET cc_start: 0.8411 (mtp) cc_final: 0.8047 (mtt) REVERT: A 213 THR cc_start: 0.7377 (OUTLIER) cc_final: 0.6979 (t) REVERT: A 250 TYR cc_start: 0.7739 (m-80) cc_final: 0.7419 (m-80) REVERT: A 335 ASP cc_start: 0.7493 (m-30) cc_final: 0.7205 (p0) REVERT: A 668 MET cc_start: 0.8088 (mmm) cc_final: 0.7689 (mpp) REVERT: A 762 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8477 (pttt) REVERT: A 879 LYS cc_start: 0.8765 (mmmm) cc_final: 0.8158 (mtmt) REVERT: A 937 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7962 (mp0) REVERT: B 39 ASP cc_start: 0.8514 (m-30) cc_final: 0.8056 (p0) REVERT: C 92 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7462 (tm-30) REVERT: D 1 MET cc_start: 0.5467 (tpt) cc_final: 0.4877 (tmm) outliers start: 18 outliers final: 15 residues processed: 122 average time/residue: 0.6209 time to fit residues: 81.6189 Evaluate side-chains 123 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 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 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 33 LYS 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 50 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 21 optimal weight: 0.0050 chunk 90 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 114 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 = 0.3745 r_free = 0.3745 target = 0.142810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.094670 restraints weight = 12479.933| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.51 r_work: 0.2941 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10347 Z= 0.121 Angle : 0.465 7.596 14011 Z= 0.241 Chirality : 0.042 0.143 1568 Planarity : 0.004 0.045 1812 Dihedral : 5.721 83.574 1408 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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 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: 1.69 (0.24), residues: 1273 helix: 1.90 (0.24), residues: 502 sheet: 0.95 (0.35), residues: 207 loop : 0.60 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 5 TYR 0.007 0.001 TYR A 736 PHE 0.013 0.001 PHE C 62 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00297 (10344) covalent geometry : angle 0.46230 (14009) SS BOND : bond 0.00687 ( 1) SS BOND : angle 4.01084 ( 2) hydrogen bonds : bond 0.03546 ( 478) hydrogen bonds : angle 4.34363 ( 1323) Misc. bond : bond 0.00065 ( 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: 3984.84 seconds wall clock time: 68 minutes 17.83 seconds (4097.83 seconds total)