Starting phenix.real_space_refine on Sat Aug 23 04:04:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5f_44210/08_2025/9b5f_44210.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5f_44210/08_2025/9b5f_44210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b5f_44210/08_2025/9b5f_44210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5f_44210/08_2025/9b5f_44210.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b5f_44210/08_2025/9b5f_44210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5f_44210/08_2025/9b5f_44210.map" } resolution = 2.78 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= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 2 5.21 5 S 42 5.16 5 C 6078 2.51 5 N 1575 2.21 5 O 1836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9536 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} 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: 2.44, per 1000 atoms: 0.26 Number of scatterers: 9536 At special positions: 0 Unit cell: (87.248, 103.208, 120.232, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 3 15.00 Mg 2 11.99 O 1836 8.00 N 1575 7.00 C 6078 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=2.90 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 372.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 10 sheets defined 47.5% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.782A pdb=" N TYR A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 36 Processing helix chain 'A' and resid 46 through 60 Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.672A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.933A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.369A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LYS A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 123 Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.734A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYS A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.181A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 304 removed outlier: 3.663A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.562A 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: 4.524A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 Processing helix chain 'A' and resid 436 through 450 Processing helix chain 'A' and resid 468 through 474 removed outlier: 3.557A pdb=" N ASN A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 474 " --> pdb=" O ASN A 471 " (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: 4.041A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 528 removed outlier: 3.953A pdb=" N LYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.616A pdb=" N ARG A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.517A pdb=" N SER A 581 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.850A 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 630 Processing helix chain 'A' and resid 632 through 641 removed outlier: 3.876A pdb=" N THR A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 656 Processing helix chain 'A' and resid 662 through 679 removed outlier: 3.779A pdb=" N CYS A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 689 Processing helix chain 'A' and resid 718 through 737 Processing helix chain 'A' and resid 743 through 753 removed outlier: 3.952A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 794 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: 3.732A pdb=" N THR A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.688A pdb=" N GLU A 882 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR A 883 " --> pdb=" O ILE A 880 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 879 through 883' Processing helix chain 'A' and resid 926 through 937 Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 969 through 979 Processing helix chain '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 removed outlier: 3.672A pdb=" N ASP C 16 " --> pdb=" O ASP C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.507A pdb=" N LEU C 89 " --> pdb=" O LEU C 86 " (cutoff:3.500A) 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 sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.714A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N THR A 129 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ILE A 43 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.244A 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: 