Starting phenix.real_space_refine on Fri Mar 14 06:24:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5w_44227/03_2025/9b5w_44227.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5w_44227/03_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_44227/03_2025/9b5w_44227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5w_44227/03_2025/9b5w_44227.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5w_44227/03_2025/9b5w_44227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5w_44227/03_2025/9b5w_44227.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.040 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.49, per 1000 atoms: 0.68 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: 2.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.38 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: 3.41 Time building geometry restraints manager: 2.92 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: 4.160 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.880 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.290 ------------------------------------------------------------------------------- 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 : 0.004 0.069 9738 Z= 0.265 Angle : 0.518 11.273 13195 Z= 0.273 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.005 0.001 TRP C 93 HIS 0.005 0.001 HIS A 458 PHE 0.011 0.001 PHE C 50 TYR 0.010 0.001 TYR A 277 ARG 0.002 0.000 ARG C 139 *********************** 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 : 1.027 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: 0.2989 time to fit residues: 69.3973 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 : 1.139 ------------------------------------------------------------------------------- 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 100 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 0.0570 chunk 30 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 93 optimal weight: 0.0980 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 overall best weight: 1.2102 ------------------------------------------------------------------------------- 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 = 0.3164 r_free = 0.3164 target = 0.047155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.037833 restraints weight = 62605.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.039150 restraints weight = 36975.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.040073 restraints weight = 25495.175| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9738 Z= 0.221 Angle : 0.597 10.148 13195 Z= 0.306 Chirality : 0.042 0.169 1471 Planarity : 0.004 0.038 1707 Dihedral : 5.774 57.407 1335 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.98 % Allowed : 8.58 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.25), residues: 1199 helix: 1.39 (0.25), residues: 496 sheet: 0.10 (0.37), residues: 215 loop : 0.51 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 33 HIS 0.005 0.001 HIS C 32 PHE 0.014 0.001 PHE C 62 TYR 0.017 0.001 TYR A 279 ARG 0.006 0.001 ARG A 841 *********************** 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 113 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 1.029 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: A 19 LEU cc_start: 0.9527 (tp) cc_final: 0.9188 (mt) REVERT: A 55 ASN cc_start: 0.8404 (m-40) cc_final: 0.7987 (m-40) REVERT: A 218 MET cc_start: 0.8261 (mtt) cc_final: 0.7566 (mtt) REVERT: A 383 TYR cc_start: 0.8387 (m-80) cc_final: 0.7979 (m-80) REVERT: A 442 MET cc_start: 0.9303 (tpp) cc_final: 0.8619 (mmm) REVERT: A 855 MET cc_start: 0.8666 (tpp) cc_final: 0.8200 (tpp) REVERT: A 913 ILE cc_start: 0.9203 (mm) cc_final: 0.9003 (mm) REVERT: A 919 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7196 (ptp90) REVERT: C 34 GLN cc_start: 0.9398 (tt0) cc_final: 0.9191 (tm-30) REVERT: C 74 TYR cc_start: 0.8275 (t80) cc_final: 0.7744 (t80) REVERT: C 81 ASN cc_start: 0.8765 (m-40) cc_final: 0.8163 (t0) REVERT: D 3 ILE cc_start: 0.9043 (pt) cc_final: 0.8769 (pt) REVERT: D 15 LEU cc_start: 0.7772 (mt) cc_final: 0.7344 (mp) outliers start: 21 outliers final: 12 residues processed: 108 average time/residue: 0.2221 time to fit residues: 33.9777 Evaluate side-chains 88 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 56 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 61 optimal weight: 0.4980 chunk 70 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 85 optimal weight: 0.2980 chunk 55 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3178 r_free = 0.3178 target = 0.048116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.038581 restraints weight = 64146.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.039922 restraints weight = 37741.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.040868 restraints weight = 26017.658| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9738 Z= 0.161 Angle : 0.535 8.365 13195 Z= 0.272 Chirality : 0.041 0.143 1471 Planarity : 0.004 0.043 1707 Dihedral : 5.292 59.830 1333 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.36 % Allowed : 8.