Starting phenix.real_space_refine on Sat Aug 23 04:18:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5w_44227/08_2025/9b5w_44227.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5w_44227/08_2025/9b5w_44227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b5w_44227/08_2025/9b5w_44227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5w_44227/08_2025/9b5w_44227.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5w_44227/08_2025/9b5w_44227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5w_44227/08_2025/9b5w_44227.cif" } resolution = 3.96 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= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 2 5.21 5 S 42 5.16 5 C 6074 2.51 5 N 1573 2.21 5 O 1833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s 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: 9527 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7734 Classifications: {'peptide': 985} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 928} Chain breaks: 1 Chain: "C" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1158 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131} Chain: "D" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 596 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'A1AIV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.91, per 1000 atoms: 0.20 Number of scatterers: 9527 At special positions: 0 Unit cell: (101.08, 97.888, 119.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 3 15.00 Mg 2 11.99 O 1833 8.00 N 1573 7.00 C 6074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS C 85 " distance=2.90 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: 0.85 Conformation dependent library (CDL) restraints added in 376.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 46.4% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.974A 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: 3.540A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.936A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.042A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.587A 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 144 removed outlier: 3.639A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 224 removed outlier: 4.201A pdb=" N GLY A 224 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.141A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 304 removed outlier: 4.010A pdb=" N GLN A 290 " --> pdb=" O MET A 286 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN A 296 " --> pdb=" O HIS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 332 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 354 through 375 Processing helix chain 'A' and resid 389 through 392 Processing helix chain 'A' and resid 399 through 404 Processing helix chain 'A' and resid 410 through 418 removed outlier: 4.473A 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: 3.868A pdb=" N ASN A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.595A 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 removed outlier: 3.583A pdb=" N CYS A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 503 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.854A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 538 through 553 Processing helix 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 removed outlier: 3.540A pdb=" N THR A 605 " --> pdb=" O ARG A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 630 Processing helix chain 'A' and resid 632 through 641 removed outlier: 3.532A 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: 3.519A pdb=" N CYS A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 689 removed outlier: 3.768A 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: 3.923A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 794 removed outlier: 4.095A pdb=" N GLN A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 794 " --> pdb=" O ILE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 834 Processing helix chain 'A' and resid 840 through 849 Processing helix chain 'A' and resid 855 through 876 removed outlier: 3.526A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 937 Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 969 through 979 Processing helix chain 'C' and resid 3 through 16 removed outlier: 3.719A pdb=" N GLY C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 112 removed outlier: 4.062A pdb=" N SER C 107 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 130 Processing helix chain 'C' and resid 130 through 145 Processing helix chain 'D' and resid 22 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 55 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.722A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N