4.025A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.249A 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: 4.025A 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: 6.572A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.180A 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 923 removed outlier: 6.426A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N VAL A 990 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N SER A 947 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLU A 992 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU A 945 " --> pdb=" O GLU A 992 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N CYS A 994 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.373A 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 923 removed outlier: 6.426A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.376A 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: 3.862A pdb=" N ARG B 42 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 21 through 26 removed outlier: 6.229A pdb=" N HIS C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1275 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: 1.76 Time building geometry restraints manager: 1.23 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: 1619 1.27 - 1.40: 2292 1.40 - 1.54: 5646 1.54 - 1.67: 125 1.67 - 1.81: 64 Bond restraints: 9746 Sorted by residual: bond pdb=" C04 A1AIV D 201 " pdb=" C05 A1AIV D 201 " ideal model delta sigma weight residual 1.453 1.525 -0.072 2.00e-02 2.50e+03 1.30e+01 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 2.65e+00 bond pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " ideal model delta sigma weight residual 1.531 1.518 0.013 1.20e-02 6.94e+03 1.13e+00 bond pdb=" C05 A1AIV D 201 " pdb=" N06 A1AIV D 201 " ideal model delta sigma weight residual 1.151 1.131 0.020 2.00e-02 2.50e+03 9.78e-01 bond pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 1.416 1.407 0.009 1.30e-02 5.92e+03 4.79e-01 ... (remaining 9741 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 13022 1.40 - 2.79: 103 2.79 - 4.19: 71 4.19 - 5.59: 4 5.59 - 6.99: 4 Bond angle restraints: 13204 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 121.70 128.58 -6.88 1.80e+00 3.09e-01 1.46e+01 angle pdb=" N ILE A 239 " pdb=" CA ILE A 239 " pdb=" C ILE A 239 " ideal model delta sigma weight residual 113.47 110.38 3.09 1.01e+00 9.80e-01 9.38e+00 angle pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 106.53 103.20 3.33 1.18e+00 7.24e-01 8.02e+00 angle pdb=" C3' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" C5' ATP A1103 " ideal model delta sigma weight residual 115.19 110.55 4.64 1.76e+00 3.23e-01 6.95e+00 angle pdb=" C2' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O3' ATP A1103 " ideal model delta sigma weight residual 111.83 104.84 6.99 2.67e+00 1.40e-01 6.85e+00 ... (remaining 13199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 5640 16.14 - 32.27: 221 32.27 - 48.41: 52 48.41 - 64.54: 15 64.54 - 80.68: 3 Dihedral angle restraints: 5931 sinusoidal: 2425 harmonic: 3506 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 -135.47 49.47 1 1.00e+01 1.00e-02 3.36e+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 -60.00 -118.52 58.52 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N CYS C 85 " pdb=" CA CYS C 85 " pdb=" CB CYS C 85 " pdb=" SG CYS C 85 " ideal model delta sinusoidal sigma weight residual -180.00 -122.28 -57.72 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 5928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1286 0.057 - 0.115: 153 0.115 - 0.172: 29 0.172 - 0.230: 0 0.230 - 0.287: 3 Chirality restraints: 1471 Sorted by residual: chirality pdb=" C3' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" O3' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.06e+00 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 -2.96 0.28 2.00e-01 2.50e+01 2.01e+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 1.37e+00 ... (remaining 1468 not shown) Planarity restraints: 1709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 288 " 0.019 5.00e-02 4.00e+02 2.81e-02 1.26e+00 pdb=" N PRO A 289 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 289 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 289 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 107 " 0.017 5.00e-02 4.00e+02 2.50e-02 9.99e-01 pdb=" N PRO A 108 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 