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.25), residues: 1199 helix: 1.60 (0.24), residues: 490 sheet: 0.20 (0.39), residues: 203 loop : 0.57 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 917 HIS 0.004 0.001 HIS C 32 PHE 0.013 0.001 PHE A 237 TYR 0.012 0.001 TYR A 279 ARG 0.004 0.000 ARG C 8 *********************** 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: 25 poor density : 80 time to evaluate : 1.157 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: 0.9494 (tp) cc_final: 0.9165 (mt) REVERT: A 55 ASN cc_start: 0.8364 (m-40) cc_final: 0.7904 (m110) REVERT: A 80 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8667 (tm-30) REVERT: A 285 MET cc_start: 0.8328 (mmm) cc_final: 0.8003 (mmm) REVERT: A 383 TYR cc_start: 0.8464 (m-80) cc_final: 0.8049 (m-80) REVERT: A 442 MET cc_start: 0.9294 (tpp) cc_final: 0.8608 (mmm) REVERT: A 855 MET cc_start: 0.8796 (tpp) cc_final: 0.8299 (tpp) REVERT: A 919 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7115 (ptp90) REVERT: C 34 GLN cc_start: 0.9384 (tt0) cc_final: 0.9181 (tm-30) REVERT: C 74 TYR cc_start: 0.8283 (t80) cc_final: 0.7782 (t80) REVERT: C 81 ASN cc_start: 0.8734 (m-40) cc_final: 0.8158 (t0) REVERT: D 15 LEU cc_start: 0.7635 (mt) cc_final: 0.7244 (mp) outliers start: 25 outliers final: 13 residues processed: 101 average time/residue: 0.2454 time to fit residues: 34.8551 Evaluate side-chains 87 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 53 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 82 optimal weight: 0.0470 chunk 69 optimal weight: 0.0470 chunk 35 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 95 optimal weight: 0.2980 overall best weight: 0.3376 ------------------------------------------------------------------------------- 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 = 0.3192 r_free = 0.3192 target = 0.048212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.039060 restraints weight = 62360.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.040377 restraints weight = 36770.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.041314 restraints weight = 25239.991| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9738 Z= 0.139 Angle : 0.510 7.690 13195 Z= 0.259 Chirality : 0.040 0.141 1471 Planarity : 0.003 0.043 1707 Dihedral : 5.062 58.272 1333 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.45 % Allowed : 9.14 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.25), residues: 1199 helix: 1.68 (0.24), residues: 491 sheet: 0.23 (0.39), residues: 198 loop : 0.56 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 917 HIS 0.009 0.001 HIS A 202 PHE 0.016 0.001 PHE A 170 TYR 0.012 0.001 TYR C 127 ARG 0.005 0.000 ARG C 8 *********************** 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 103 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 1.056 Fit side-chains revert: symmetry clash 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: 0.8368 (m-40) cc_final: 0.7854 (m110) REVERT: A 80 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8673 (tm-30) REVERT: A 383 TYR cc_start: 0.8408 (m-80) cc_final: 0.8001 (m-80) REVERT: A 442 MET cc_start: 0.9304 (tpp) cc_final: 0.8607 (mmm) REVERT: A 919 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7117 (ptp90) REVERT: C 34 GLN cc_start: 0.9335 (tt0) cc_final: 0.9122 (tm-30) REVERT: C 74 TYR cc_start: 0.8239 (t80) cc_final: 0.7797 (t80) REVERT: C 81 ASN cc_start: 0.8592 (m-40) cc_final: 0.8122 (t0) REVERT: C 101 LYS cc_start: 0.8636 (mttt) cc_final: 0.8302 (mttt) REVERT: D 31 GLN cc_start: 0.9005 (tt0) cc_final: 0.8520 (tp40) outliers start: 26 outliers final: 13 residues processed: 100 average time/residue: 0.2330 time to fit residues: 33.9100 Evaluate side-chains 85 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 120 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 85 optimal weight: 0.0870 chunk 33 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 17 optimal weight: 0.0060 chunk 104 optimal weight: 0.0570 chunk 59 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.3692 ------------------------------------------------------------------------------- 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 = 0.3179 r_free = 0.3179 target = 0.048113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.038847 restraints weight = 62648.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.040131 restraints weight = 36889.