THR A 129 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE A 43 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.549A 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: 4.298A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.354A 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: 4.298A 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: 3.545A pdb=" N SER A 460 " --> pdb=" O THR A 430 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.324A 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: 6.425A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N VAL A 990 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N SER A 947 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU A 992 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU A 945 " --> pdb=" O GLU A 992 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N CYS A 994 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.504A 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: 6.425A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N CYS A 995 " --> pdb=" O VAL A1003 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 24 through 26 removed outlier: 3.605A pdb=" N GLY C 24 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N HIS C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 12 through 16 461 hydrogen bonds defined for protein. 1260 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: 1.61 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1616 1.27 - 1.40: 2291 1.40 - 1.54: 5666 1.54 - 1.67: 101 1.67 - 1.81: 64 Bond restraints: 9738 Sorted by residual: bond pdb=" C04 A1AIV D 101 " pdb=" C05 A1AIV D 101 " ideal model delta sigma weight residual 1.453 1.522 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.30e+00 bond pdb=" CB TRP C 33 " pdb=" CG TRP C 33 " ideal model delta sigma weight residual 1.498 1.456 0.042 3.10e-02 1.04e+03 1.81e+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 1.12e+00 bond pdb=" C05 A1AIV D 101 " pdb=" N06 A1AIV D 101 " ideal model delta sigma weight residual 1.151 1.131 0.020 2.00e-02 2.50e+03 9.60e-01 ... (remaining 9733 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 13095 2.25 - 4.51: 92 4.51 - 6.76: 7 6.76 - 9.02: 0 9.02 - 11.27: 1 Bond angle restraints: 13195 Sorted by residual: angle pdb=" C03 A1AIV D 101 " pdb=" C02 A1AIV D 101 " pdb=" N01 A1AIV D 101 " ideal model delta sigma weight residual 111.06 99.79 11.27 3.00e+00 1.11e-01 1.41e+01 angle pdb=" C LYS A 381 " pdb=" N GLN A 382 " pdb=" CA GLN A 382 " ideal model delta sigma weight residual 121.70 127.81 -6.11 1.80e+00 3.09e-01 1.15e+01 angle pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 106.53 103.32 3.21 1.18e+00 7.24e-01 7.46e+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=" N LEU C 104 " pdb=" CA LEU C 104 " pdb=" C LEU C 104 " ideal model delta sigma weight residual 113.72 110.61 3.11 1.30e+00 5.92e-01 5.73e+00 ... (remaining 13190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 5709 17.44 - 34.88: 177 34.88 - 52.32: 35 52.32 - 69.76: 6 69.76 - 87.21: 2 Dihedral angle restraints: 5929 sinusoidal: 2424 harmonic: 3505 Sorted by residual: dihedral pdb=" CB CYS A 593 " pdb=" SG CYS A 593 " pdb=" SG CYS C 85 " pdb=" CB CYS C 85 " ideal model delta sinusoidal sigma weight residual 93.00 135.03 -42.03 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" SG CYS A 593 " pdb=" CB CYS C 85 " pdb=" SG CYS C 85 " pdb=" CA CYS C 85 " ideal model delta sinusoidal sigma weight residual -73.00 -4.19 -68.81 1 2.00e+01 2.50e-03 1.53e+01 dihedral pdb=" CA LYS A 884 " pdb=" C LYS A 884 " pdb=" N ASN A 885 " pdb=" CA ASN A 885 " ideal model delta harmonic sigma weight residual 180.00 163.55 16.45 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 5926 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1284 0.056 - 0.112: 168 0.112 - 0.169: 16 0.169 - 0.225: 1 0.225 - 0.281: 2 Chirality restraints: 1471 Sorted by residual: chirality pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O2' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.68 -2.96 0.28 2.00e-01 2.50e+01 1.97e+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 -2.89 0.26 2.00e-01 2.50e+01 1.68e+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 -2.71 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1468 not shown) Planarity restraints: 1707 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 104 " 0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C LEU C 104 " -0.065 2.00e-02 2.50e+03 pdb=" O LEU C 104 " 0.024 2.00e-02 2.50e+03 pdb=" N SER C 105 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 35 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C ALA C 35 " -0.030 2.00e-02 2.50e+03 pdb=" O ALA C 35 " 0.011 