108 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 108 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 75 " -0.016 5.00e-02 4.00e+02 2.42e-02 9.40e-01 pdb=" N PRO C 76 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO C 76 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 76 " -0.014 5.00e-02 4.00e+02 ... (remaining 1706 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 67 2.60 - 3.18: 8126 3.18 - 3.75: 13977 3.75 - 4.33: 20919 4.33 - 4.90: 35359 Nonbonded interactions: 78448 Sorted by model distance: nonbonded pdb=" OD2 ASP A 465 " pdb="MG MG A1102 " model vdw 2.027 2.170 nonbonded pdb="MG MG A1101 " pdb=" O2B ATP A1103 " model vdw 2.046 2.170 nonbonded pdb="MG MG A1101 " pdb=" O2A ATP A1103 " model vdw 2.082 2.170 nonbonded pdb=" OD2 ASP A 537 " pdb="MG MG A1101 " model vdw 2.106 2.170 nonbonded pdb=" O PRO C 18 " pdb=" OG SER C 19 " model vdw 2.127 3.040 ... (remaining 78443 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.560 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.870 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.871 9749 Z= 0.483 Angle : 0.619 44.421 13206 Z= 0.310 Chirality : 0.043 0.287 1471 Planarity : 0.003 0.033 1709 Dihedral : 9.870 80.677 3664 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.94 % Allowed : 2.73 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.25), residues: 1200 helix: 1.99 (0.25), residues: 482 sheet: 0.99 (0.35), residues: 183 loop : 0.13 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 72 TYR 0.009 0.001 TYR A 20 PHE 0.011 0.001 PHE A 360 TRP 0.007 0.001 TRP A 608 HIS 0.003 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 9746) covalent geometry : angle 0.47386 (13204) SS BOND : bond 0.87139 ( 1) SS BOND : angle 32.40025 ( 2) hydrogen bonds : bond 0.14672 ( 456) hydrogen bonds : angle 5.80971 ( 1275) Misc. bond : bond 0.07973 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8387 (t) cc_final: 0.8029 (p) REVERT: A 114 GLU cc_start: 0.7628 (tt0) cc_final: 0.7358 (tm-30) REVERT: A 190 ASP cc_start: 0.7434 (t0) cc_final: 0.7146 (t0) REVERT: A 196 MET cc_start: 0.8568 (mmp) cc_final: 0.8342 (mmm) REVERT: A 214 GLU cc_start: 0.7687 (mt-10) cc_final: 0.6883 (tt0) REVERT: A 216 LYS cc_start: 0.6259 (mtmm) cc_final: 0.5839 (pttp) REVERT: A 218 MET cc_start: 0.7748 (mtt) cc_final: 0.7496 (mtt) REVERT: A 286 MET cc_start: 0.7625 (mmm) cc_final: 0.6608 (pmt) REVERT: A 306 GLU cc_start: 0.8286 (mp0) cc_final: 0.7803 (mp0) REVERT: A 387 ASP cc_start: 0.8676 (p0) cc_final: 0.8462 (p0) REVERT: A 397 THR cc_start: 0.8241 (m) cc_final: 0.7934 (t) REVERT: A 524 GLU cc_start: 0.7530 (mp0) cc_final: 0.7235 (mp0) REVERT: A 583 GLN cc_start: 0.7813 (mt0) cc_final: 0.7094 (mp10) REVERT: A 878 LYS cc_start: 0.8261 (mmtp) cc_final: 0.8037 (mmtp) REVERT: A 879 LYS cc_start: 0.7917 (mttm) cc_final: 0.7486 (mttm) REVERT: A 919 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7927 (pmm-80) REVERT: A 1004 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7791 (mt-10) REVERT: A 1011 LYS cc_start: 0.7948 (ttmm) cc_final: 0.7682 (ttmt) outliers start: 10 outliers final: 4 residues processed: 144 average time/residue: 0.7469 time to fit residues: 113.8148 Evaluate side-chains 121 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 97 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.125694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.087948 restraints weight = 11811.218| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.32 r_work: 0.2875 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9749 Z= 0.184 Angle : 0.525 10.257 13206 Z= 0.274 Chirality : 0.044 0.155 1471 Planarity : 0.004 0.042 1709 Dihedral : 6.573 87.467 1336 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.98 % Allowed : 6.69 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.24), residues: 1200 helix: 1.76 (0.24), residues: 490 sheet: 1.08 (0.35), residues: 187 loop : 0.16 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 72 TYR 0.010 0.001 TYR A 953 PHE 0.013 0.001 PHE A 237 TRP 0.006 0.001 TRP A 608 HIS 0.003 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 9746) covalent geometry : angle 0.51648 (13204) SS BOND : bond 0.02537 ( 1) SS BOND : angle 7.64608 ( 2) hydrogen bonds : bond 0.05073 ( 456) hydrogen bonds : angle 4.80310 ( 1275) Misc. bond : bond 0.00181 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.387 Fit side-chains