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.041091 restraints weight = 25690.994| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9738 Z= 0.140 Angle : 0.506 7.081 13195 Z= 0.254 Chirality : 0.040 0.128 1471 Planarity : 0.003 0.042 1707 Dihedral : 4.696 57.485 1332 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.26 % Allowed : 10.56 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.25), residues: 1199 helix: 1.80 (0.24), residues: 490 sheet: 0.32 (0.39), residues: 198 loop : 0.54 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 917 HIS 0.003 0.001 HIS C 32 PHE 0.012 0.001 PHE A 237 TYR 0.014 0.001 TYR C 127 ARG 0.004 0.000 ARG C 8 *********************** 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 101 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9453 (tp) cc_final: 0.9136 (mt) REVERT: A 55 ASN cc_start: 0.8395 (m-40) cc_final: 0.7877 (m110) REVERT: A 80 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8457 (tm-30) REVERT: A 285 MET cc_start: 0.8354 (mmm) cc_final: 0.8136 (mmm) REVERT: A 383 TYR cc_start: 0.8390 (m-80) cc_final: 0.7917 (m-80) REVERT: A 442 MET cc_start: 0.9318 (tpp) cc_final: 0.8598 (mmm) REVERT: A 919 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7135 (ptp90) REVERT: C 8 ARG cc_start: 0.9223 (mmm160) cc_final: 0.8856 (tpt90) REVERT: C 34 GLN cc_start: 0.9365 (tt0) cc_final: 0.9075 (tm-30) REVERT: C 74 TYR cc_start: 0.8313 (t80) cc_final: 0.7884 (t80) REVERT: C 81 ASN cc_start: 0.8584 (m-40) cc_final: 0.8081 (t0) REVERT: C 101 LYS cc_start: 0.8629 (mttt) cc_final: 0.8318 (mttt) REVERT: D 31 GLN cc_start: 0.9045 (tt0) cc_final: 0.8595 (tp40) outliers start: 24 outliers final: 13 residues processed: 99 average time/residue: 0.2187 time to fit residues: 31.0822 Evaluate side-chains 80 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 120 VAL 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 84 optimal weight: 0.8980 chunk 7 optimal weight: 0.1980 chunk 90 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.047521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.038300 restraints weight = 63309.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.039578 restraints weight = 37442.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.040545 restraints weight = 26008.942| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9738 Z= 0.167 Angle : 0.507 7.953 13195 Z= 0.257 Chirality : 0.040 0.130 1471 Planarity : 0.003 0.044 1707 Dihedral : 4.677 57.366 1332 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.17 % Allowed : 10.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.26), residues: 1199 helix: 1.90 (0.24), residues: 490 sheet: 0.41 (0.40), residues: 188 loop : 0.49 (0.29), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 93 HIS 0.010 0.001 HIS A 202 PHE 0.009 0.001 PHE A 985 TYR 0.016 0.001 TYR C 127 ARG 0.003 0.000 ARG C 8 *********************** 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 88 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9493 (tp) cc_final: 0.9181 (mt) REVERT: A 55 ASN cc_start: 0.8355 (m-40) cc_final: 0.7839 (m110) REVERT: A 80 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8427 (tm-30) REVERT: A 285 MET cc_start: 0.8377 (mmm) cc_final: 0.8165 (mmm) REVERT: A 383 TYR cc_start: 0.8426 (m-80) cc_final: 0.8039 (m-80) REVERT: A 442 MET cc_start: 0.9336 (tpp) cc_final: 0.8626 (mmm) REVERT: A 448 MET cc_start: 0.8229 (tpp) cc_final: 0.7766 (tpt) REVERT: A 919 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7108 (ptp90) REVERT: C 8 ARG cc_start: 0.9235 (mmm160) cc_final: 0.8880 (tpt90) REVERT: C 74 TYR cc_start: 0.8241 (t80) cc_final: 0.7810 (t80) REVERT: C 81 ASN cc_start: 0.8540 (m-40) cc_final: 0.8088 (t0) REVERT: D 31 GLN cc_start: 0.9017 (tt0) cc_final: 0.8553 (tp40) outliers start: 23 outliers final: 13 residues processed: 84 average time/residue: 0.2154 time to fit residues: 26.4391 Evaluate side-chains 78 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 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 D residue 56 LEU Chi-restraints excluded: chain D residue 67 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 79 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3160 r_free = 0.3160 target = 0.047416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.038203 restraints weight = 63836.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.039472 restraints weight = 37934.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.040421 restraints weight = 26370.861| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9738 Z= 0.156 Angle : 0.506 8.738 13195 Z= 0.253 Chirality : 0.040 0.146 1471 Planarity : 0.003 0.043 1707 Dihedral : 4.657 56.950 1332 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.79 % Allowed : 10.93 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.26), residues: 1199 helix: 1.98 (0.24), residues: 491 sheet: 0.36 (0.40), residues: 188 loop : 0.49 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 141 HIS 0.007 0.001 HIS A 202 PHE 0.010 0.001 PHE A 237 TYR 0.017 0.001 TYR C 127 ARG 0.002 0.000 ARG C 8 *********************** 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 84 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9502 (tp) cc_final: 