2.00e-02 2.50e+03 pdb=" N THR C 36 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 5 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.50e+00 pdb=" C ARG C 5 " -0.027 2.00e-02 2.50e+03 pdb=" O ARG C 5 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE C 6 " 0.009 2.00e-02 2.50e+03 ... (remaining 1704 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 88 2.56 - 3.15: 8083 3.15 - 3.73: 14297 3.73 - 4.32: 20301 4.32 - 4.90: 34238 Nonbonded interactions: 77007 Sorted by model distance: nonbonded pdb="MG MG A1102 " pdb=" O1B ATP A1103 " model vdw 1.979 2.170 nonbonded pdb="MG MG A1101 " pdb=" O3G ATP A1103 " model vdw 2.006 2.170 nonbonded pdb="MG MG A1101 " pdb=" O2A ATP A1103 " model vdw 2.018 2.170 nonbonded pdb=" O PRO C 18 " pdb=" OG SER C 19 " model vdw 2.069 3.040 nonbonded pdb=" OD2 ASP A 465 " pdb="MG MG A1102 " model vdw 2.097 2.170 ... (remaining 77002 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.590 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: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.900 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 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 0.874 9741 Z= 0.501 Angle : 0.738 59.783 13197 Z= 0.370 Chirality : 0.041 0.281 1471 Planarity : 0.004 0.038 1707 Dihedral : 9.277 87.206 3662 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.25 % Favored : 97.58 % Rotamer: Outliers : 1.32 % Allowed : 3.39 % Favored : 95.29 % 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: 0.94 (0.25), residues: 1199 helix: 1.52 (0.26), residues: 479 sheet: -0.16 (0.36), residues: 209 loop : 0.25 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 139 TYR 0.010 0.001 TYR A 277 PHE 0.011 0.001 PHE C 50 TRP 0.005 0.001 TRP C 93 HIS 0.005 0.001 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 9738) covalent geometry : angle 0.51761 (13195) SS BOND : bond 0.87362 ( 1) SS BOND : angle 42.70603 ( 2) hydrogen bonds : bond 0.13993 ( 448) hydrogen bonds : angle 5.87845 ( 1260) Misc. bond : bond 0.08531 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9459 (tp) cc_final: 0.9079 (mt) REVERT: A 55 ASN cc_start: 0.8425 (m-40) cc_final: 0.8005 (m-40) REVERT: A 218 MET cc_start: 0.8097 (mtt) cc_final: 0.7199 (mtt) REVERT: A 383 TYR cc_start: 0.8520 (m-80) cc_final: 0.8239 (m-80) REVERT: A 442 MET cc_start: 0.9270 (tpp) cc_final: 0.8697 (mmm) REVERT: A 913 ILE cc_start: 0.9266 (mm) cc_final: 0.8831 (mm) REVERT: A 919 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7380 (ptp90) REVERT: C 26 VAL cc_start: 0.8904 (t) cc_final: 0.8560 (t) REVERT: C 34 GLN cc_start: 0.9477 (tt0) cc_final: 0.9171 (tm-30) REVERT: C 81 ASN cc_start: 0.8811 (m-40) cc_final: 0.8335 (t0) REVERT: D 1 MET cc_start: 0.8948 (ptt) cc_final: 0.8661 (ptp) REVERT: D 50 LEU cc_start: 0.8755 (mt) cc_final: 0.8487 (mp) outliers start: 14 outliers final: 3 residues processed: 179 average time/residue: 0.1281 time to fit residues: 30.0339 Evaluate side-chains 91 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 919 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.0770 chunk 117 optimal weight: 4.9990 overall best weight: 1.1940 ------------------------------------------------------------------------------- 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 = 0.3165 r_free = 0.3165 target = 0.047207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.037872 restraints weight = 62902.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.039189 restraints weight = 37090.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.040109 restraints weight = 25557.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.040755 restraints weight = 19497.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.041250 restraints weight = 16007.317| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9741 Z= 0.150 Angle : 0.595 9.730 13197 Z= 0.306 Chirality : 0.042 0.167 1471 Planarity : 0.004 0.039 1707 Dihedral : 5.637 57.109 1335 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.79 % Allowed : 8.86 % Favored : 89.35 % 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: 1.11 (0.25), residues: 1199 helix: 1.40 (0.25), residues: 497 sheet: 0.10 (0.37), residues: 215 loop : 0.52 (0.30), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 841 TYR 0.016 0.001 TYR A 279 PHE 0.014 0.001 PHE C 62 TRP 0.009 0.001 TRP C 33 HIS 0.005 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9738) covalent geometry : angle 0.59164 (13195) SS BOND : bond 0.00424 ( 1) SS BOND : angle 5.09353 ( 2) hydrogen bonds : bond 0.03720 ( 448) hydrogen bonds : angle 4.65917 ( 1260) Misc. bond : bond 0.00105 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9501 (tp) cc_final: 0.9162 (mt) REVERT: A 55 ASN