REVERT: A 110 SER cc_start: 0.8533 (t) cc_final: 0.8121 (p) REVERT: A 114 GLU cc_start: 0.7890 (tt0) cc_final: 0.7580 (tm-30) REVERT: A 214 GLU cc_start: 0.7841 (mt-10) cc_final: 0.6991 (tt0) REVERT: A 216 LYS cc_start: 0.6380 (mtmm) cc_final: 0.5945 (pttp) REVERT: A 286 MET cc_start: 0.7980 (mmm) cc_final: 0.6858 (pmt) REVERT: A 306 GLU cc_start: 0.8466 (mp0) cc_final: 0.7974 (mp0) REVERT: A 397 THR cc_start: 0.8237 (m) cc_final: 0.7878 (t) REVERT: A 524 GLU cc_start: 0.7756 (mp0) cc_final: 0.7387 (mp0) REVERT: A 583 GLN cc_start: 0.7859 (mt0) cc_final: 0.7039 (mp10) REVERT: A 601 ARG cc_start: 0.7297 (mtp180) cc_final: 0.6720 (mtm-85) REVERT: A 878 LYS cc_start: 0.8316 (mmtp) cc_final: 0.8102 (mmtp) REVERT: A 879 LYS cc_start: 0.7861 (mttm) cc_final: 0.7469 (mttm) REVERT: A 1004 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7896 (mt-10) REVERT: A 1011 LYS cc_start: 0.8057 (ttmm) cc_final: 0.7739 (ttmt) REVERT: B 31 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.6907 (tt0) outliers start: 21 outliers final: 10 residues processed: 123 average time/residue: 0.7860 time to fit residues: 102.2132 Evaluate side-chains 120 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 10 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 0.0770 chunk 60 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 25 optimal weight: 0.2980 chunk 89 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.127030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.089352 restraints weight = 11709.719| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.32 r_work: 0.2895 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9749 Z= 0.121 Angle : 0.480 8.209 13206 Z= 0.251 Chirality : 0.042 0.146 1471 Planarity : 0.004 0.044 1709 Dihedral : 6.215 83.013 1332 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.89 % Allowed : 7.63 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.24), residues: 1200 helix: 1.78 (0.24), residues: 491 sheet: 1.13 (0.36), residues: 186 loop : 0.20 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 72 TYR 0.008 0.001 TYR C 74 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 0.00286 ( 9746) covalent geometry : angle 0.47366 (13204) SS BOND : bond 0.01239 ( 1) SS BOND : angle 6.20341 ( 2) hydrogen bonds : bond 0.04124 ( 456) hydrogen bonds : angle 4.54053 ( 1275) Misc. bond : bond 0.00236 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.421 Fit side-chains REVERT: A 110 SER cc_start: 0.8436 (t) cc_final: 0.8022 (p) REVERT: A 114 GLU cc_start: 0.7880 (tt0) cc_final: 0.7569 (tm-30) REVERT: A 214 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7033 (tt0) REVERT: A 216 LYS cc_start: 0.6303 (mtmm) cc_final: 0.5873 (pttp) REVERT: A 274 ASP cc_start: 0.8103 (p0) cc_final: 0.7887 (p0) REVERT: A 286 MET cc_start: 0.7918 (mmm) cc_final: 0.6885 (pmt) REVERT: A 306 GLU cc_start: 0.8488 (mp0) cc_final: 0.8047 (mp0) REVERT: A 353 ASP cc_start: 0.8476 (t70) cc_final: 0.8020 (t0) REVERT: A 387 ASP cc_start: 0.8762 (p0) cc_final: 0.8511 (p0) REVERT: A 397 THR cc_start: 0.8244 (m) cc_final: 0.7893 (t) REVERT: A 524 GLU cc_start: 0.7807 (mp0) cc_final: 0.7408 (mp0) REVERT: A 583 GLN cc_start: 0.7855 (mt0) cc_final: 0.7026 (mp10) REVERT: A 601 ARG cc_start: 0.7266 (mtp180) cc_final: 0.6716 (mtm-85) REVERT: A 878 LYS cc_start: 0.8309 (mmtp) cc_final: 0.8102 (mmtp) REVERT: A 879 LYS cc_start: 0.7846 (mttm) cc_final: 0.7450 (mttm) REVERT: A 1004 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7874 (mt-10) REVERT: A 1011 LYS cc_start: 0.8064 (ttmm) cc_final: 0.7742 (ttmt) REVERT: B 31 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.7086 (tt0) outliers start: 20 outliers final: 12 residues processed: 125 average time/residue: 0.7294 time to fit residues: 96.8729 Evaluate side-chains 124 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 992 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 97 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 77 optimal weight: 0.0670 chunk 104 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.126628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.088834 restraints weight = 11896.745| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.34 r_work: 0.2888 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9749 Z= 0.139 Angle : 0.483 7.302 13206 Z= 0.251 Chirality : 0.042 0.148 1471 Planarity : 0.004 0.045 1709 Dihedral : 6.300 87.249 1332 