0.9162 (mt) REVERT: A 55 ASN cc_start: 0.8348 (m-40) cc_final: 0.7831 (m110) REVERT: A 80 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8446 (tm-30) REVERT: A 285 MET cc_start: 0.8436 (mmm) cc_final: 0.8229 (mmm) REVERT: A 383 TYR cc_start: 0.8419 (m-80) cc_final: 0.8042 (m-80) REVERT: A 442 MET cc_start: 0.9350 (tpp) cc_final: 0.8640 (mmm) REVERT: A 448 MET cc_start: 0.8337 (tpp) cc_final: 0.7942 (tpt) REVERT: A 919 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7095 (ptp90) REVERT: C 8 ARG cc_start: 0.9215 (mmm160) cc_final: 0.8901 (tpt90) REVERT: C 74 TYR cc_start: 0.8263 (t80) cc_final: 0.7858 (t80) REVERT: C 81 ASN cc_start: 0.8542 (m-40) cc_final: 0.8070 (t0) REVERT: C 101 LYS cc_start: 0.8606 (mttt) cc_final: 0.8179 (mttt) REVERT: D 2 GLN cc_start: 0.8469 (pp30) cc_final: 0.8022 (pp30) REVERT: D 31 GLN cc_start: 0.9008 (tt0) cc_final: 0.8545 (tp40) outliers start: 19 outliers final: 13 residues processed: 81 average time/residue: 0.2229 time to fit residues: 26.3558 Evaluate side-chains 79 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 1.187 ------------------------------------------------------------------------------- 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 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 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 82 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3147 r_free = 0.3147 target = 0.046970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.037505 restraints weight = 65243.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.038769 restraints weight = 38724.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.039724 restraints weight = 27172.182| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9738 Z= 0.198 Angle : 0.533 9.518 13195 Z= 0.267 Chirality : 0.041 0.194 1471 Planarity : 0.003 0.044 1707 Dihedral : 4.670 56.943 1332 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.07 % Allowed : 11.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.26), residues: 1199 helix: 2.02 (0.24), residues: 490 sheet: 0.28 (0.40), residues: 188 loop : 0.53 (0.29), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 93 HIS 0.004 0.001 HIS A 202 PHE 0.011 0.001 PHE A 237 TYR 0.016 0.001 TYR C 127 ARG 0.002 0.000 ARG A 841 *********************** 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 87 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9529 (tp) cc_final: 0.9148 (mt) REVERT: A 55 ASN cc_start: 0.8357 (m-40) cc_final: 0.7845 (m110) REVERT: A 80 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8436 (tm-30) REVERT: A 250 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.7841 (m-80) REVERT: A 285 MET cc_start: 0.8551 (mmm) cc_final: 0.8211 (mmm) REVERT: A 383 TYR cc_start: 0.8454 (m-80) cc_final: 0.8074 (m-80) REVERT: A 442 MET cc_start: 0.9377 (tpp) cc_final: 0.8655 (mmm) REVERT: A 448 MET cc_start: 0.8395 (tpp) cc_final: 0.7962 (tpt) REVERT: A 919 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7070 (ptp90) REVERT: A 982 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8928 (mm) REVERT: C 8 ARG cc_start: 0.9234 (mmm160) cc_final: 0.8920 (tpt90) REVERT: C 74 TYR cc_start: 0.8346 (t80) cc_final: 0.7962 (t80) REVERT: C 81 ASN cc_start: 0.8570 (m-40) cc_final: 0.8000 (t0) REVERT: C 101 LYS cc_start: 0.8646 (mttt) cc_final: 0.8270 (mttt) REVERT: D 2 GLN cc_start: 0.8508 (pp30) cc_final: 0.8054 (pp30) REVERT: D 31 GLN cc_start: 0.9016 (tt0) cc_final: 0.8552 (tp40) outliers start: 22 outliers final: 13 residues processed: 83 average time/residue: 0.2207 time to fit residues: 26.8549 Evaluate side-chains 77 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 462 THR 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 919 ARG Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1003 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 19 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.3121 r_free = 0.3121 target = 0.046046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.036799 restraints weight = 64623.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.038052 restraints weight = 38351.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.038982 restraints weight = 26828.454| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9738 Z= 0.240 Angle : 0.563 9.564 13195 Z= 0.283 Chirality : 0.041 0.159 1471 Planarity : 0.004 0.044 1707 Dihedral : 4.868 56.553 1332 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.25), residues: 1199 helix: 1.92 (0.24), residues: 496 sheet: 0.22 (0.40), residues: 188 loop : 0.41 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 93 HIS 0.005 0.001 HIS C 75 PHE 0.013 0.001 PHE A 282 TYR 0.016 0.001 TYR C 127 ARG 0.003 0.000 ARG A 227 *********************** 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 79 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.8440 (m-40) cc_final: 0.7989 (m-40) REVERT: A 80 