cc_start: 0.8406 (m-40) cc_final: 0.7981 (m-40) REVERT: A 218 MET cc_start: 0.8299 (mtt) cc_final: 0.7556 (mtt) REVERT: A 383 TYR cc_start: 0.8404 (m-80) cc_final: 0.7980 (m-80) REVERT: A 442 MET cc_start: 0.9301 (tpp) cc_final: 0.8609 (mmm) REVERT: A 448 MET cc_start: 0.8023 (tpp) cc_final: 0.7695 (tpt) REVERT: A 855 MET cc_start: 0.8685 (tpp) cc_final: 0.8218 (tpp) REVERT: A 919 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7191 (ptp90) REVERT: C 34 GLN cc_start: 0.9411 (tt0) cc_final: 0.9178 (tm-30) REVERT: C 74 TYR cc_start: 0.8293 (t80) cc_final: 0.7779 (t80) REVERT: C 81 ASN cc_start: 0.8742 (m-40) cc_final: 0.8181 (t0) REVERT: D 3 ILE cc_start: 0.9047 (pt) cc_final: 0.8783 (pt) REVERT: D 15 LEU cc_start: 0.7787 (mt) cc_final: 0.7373 (mp) outliers start: 19 outliers final: 11 residues processed: 108 average time/residue: 0.1037 time to fit residues: 15.8911 Evaluate side-chains 87 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 5 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 17 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 89 optimal weight: 0.1980 chunk 15 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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 = 0.3176 r_free = 0.3176 target = 0.048016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.038611 restraints weight = 62476.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.039941 restraints weight = 36736.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.040869 restraints weight = 25331.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.041528 restraints weight = 19365.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.041988 restraints weight = 15872.885| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9741 Z= 0.110 Angle : 0.538 8.358 13197 Z= 0.274 Chirality : 0.041 0.156 1471 Planarity : 0.004 0.043 1707 Dihedral : 5.313 59.901 1333 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.26 % Allowed : 8.95 % 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: 1.23 (0.25), residues: 1199 helix: 1.54 (0.24), residues: 497 sheet: 0.18 (0.39), residues: 203 loop : 0.51 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 8 TYR 0.013 0.001 TYR A 279 PHE 0.014 0.001 PHE A 237 TRP 0.006 0.001 TRP A 917 HIS 0.004 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9738) covalent geometry : angle 0.53678 (13195) SS BOND : bond 0.01171 ( 1) SS BOND : angle 2.93927 ( 2) hydrogen bonds : bond 0.03187 ( 448) hydrogen bonds : angle 4.36540 ( 1260) Misc. bond : bond 0.00075 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9467 (tp) cc_final: 0.9141 (mt) REVERT: A 55 ASN cc_start: 0.8362 (m-40) cc_final: 0.7893 (m110) REVERT: A 80 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8530 (tm-30) REVERT: A 285 MET cc_start: 0.8378 (mmm) cc_final: 0.8140 (mmm) REVERT: A 383 TYR cc_start: 0.8479 (m-80) cc_final: 0.8002 (m-80) REVERT: A 442 MET cc_start: 0.9306 (tpp) cc_final: 0.8602 (mmm) REVERT: A 448 MET cc_start: 0.8184 (tpp) cc_final: 0.7778 (tpt) REVERT: A 855 MET cc_start: 0.8810 (tpp) cc_final: 0.8308 (tpp) REVERT: A 919 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7117 (ptp90) REVERT: C 34 GLN cc_start: 0.9397 (tt0) cc_final: 0.9033 (tm-30) REVERT: C 74 TYR cc_start: 0.8308 (t80) cc_final: 0.7800 (t80) REVERT: C 81 ASN cc_start: 0.8716 (m-40) cc_final: 0.8139 (t0) REVERT: D 15 LEU cc_start: 0.7702 (mt) cc_final: 0.7371 (mp) outliers start: 24 outliers final: 13 residues processed: 101 average time/residue: 0.0973 time to fit residues: 13.8337 Evaluate side-chains 86 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 44 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 87 optimal weight: 0.0050 chunk 102 optimal weight: 0.0970 chunk 27 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 overall best weight: 0.4592 ------------------------------------------------------------------------------- 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 = 0.3189 r_free = 0.3189 target = 0.048171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.038812 restraints weight = 63255.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.040132 restraints weight = 37397.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.041080 restraints weight = 25789.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.041788 restraints weight = 19734.