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.79 % Allowed : 8.01 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.24), residues: 1200 helix: 1.75 (0.24), residues: 491 sheet: 1.09 (0.36), residues: 186 loop : 0.17 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 72 TYR 0.008 0.001 TYR C 74 PHE 0.011 0.001 PHE A 360 TRP 0.005 0.001 TRP A 608 HIS 0.002 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9746) covalent geometry : angle 0.47847 (13204) SS BOND : bond 0.00997 ( 1) SS BOND : angle 5.53153 ( 2) hydrogen bonds : bond 0.04151 ( 456) hydrogen bonds : angle 4.50350 ( 1275) Misc. bond : bond 0.00137 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8511 (t) cc_final: 0.8097 (p) REVERT: A 114 GLU cc_start: 0.7890 (tt0) cc_final: 0.7578 (tm-30) REVERT: A 214 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7131 (tt0) REVERT: A 216 LYS cc_start: 0.6173 (mtmm) cc_final: 0.5766 (pttp) REVERT: A 286 MET cc_start: 0.7917 (mmm) cc_final: 0.6875 (pmt) REVERT: A 306 GLU cc_start: 0.8488 (mp0) cc_final: 0.8047 (mp0) REVERT: A 387 ASP cc_start: 0.8793 (p0) cc_final: 0.8524 (p0) REVERT: A 397 THR cc_start: 0.8248 (m) cc_final: 0.7911 (t) REVERT: A 524 GLU cc_start: 0.7818 (mp0) cc_final: 0.7404 (mp0) REVERT: A 583 GLN cc_start: 0.7847 (mt0) cc_final: 0.6989 (mp10) REVERT: A 601 ARG cc_start: 0.7297 (mtp180) cc_final: 0.6756 (mtm-85) REVERT: A 878 LYS cc_start: 0.8306 (mmtp) cc_final: 0.8096 (mmtp) REVERT: A 879 LYS cc_start: 0.7862 (mttm) cc_final: 0.7460 (mttm) REVERT: A 1004 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7891 (mt-10) REVERT: A 1011 LYS cc_start: 0.8048 (ttmm) cc_final: 0.7721 (ttmt) outliers start: 19 outliers final: 16 residues processed: 123 average time/residue: 0.7172 time to fit residues: 93.5638 Evaluate side-chains 126 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 992 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 77 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 79 optimal weight: 0.4980 chunk 72 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 chunk 75 optimal weight: 0.0570 chunk 49 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.126725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.088969 restraints weight = 11765.471| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.32 r_work: 0.2891 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9749 Z= 0.133 Angle : 0.483 6.634 13206 Z= 0.252 Chirality : 0.042 0.142 1471 Planarity : 0.004 0.046 1709 Dihedral : 6.306 87.789 1332 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.79 % Allowed : 8.39 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.24), residues: 1200 helix: 1.75 (0.24), residues: 491 sheet: 1.10 (0.36), residues: 186 loop : 0.22 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 72 TYR 0.008 0.001 TYR C 74 PHE 0.012 0.001 PHE A 360 TRP 0.005 0.001 TRP C 93 HIS 0.002 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9746) covalent geometry : angle 0.47928 (13204) SS BOND : bond 0.01022 ( 1) SS BOND : angle 5.04863 ( 2) hydrogen bonds : bond 0.04068 ( 456) hydrogen bonds : angle 4.46263 ( 1275) Misc. bond : bond 0.00097 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8430 (t) cc_final: 0.8001 (p) REVERT: A 114 GLU cc_start: 0.7865 (tt0) cc_final: 0.7552 (tm-30) REVERT: A 214 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7140 (tt0) REVERT: A 216 LYS cc_start: 0.5994 (mtmm) cc_final: 0.5594 (pttp) REVERT: A 286 MET cc_start: 0.7888 (mmm) cc_final: 0.6847 (pmt) REVERT: A 306 GLU cc_start: 0.8484 (mp0) cc_final: 0.8039 (mp0) REVERT: A 387 ASP cc_start: 0.8789 (p0) cc_final: 0.8512 (p0) REVERT: A 524 GLU cc_start: 0.7797 (mp0) cc_final: 0.7478 (mp0) REVERT: A 583 GLN cc_start: 0.7837 (mt0) cc_final: 0.6974 (mp10) REVERT: A 601 ARG cc_start: 0.7274 (mtp180) cc_final: 0.6773 (mtm-85) REVERT: A 646 GLU cc_start: 0.8198 (pp20) cc_final: 0.7973 (pp20) REVERT: A 878 LYS cc_start: 0.8306 (mmtp) cc_final: 0.8091 (mmtp) REVERT: A 879 LYS cc_start: 0.7866 (mttm) cc_final: 0.7441 (mttm) REVERT: A 1004 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7890 (mt-10) REVERT: A 1011 LYS cc_start: 0.8041 (ttmm) cc_final: 0.7709 (ttmt) outliers start: 19 outliers final: 16 residues processed: 120 average time/residue: 0.7172 time to fit residues: 91.6093 Evaluate side-chains 124 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 992 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 