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8349 (tm-30) REVERT: A 250 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.7902 (m-80) REVERT: A 285 MET cc_start: 0.8598 (mmm) cc_final: 0.8355 (mmm) REVERT: A 383 TYR cc_start: 0.8473 (m-80) cc_final: 0.8129 (m-80) REVERT: A 442 MET cc_start: 0.9415 (tpp) cc_final: 0.8702 (mmm) REVERT: A 448 MET cc_start: 0.8403 (tpp) cc_final: 0.7956 (tpt) REVERT: A 919 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7027 (ptp90) REVERT: A 982 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8934 (mm) REVERT: C 8 ARG cc_start: 0.9235 (mmm160) cc_final: 0.8946 (tpt90) REVERT: C 74 TYR cc_start: 0.8342 (t80) cc_final: 0.7957 (t80) REVERT: C 81 ASN cc_start: 0.8522 (m-40) cc_final: 0.7943 (t0) REVERT: D 31 GLN cc_start: 0.9023 (tt0) cc_final: 0.8550 (tp40) outliers start: 18 outliers final: 13 residues processed: 75 average time/residue: 0.2525 time to fit residues: 26.9678 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 : 1.131 ------------------------------------------------------------------------------- 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 461 VAL Chi-restraints excluded: chain A residue 462 THR 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 919 ARG Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 140 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3133 r_free = 0.3133 target = 0.046277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.037201 restraints weight = 65087.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.038471 restraints weight = 38440.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.039407 restraints weight = 26618.933| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9738 Z= 0.170 Angle : 0.545 10.748 13195 Z= 0.275 Chirality : 0.041 0.164 1471 Planarity : 0.003 0.044 1707 Dihedral : 4.797 56.344 1332 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.51 % Allowed : 12.54 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.25), residues: 1199 helix: 1.94 (0.24), residues: 497 sheet: 0.23 (0.40), residues: 188 loop : 0.44 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 93 HIS 0.003 0.001 HIS A 202 PHE 0.012 0.001 PHE A 237 TYR 0.015 0.001 TYR C 127 ARG 0.002 0.000 ARG A 610 ********************** 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 81 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9444 (tp) cc_final: 0.9002 (mt) REVERT: A 55 ASN cc_start: 0.8403 (m-40) cc_final: 0.7887 (m110) REVERT: A 80 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.7818 (tm-30) REVERT: A 250 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.7699 (m-80) REVERT: A 285 MET cc_start: 0.8562 (mmm) cc_final: 0.8339 (mmm) REVERT: A 357 MET cc_start: 0.8258 (mtm) cc_final: 0.8007 (ttp) REVERT: A 383 TYR cc_start: 0.8416 (m-80) cc_final: 0.8093 (m-80) REVERT: A 442 MET cc_start: 0.9391 (tpp) cc_final: 0.8741 (mmm) REVERT: A 448 MET cc_start: 0.8368 (tpp) cc_final: 0.7933 (tpt) REVERT: A 919 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7061 (ptp90) REVERT: A 982 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8951 (mm) REVERT: C 8 ARG cc_start: 0.9199 (mmm160) cc_final: 0.8896 (tpt90) REVERT: C 74 TYR cc_start: 0.8262 (t80) cc_final: 0.7899 (t80) REVERT: C 81 ASN cc_start: 0.8506 (m-40) cc_final: 0.7917 (t0) REVERT: C 101 LYS cc_start: 0.8609 (mttt) cc_final: 0.8270 (mttt) REVERT: D 31 GLN cc_start: 0.9017 (tt0) cc_final: 0.8554 (tp40) outliers start: 16 outliers final: 11 residues processed: 78 average time/residue: 0.2494 time to fit residues: 28.1400 Evaluate side-chains 77 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 461 VAL Chi-restraints excluded: chain A residue 462 THR 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 919 ARG Chi-restraints excluded: chain A residue 982 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 44 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3123 r_free = 0.3123 target = 0.045928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.036948 restraints weight = 64756.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.038187 restraints weight = 38444.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.039110 restraints weight = 26689.144| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9738 Z= 0.201 Angle : 0.566 11.516 13195 Z= 0.285 Chirality : 0.041 0.210 1471 Planarity : 0.004 0.044 1707 Dihedral : 4.820 56.266 1332 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.60 % Allowed : 12.35 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.25), residues: 1199 helix: 1.91 (0.24), residues: 497 sheet: 0.21 (0.40), residues: 188 loop : 0.44 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 93 HIS 0.004 0.001 HIS C 75 PHE 0.011 0.001 PHE A 237 TYR 0.015 0.001 TYR C 127 ARG 0.002 0.000 ARG A 227 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2632.62 seconds wall clock time: 47 minutes 9.45 seconds (2829.45 seconds total)