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.042285 restraints weight = 16173.866| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9741 Z= 0.099 Angle : 0.511 7.661 13197 Z= 0.260 Chirality : 0.040 0.138 1471 Planarity : 0.003 0.043 1707 Dihedral : 5.092 58.568 1333 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.45 % Allowed : 9.52 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.25), residues: 1199 helix: 1.61 (0.24), residues: 497 sheet: 0.24 (0.40), residues: 198 loop : 0.49 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 8 TYR 0.012 0.001 TYR C 127 PHE 0.013 0.001 PHE A 237 TRP 0.006 0.001 TRP A 917 HIS 0.004 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 9738) covalent geometry : angle 0.51004 (13195) SS BOND : bond 0.00234 ( 1) SS BOND : angle 2.07939 ( 2) hydrogen bonds : bond 0.02859 ( 448) hydrogen bonds : angle 4.25659 ( 1260) Misc. bond : bond 0.00103 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9413 (tp) cc_final: 0.9078 (mt) REVERT: A 55 ASN cc_start: 0.8313 (m-40) cc_final: 0.7812 (m110) REVERT: A 80 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8566 (tm-30) REVERT: A 383 TYR cc_start: 0.8443 (m-80) cc_final: 0.8044 (m-80) REVERT: A 442 MET cc_start: 0.9302 (tpp) cc_final: 0.8597 (mmm) REVERT: A 448 MET cc_start: 0.8258 (tpp) cc_final: 0.7821 (tpt) REVERT: A 919 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7122 (ptp90) REVERT: C 34 GLN cc_start: 0.9329 (tt0) cc_final: 0.9115 (tm-30) REVERT: C 74 TYR cc_start: 0.8237 (t80) cc_final: 0.7804 (t80) REVERT: C 81 ASN cc_start: 0.8566 (m-40) cc_final: 0.8100 (t0) REVERT: C 101 LYS cc_start: 0.8638 (mttt) cc_final: 0.8294 (mttt) REVERT: D 31 GLN cc_start: 0.8972 (tt0) cc_final: 0.8520 (tp40) outliers start: 26 outliers final: 15 residues processed: 101 average time/residue: 0.0844 time to fit residues: 12.4258 Evaluate side-chains 86 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 21 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3165 r_free = 0.3165 target = 0.047364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.038142 restraints weight = 64099.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.039425 restraints weight = 38369.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.040252 restraints weight = 26717.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.041007 restraints weight = 20976.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.041514 restraints weight = 16933.991| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9741 Z= 0.114 Angle : 0.510 7.389 13197 Z= 0.258 Chirality : 0.040 0.132 1471 Planarity : 0.003 0.044 1707 Dihedral : 4.840 58.174 1332 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.54 % Allowed : 10.37 % Favored : 87.09 % 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: 1.37 (0.25), residues: 1199 helix: 1.70 (0.24), residues: 497 sheet: 0.32 (0.39), residues: 198 loop : 0.51 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 8 TYR 0.013 0.001 TYR C 127 PHE 0.014 0.001 PHE A 237 TRP 0.004 0.001 TRP A 917 HIS 0.003 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9738) covalent geometry : angle 0.50853 (13195) SS BOND : bond 0.00388 ( 1) SS BOND : angle 3.16680 ( 2) hydrogen bonds : bond 0.02738 ( 448) hydrogen bonds : angle 4.23882 ( 1260) Misc. bond : bond 0.00123 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9450 (tp) cc_final: 0.9138 (mt) REVERT: A 55 ASN cc_start: 0.8342 (m-40) cc_final: 0.7821 (m110) REVERT: A 80 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.7957 (tm-30) REVERT: A 285 MET cc_start: 0.8193 (mmm) cc_final: 0.7985 (mmm) REVERT: A 383 TYR cc_start: 0.8446 (m-80) cc_final: 0.8071 (m-80) REVERT: A 442 MET cc_start: 0.9328 (tpp) cc_final: 0.8642 (mmm) REVERT: A 448 MET cc_start: 0.8291 (tpp) cc_final: 0.7851 (tpt) REVERT: A 919 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7150 (ptp90) REVERT: C 8 ARG cc_start: 0.9176 (mmm160) cc_final: 0.8798 (tpt90) REVERT: C 34 GLN cc_start: 0.9293 (tt0) cc_final: 0.9088 (tp-100) REVERT: C 74 TYR cc_start: 0.8235 (t80) cc_final: 0.7802 (t80) REVERT: C 81 ASN cc_start: 0.8538 (m-40) cc_final: 0.8082 (t0) REVERT: C 101 LYS cc_start: 0.8574 (mttt) cc_final: 0.8251 (mttt) REVERT: D 31 GLN cc_start: 0.9010 (tt0) cc_final: 0.8541 (tp40) outliers start: 27 outliers final: 16 residues processed: 93 average time/residue: 0.0797 time to fit residues: 10.7342 Evaluate side-chains 85 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 43 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3162 r_free = 0.3162 target = 0.047189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.038008 restraints weight = 63924.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.039277 restraints weight = 38169.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.040172 restraints weight = 26735.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.040851 restraints weight = 20700.