18 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3462 r_free = 0.3462 target = 0.124961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.087121 restraints weight = 11853.375| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.32 r_work: 0.2863 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9749 Z= 0.207 Angle : 0.529 6.812 13206 Z= 0.275 Chirality : 0.044 0.195 1471 Planarity : 0.004 0.047 1709 Dihedral : 6.535 86.858 1332 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.98 % Allowed : 8.39 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.24), residues: 1200 helix: 1.62 (0.24), residues: 490 sheet: 1.01 (0.35), residues: 186 loop : 0.14 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 72 TYR 0.011 0.001 TYR A 20 PHE 0.014 0.002 PHE A 237 TRP 0.007 0.001 TRP A 608 HIS 0.003 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 9746) covalent geometry : angle 0.52541 (13204) SS BOND : bond 0.01350 ( 1) SS BOND : angle 5.27683 ( 2) hydrogen bonds : bond 0.04790 ( 456) hydrogen bonds : angle 4.57276 ( 1275) Misc. bond : bond 0.00091 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8567 (t) cc_final: 0.8124 (p) REVERT: A 114 GLU cc_start: 0.7849 (tt0) cc_final: 0.7573 (tm-30) REVERT: A 214 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7105 (tt0) REVERT: A 216 LYS cc_start: 0.6015 (mtmm) cc_final: 0.5632 (pttp) REVERT: A 286 MET cc_start: 0.7995 (mmm) cc_final: 0.6871 (pmt) REVERT: A 306 GLU cc_start: 0.8497 (mp0) cc_final: 0.8049 (mp0) REVERT: A 524 GLU cc_start: 0.7827 (mp0) cc_final: 0.7516 (mp0) REVERT: A 583 GLN cc_start: 0.7880 (mt0) cc_final: 0.7027 (mp10) REVERT: A 601 ARG cc_start: 0.7438 (mtp180) cc_final: 0.6834 (mtm-85) REVERT: A 646 GLU cc_start: 0.8299 (pp20) cc_final: 0.8018 (pp20) REVERT: A 879 LYS cc_start: 0.7905 (mttm) cc_final: 0.7515 (mttm) REVERT: A 1004 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7892 (mt-10) REVERT: C 72 ARG cc_start: 0.8268 (mmm-85) cc_final: 0.8045 (mmm-85) outliers start: 21 outliers final: 18 residues processed: 120 average time/residue: 0.6183 time to fit residues: 79.0127 Evaluate side-chains 122 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 992 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 0.5980 chunk 82 optimal weight: 0.4980 chunk 60 optimal weight: 0.6980 chunk 114 optimal weight: 0.0170 chunk 117 optimal weight: 0.9980 chunk 109 optimal weight: 0.0770 chunk 24 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 overall best weight: 0.3576 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.127290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.089437 restraints weight = 11836.110| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.34 r_work: 0.2899 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9749 Z= 0.105 Angle : 0.468 5.943 13206 Z= 0.243 Chirality : 0.041 0.173 1471 Planarity : 0.004 0.045 1709 Dihedral : 6.285 89.734 1332 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.70 % Allowed : 8.58 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.24), residues: 1200 helix: 1.75 (0.24), residues: 492 sheet: 1.12 (0.36), residues: 184 loop : 0.23 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 72 TYR 0.008 0.001 TYR C 74 PHE 0.011 0.001 PHE A 360 TRP 0.005 0.001 TRP A 669 HIS 0.001 0.000 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9746) covalent geometry : angle 0.46456 (13204) SS BOND : bond 0.00828 ( 1) SS BOND : angle 4.40836 ( 2) hydrogen bonds : bond 0.03749 ( 456) hydrogen bonds : angle 4.39920 ( 1275) Misc. bond : bond 0.00005 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8322 (t) cc_final: 0.7902 (p) REVERT: A 114 GLU cc_start: 0.7837 (tt0) cc_final: 0.7565 (tm-30) REVERT: A 214 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7108 (tt0) REVERT: A 216 LYS cc_start: 0.5969 (mtmm) cc_final: 0.5544 (pttp) REVERT: A 286 MET cc_start: 0.7901 (mmm) cc_final: 0.6836 (pmt) REVERT: A 306 GLU cc_start: 0.8497 (mp0) cc_final: 0.8052 (mp0) REVERT: A 327 LYS cc_start: 0.6496 (ttmm) cc_final: 0.6225 (ttmm) REVERT: A 328 ILE cc_start: 0.7083 (mt) cc_final: 0.6830 (mt) REVERT: A 524 GLU cc_start: 0.7830 (mp0) cc_final: 0.7440 (mp0) REVERT: A 583 GLN cc_start: 0.7860 (mt0) cc_final: 0.6998 (mp10) REVERT: A 601 ARG cc_start: 0.7337 (mtp180) cc_final: 0.6789 (mtm-85) REVERT: A 879 LYS cc_start: 0.7860 (mttm) cc_final: 0.7427 (mttm) REVERT: A 1004 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7865 (mt-10) REVERT: B 31 GLN cc_start: 0.7121 (OUTLIER) cc_final: 0.6902 (tt0) REVERT: C 72 ARG cc_start: 0.8232 (mmm-85) cc_final: 0.8000 (mmm-85) outliers start: 18 outliers final: 16 residues processed: 118 average time/residue: 0.7070 time to fit residues: 88.7879 Evaluate side-chains 121 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 992 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 66 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 78 optimal weight: 0.3980 chunk 18 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 96 optimal weight: 0.1980 chunk 113 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 = 0.3471 r_free = 0.3471 target = 0.125627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.087829 restraints weight = 11748.224| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.32 r_work: 0.2877 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9749 Z= 0.179 Angle : 0.502 6.129 13206 Z= 0.260 Chirality : 0.043 0.190 1471 Planarity : 0.004 0.047 1709 Dihedral : 6.368 88.338 1332 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.79 % Allowed : 8.77 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.24), residues: 1200 helix: 1.70 (0.24), residues: 490 sheet: 1.01 (0.36), residues: 186 loop : 0.18 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 72 TYR 0.009 0.001 TYR A 20 PHE 0.012 0.001 PHE A 237 TRP 0.007 0.001 TRP A 608 HIS 0.002 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 9746) covalent geometry : angle 0.49886 (13204) SS BOND : bond 0.00759 ( 1) SS BOND : angle 4.77375 ( 2) hydrogen bonds : bond 0.04346 ( 456) hydrogen bonds : angle 4.47027 ( 1275) Misc. bond : bond 0.00064 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8509 (t) cc_final: 0.8079 (p) REVERT: A 114 GLU cc_start: 0.7839 (tt0) cc_final: 0.7560 (tm-30) REVERT: A 190 ASP cc_start: 0.7646 (t70) cc_final: 0.7322 (t0) REVERT: A 214 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7106 (tt0) REVERT: A 216 LYS cc_start: 0.5952 (mtmm) cc_final: 0.5504 (tttm) REVERT: A 286 MET cc_start: 0.7934 (mmm) cc_final: 0.6888 (pmt) REVERT: A 306 GLU cc_start: 0.8498 (mp0) cc_final: 0.8082 (mp0) REVERT: A 524 GLU cc_start: 0.7827 (mp0) cc_final: 0.7508 (mp0) REVERT: A 583 GLN cc_start: 0.7882 (mt0) cc_final: 0.7013 (mp10) REVERT: A 601 ARG cc_start: 0.7403 (mtp180) cc_final: 0.6854 (mtm-85) REVERT: A 879 LYS cc_start: 0.7900 (mttm) cc_final: 0.7491 (mttm) REVERT: A 1004 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7927 (mt-10) REVERT: C 72 ARG cc_start: 0.8288 (mmm-85) cc_final: 0.8049 (mmm-85) outliers start: 19 outliers final: 18 residues processed: 117 average time/residue: 0.5561 time to fit residues: 69.1665 Evaluate side-chains 125 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 992 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 101 optimal weight: 0.0970 chunk 61 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 46 optimal weight: 0.1980 chunk 60 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.126917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.089246 restraints weight = 11799.435| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.33 r_work: 0.2899 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9749 Z= 0.118 Angle : 0.476 5.918 13206 Z= 0.248 Chirality : 0.042 0.212 1471 Planarity : 0.004 0.046 1709 Dihedral : 6.264 89.929 1332 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.51 % Allowed : 9.33 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.24), residues: 1200 helix: 1.77 (0.24), residues: 492 sheet: 1.07 (0.36), residues: 184 loop : 0.23 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 72 TYR 0.007 0.001 TYR C 74 PHE 0.011 0.001 PHE A 360 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9746) covalent geometry : angle 0.47271 (13204) SS BOND : bond 0.00838 ( 1) SS BOND : angle 4.36330 ( 2) hydrogen bonds : bond 0.03825 ( 456) hydrogen bonds : angle 4.38867 ( 1275) Misc. bond : bond 0.00072 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8400 (t) cc_final: 0.7983 (p) REVERT: A 114 GLU cc_start: 0.7823 (tt0) cc_final: 0.7548 (tm-30) REVERT: A 182 THR cc_start: 0.8508 (t) cc_final: 0.8304 (m) REVERT: A 190 ASP cc_start: 0.7645 (t70) cc_final: 0.7322 (t0) REVERT: A 214 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7113 (tt0) REVERT: A 216 LYS cc_start: 0.5961 (mtmm) cc_final: 0.5479 (tttm) REVERT: A 286 MET cc_start: 0.7890 (mmm) cc_final: 0.6864 (pmt) REVERT: A 306 GLU cc_start: 0.8504 (mp0) cc_final: 0.8093 (mp0) REVERT: A 327 LYS cc_start: 0.6529 (ttmm) cc_final: 0.6197 (ttmm) REVERT: A 524 GLU cc_start: 0.7812 (mp0) cc_final: 0.7418 (mp0) REVERT: A 583 GLN cc_start: 0.7860 (mt0) cc_final: 0.6996 (mp10) REVERT: A 601 ARG cc_start: 0.7355 (mtp180) cc_final: 0.6801 (mtm-85) REVERT: A 879 LYS cc_start: 0.7919 (mttm) cc_final: 0.7480 (mttm) REVERT: A 1004 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7890 (mt-10) REVERT: C 72 ARG cc_start: 0.8283 (mmm-85) cc_final: 0.8046 (mmm-85) outliers start: 16 outliers final: 16 residues processed: 118 average time/residue: 0.6104 time to fit residues: 76.8711 Evaluate side-chains 120 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 992 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.125781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.087987 restraints weight = 11786.084| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.33 r_work: 0.2877 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9749 Z= 0.167 Angle : 0.508 6.106 13206 Z= 0.263 Chirality : 0.044 0.229 1471 Planarity : 0.004 0.046 1709 Dihedral : 6.291 87.827 1331 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.60 % Allowed : 9.33 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.24), residues: 1200 helix: 1.71 (0.24), residues: 490 sheet: 0.96 (0.36), residues: 186 loop : 0.19 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 72 TYR 0.009 0.001 TYR A 150 PHE 0.012 0.001 PHE A 237 TRP 0.006 0.001 TRP A 669 HIS 0.003 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 9746) covalent geometry : angle 0.50443 (13204) SS BOND : bond 0.00891 ( 1) SS BOND : angle 4.67919 ( 2) hydrogen bonds : bond 0.04303 ( 456) hydrogen bonds : angle 4.46702 ( 1275) Misc. bond : bond 0.00063 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8492 (t) cc_final: 0.8065 (p) REVERT: A 114 GLU cc_start: 0.7809 (tt0) cc_final: 0.7523 (tm-30) REVERT: A 190 ASP cc_start: 0.7652 (t70) cc_final: 0.7334 (t0) REVERT: A 214 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7107 (tt0) REVERT: A 216 LYS cc_start: 0.6078 (mtmm) cc_final: 0.5565 (tttp) REVERT: A 286 MET cc_start: 0.7902 (mmm) cc_final: 0.6865 (pmt) REVERT: A 306 GLU cc_start: 0.8490 (mp0) cc_final: 0.8078 (mp0) REVERT: A 327 LYS cc_start: 0.6480 (ttmm) cc_final: 0.6220 (ttmm) REVERT: A 524 GLU cc_start: 0.7796 (mp0) cc_final: 0.7475 (mp0) REVERT: A 583 GLN cc_start: 0.7867 (mt0) cc_final: 0.6995 (mp10) REVERT: A 601 ARG cc_start: 0.7379 (mtp180) cc_final: 0.6828 (mtm-85) REVERT: A 879 LYS cc_start: 0.7854 (mttm) cc_final: 0.7461 (mttm) REVERT: A 1004 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7927 (mt-10) REVERT: C 72 ARG cc_start: 0.8339 (mmm-85) cc_final: 0.8120 (mmm-85) outliers start: 17 outliers final: 16 residues processed: 116 average time/residue: 0.6156 time to fit residues: 76.1078 Evaluate side-chains 120 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 992 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 8 optimal weight: 0.1980 chunk 56 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 116 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 101 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.126844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.089085 restraints weight = 11774.208| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.33 r_work: 0.2895 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9749 Z= 0.118 Angle : 0.486 7.940 13206 Z= 0.251 Chirality : 0.042 0.240 1471 Planarity : 0.004 0.046 1709 Dihedral : 6.224 88.942 1331 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.51 % Allowed : 9.71 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.24), residues: 1200 helix: 1.78 (0.24), residues: 490 sheet: 1.02 (0.36), residues: 184 loop : 0.21 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 72 TYR 0.008 0.001 TYR C 74 PHE 0.011 0.001 PHE A 360 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9746) covalent geometry : angle 0.48273 (13204) SS BOND : bond 0.00779 ( 1) SS BOND : angle 4.41123 ( 2) hydrogen bonds : bond 0.03853 ( 456) hydrogen bonds : angle 4.40761 ( 1275) Misc. bond : bond 0.00057 ( 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: 3328.40 seconds wall clock time: 57 minutes 10.26 seconds (3430.26 seconds total)