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.041321 restraints weight = 17058.679| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9741 Z= 0.113 Angle : 0.506 8.423 13197 Z= 0.258 Chirality : 0.040 0.135 1471 Planarity : 0.003 0.044 1707 Dihedral : 4.794 57.541 1332 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.70 % Allowed : 11.40 % Favored : 86.90 % 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 (0.25), residues: 1199 helix: 1.74 (0.24), residues: 498 sheet: 0.26 (0.39), residues: 198 loop : 0.53 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 90 TYR 0.011 0.001 TYR C 127 PHE 0.012 0.001 PHE A 237 TRP 0.003 0.001 TRP C 93 HIS 0.006 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9738) covalent geometry : angle 0.50321 (13195) SS BOND : bond 0.00660 ( 1) SS BOND : angle 4.48684 ( 2) hydrogen bonds : bond 0.02713 ( 448) hydrogen bonds : angle 4.18966 ( 1260) Misc. bond : bond 0.00054 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9445 (tp) cc_final: 0.9132 (mt) REVERT: A 55 ASN cc_start: 0.8341 (m-40) cc_final: 0.7831 (m110) REVERT: A 80 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.7907 (tm-30) REVERT: A 383 TYR cc_start: 0.8428 (m-80) cc_final: 0.8079 (m-80) REVERT: A 442 MET cc_start: 0.9330 (tpp) cc_final: 0.8651 (mmm) REVERT: A 448 MET cc_start: 0.8223 (tpp) cc_final: 0.7734 (tpt) REVERT: A 919 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7137 (ptp90) REVERT: C 8 ARG cc_start: 0.9145 (mmm160) cc_final: 0.8850 (tpt90) REVERT: C 74 TYR cc_start: 0.8212 (t80) cc_final: 0.7817 (t80) REVERT: C 81 ASN cc_start: 0.8511 (m-40) cc_final: 0.8054 (t0) REVERT: C 101 LYS cc_start: 0.8589 (mttt) cc_final: 0.8204 (mttt) REVERT: D 31 GLN cc_start: 0.8995 (tt0) cc_final: 0.8543 (tp40) outliers start: 18 outliers final: 12 residues processed: 83 average time/residue: 0.0940 time to fit residues: 11.3594 Evaluate side-chains 81 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 57 optimal weight: 0.0040 chunk 43 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.6792 ------------------------------------------------------------------------------- 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 = 0.3172 r_free = 0.3172 target = 0.047418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.038267 restraints weight = 63684.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.039568 restraints weight = 37920.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.040455 restraints weight = 26378.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.041139 restraints weight = 20247.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.041652 restraints weight = 16731.909| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9741 Z= 0.099 Angle : 0.506 8.604 13197 Z= 0.256 Chirality : 0.040 0.132 1471 Planarity : 0.003 0.044 1707 Dihedral : 4.732 57.087 1332 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.89 % Allowed : 11.40 % Favored : 86.71 % 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: 1199 helix: 1.88 (0.24), residues: 490 sheet: 0.33 (0.40), residues: 188 loop : 0.52 (0.29), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 90 TYR 0.017 0.001 TYR C 127 PHE 0.013 0.001 PHE A 237 TRP 0.003 0.001 TRP C 141 HIS 0.010 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 9738) covalent geometry : angle 0.50511 (13195) SS BOND : bond 0.00384 ( 1) SS BOND : angle 2.76101 ( 2) hydrogen bonds : bond 0.02615 ( 448) hydrogen bonds : angle 4.17146 ( 1260) Misc. bond : bond 0.00016 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9448 (tp) cc_final: 0.9115 (mt) REVERT: A 55 ASN cc_start: 0.8321 (m-40) cc_final: 0.7797 (m110) REVERT: A 80 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.7859 (tm-30) REVERT: A 250 TYR cc_start: 0.8144 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: A 383 TYR cc_start: 0.8409 (m-80) cc_final: 0.8048 (m-80) REVERT: A 442 MET cc_start: 0.9338 (tpp) cc_final: 0.8650 (mmm) REVERT: A 448 MET cc_start: 0.8243 (tpp) cc_final: 0.7751 (tpt) REVERT: A 919 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7105 (ptp90) REVERT: C 8 ARG cc_start: 0.9177 (mmm160) cc_final: 0.8863 (tpt90) REVERT: C 74 TYR cc_start: 0.8226 (t80) cc_final: 0.7817 (t80) REVERT: C 81 ASN cc_start: 0.8517 (m-40) cc_final: 0.8013 (t0) REVERT: D 31 GLN cc_start: 0.8992 (tt0) cc_final: 0.8541 (tp40) outliers start: 20 outliers final: 13 residues processed: 87 average time/residue: 0.0799 time to fit residues: 10.1866 Evaluate side-chains 80 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 63 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 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 = 0.3166 r_free = 0.3166 target = 0.047233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.038199 restraints weight = 63077.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.039457 restraints weight = 37675.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.040286 restraints weight = 26334.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.040991 restraints weight = 20629.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.041499 restraints weight = 16905.310| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9741 Z= 0.105 Angle : 0.519 9.138 13197 Z= 0.263 Chirality : 0.041 0.174 1471 Planarity : 0.003 0.044 1707 Dihedral : 4.712 56.782 1332 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.98 % Allowed : 11.78 % Favored : 86.24 % 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: 1.51 (0.25), residues: 1199 helix: 1.94 (0.24), residues: 490 sheet: 0.26 (0.40), residues: 188 loop : 0.52 (0.29), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 90 TYR 0.017 0.001 TYR C 127 PHE 0.013 0.001 PHE A 237 TRP 0.007 0.001 TRP C 141 HIS 0.009 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 9738) covalent geometry : angle 0.51818 (13195) SS BOND : bond 0.01063 ( 1) SS BOND : angle 2.25541 ( 2) hydrogen bonds : bond 0.02604 ( 448) hydrogen bonds : angle 4.18935 ( 1260) Misc. bond : bond 0.00069 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9440 (tp) cc_final: 0.9063 (mt) REVERT: A 55 ASN cc_start: 0.8282 (m-40) cc_final: 0.7764 (m110) REVERT: A 80 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.7815 (tm-30) REVERT: A 250 TYR cc_start: 0.8200 (OUTLIER) cc_final: 0.7649 (m-80) REVERT: A 334 PHE cc_start: 0.7582 (m-10) cc_final: 0.7255 (m-10) REVERT: A 357 MET cc_start: 0.8387 (mtm) cc_final: 0.8181 (ttp) REVERT: A 383 TYR cc_start: 0.8418 (m-80) cc_final: 0.8053 (m-80) REVERT: A 442 MET cc_start: 0.9348 (tpp) cc_final: 0.8652 (mmm) REVERT: A 448 MET cc_start: 0.8268 (tpp) cc_final: 0.7778 (tpt) REVERT: A 919 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7118 (ptp90) REVERT: C 8 ARG cc_start: 0.9194 (mmm160) cc_final: 0.8883 (tpt90) REVERT: C 74 TYR cc_start: 0.8255 (t80) cc_final: 0.7829 (t80) REVERT: C 81 ASN cc_start: 0.8506 (m-40) cc_final: 0.7937 (t0) REVERT: D 31 GLN cc_start: 0.8994 (tt0) cc_final: 0.8545 (tp40) outliers start: 21 outliers final: 16 residues processed: 81 average time/residue: 0.0822 time to fit residues: 9.8129 Evaluate side-chains 83 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain D residue 67 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 95 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 97 optimal weight: 0.0870 chunk 118 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.3174 r_free = 0.3174 target = 0.047711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.038114 restraints weight = 63399.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.039445 restraints weight = 37721.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.040369 restraints weight = 26330.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.041067 restraints weight = 20267.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.041609 restraints weight = 16770.902| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9741 Z= 0.098 Angle : 0.520 10.214 13197 Z= 0.261 Chirality : 0.040 0.164 1471 Planarity : 0.003 0.044 1707 Dihedral : 4.652 56.341 1332 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.70 % Allowed : 11.78 % Favored : 86.52 % 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: 1.50 (0.25), residues: 1199 helix: 1.96 (0.24), residues: 494 sheet: 0.26 (0.40), residues: 188 loop : 0.45 (0.29), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 90 TYR 0.016 0.001 TYR C 127 PHE 0.013 0.001 PHE A 237 TRP 0.003 0.001 TRP A 917 HIS 0.009 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 9738) covalent geometry : angle 0.51947 (13195) SS BOND : bond 0.00957 ( 1) SS BOND : angle 2.02408 ( 2) hydrogen bonds : bond 0.02517 ( 448) hydrogen bonds : angle 4.20888 ( 1260) Misc. bond : bond 0.00031 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9451 (tp) cc_final: 0.9062 (mt) REVERT: A 55 ASN cc_start: 0.8342 (m-40) cc_final: 0.7814 (m110) REVERT: A 80 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.7792 (tm-30) REVERT: A 250 TYR cc_start: 0.8255 (OUTLIER) cc_final: 0.7726 (m-80) REVERT: A 357 MET cc_start: 0.8242 (mtm) cc_final: 0.8017 (ttp) REVERT: A 383 TYR cc_start: 0.8423 (m-80) cc_final: 0.7990 (m-80) REVERT: A 442 MET cc_start: 0.9358 (tpp) cc_final: 0.8652 (mmm) REVERT: A 448 MET cc_start: 0.8280 (tpp) cc_final: 0.7794 (tpt) REVERT: A 919 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7056 (ptp90) REVERT: C 8 ARG cc_start: 0.9222 (mmm160) cc_final: 0.8914 (tpt90) REVERT: C 74 TYR cc_start: 0.8327 (t80) cc_final: 0.7888 (t80) REVERT: C 81 ASN cc_start: 0.8459 (m-40) cc_final: 0.7876 (t0) REVERT: C 101 LYS cc_start: 0.8633 (mttt) cc_final: 0.8252 (mttt) REVERT: C 120 VAL cc_start: 0.9222 (OUTLIER) cc_final: 0.9010 (m) REVERT: D 31 GLN cc_start: 0.9056 (tt0) cc_final: 0.8616 (tp40) outliers start: 18 outliers final: 13 residues processed: 80 average time/residue: 0.0876 time to fit residues: 10.0580 Evaluate side-chains 78 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain D residue 67 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 1 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 82 optimal weight: 0.3980 chunk 45 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3167 r_free = 0.3167 target = 0.047243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.038159 restraints weight = 63453.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.039415 restraints weight = 38048.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.040322 restraints weight = 26691.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.040980 restraints weight = 20526.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.041497 restraints weight = 16876.476| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 9741 Z= 0.107 Angle : 0.546 12.094 13197 Z= 0.273 Chirality : 0.041 0.170 1471 Planarity : 0.003 0.044 1707 Dihedral : 4.629 56.255 1332 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.70 % Allowed : 11.97 % Favored : 86.33 % 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: 1.46 (0.25), residues: 1199 helix: 1.87 (0.24), residues: 497 sheet: 0.26 (0.39), residues: 188 loop : 0.48 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 90 TYR 0.015 0.001 TYR C 127 PHE 0.013 0.001 PHE A 237 TRP 0.003 0.000 TRP C 93 HIS 0.006 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 9738) covalent geometry : angle 0.54569 (13195) SS BOND : bond 0.00351 ( 1) SS BOND : angle 2.42655 ( 2) hydrogen bonds : bond 0.02567 ( 448) hydrogen bonds : angle 4.25145 ( 1260) Misc. bond : bond 0.00123 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9428 (tp) cc_final: 0.9044 (mt) REVERT: A 55 ASN cc_start: 0.8289 (m-40) cc_final: 0.7768 (m110) REVERT: A 80 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.7821 (tm-30) REVERT: A 250 TYR cc_start: 0.8230 (OUTLIER) cc_final: 0.7637 (m-80) REVERT: A 383 TYR cc_start: 0.8388 (m-80) cc_final: 0.7966 (m-80) REVERT: A 442 MET cc_start: 0.9343 (tpp) cc_final: 0.8631 (mmm) REVERT: A 448 MET cc_start: 0.8269 (tpp) cc_final: 0.7783 (tpt) REVERT: A 919 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7076 (ptp90) REVERT: C 8 ARG cc_start: 0.9176 (mmm160) cc_final: 0.8875 (tpt90) REVERT: C 74 TYR cc_start: 0.8269 (t80) cc_final: 0.7857 (t80) REVERT: C 81 ASN cc_start: 0.8410 (m-40) cc_final: 0.7866 (t0) REVERT: C 101 LYS cc_start: 0.8617 (mttt) cc_final: 0.8170 (mttt) REVERT: C 120 VAL cc_start: 0.9237 (OUTLIER) cc_final: 0.9027 (m) REVERT: D 31 GLN cc_start: 0.9014 (tt0) cc_final: 0.8561 (tp40) outliers start: 18 outliers final: 12 residues processed: 77 average time/residue: 0.1050 time to fit residues: 11.7613 Evaluate side-chains 76 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain D residue 67 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 66 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 72 optimal weight: 0.0870 chunk 41 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.3169 r_free = 0.3169 target = 0.047322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.038195 restraints weight = 63276.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.039472 restraints weight = 37622.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.040393 restraints weight = 26182.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.040902 restraints weight = 20030.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.041503 restraints weight = 16848.381| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9741 Z= 0.100 Angle : 0.540 10.776 13197 Z= 0.270 Chirality : 0.041 0.201 1471 Planarity : 0.003 0.044 1707 Dihedral : 4.600 55.901 1332 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.60 % Allowed : 11.97 % Favored : 86.43 % 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: 1.50 (0.26), residues: 1199 helix: 1.91 (0.24), residues: 496 sheet: 0.28 (0.39), residues: 188 loop : 0.51 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 90 TYR 0.016 0.001 TYR C 127 PHE 0.009 0.001 PHE A 237 TRP 0.003 0.001 TRP C 141 HIS 0.006 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 9738) covalent geometry : angle 0.53897 (13195) SS BOND : bond 0.00771 ( 1) SS BOND : angle 2.02856 ( 2) hydrogen bonds : bond 0.02564 ( 448) hydrogen bonds : angle 4.24925 ( 1260) Misc. bond : bond 0.00157 ( 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: 1316.57 seconds wall clock time: 23 minutes 18.36 seconds (1398.36 seconds total)