Starting phenix.real_space_refine on Thu Mar 13 15:56:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5s_44223/03_2025/9b5s_44223.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5s_44223/03_2025/9b5s_44223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b5s_44223/03_2025/9b5s_44223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5s_44223/03_2025/9b5s_44223.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5s_44223/03_2025/9b5s_44223.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5s_44223/03_2025/9b5s_44223.cif" } resolution = 2.96 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= 0.064 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 41 5.16 5 C 5703 2.51 5 N 1470 2.21 5 O 1716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 8935 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'A1AIV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.30, per 1000 atoms: 0.71 Number of scatterers: 8935 At special positions: 0 Unit cell: (85.12, 98.952, 119.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 41 16.00 P 3 15.00 Mg 2 11.99 O 1716 8.00 N 1470 7.00 C 5703 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=2.89 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: 2.74 Conformation dependent library (CDL) restraints added in 1.3 seconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 10 sheets defined 48.5% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.868A 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: 3.708A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 4.005A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.429A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LYS A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 123 Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.759A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LYS A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 224 removed outlier: 4.101A pdb=" N GLY A 224 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.259A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 304 removed outlier: 3.647A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.593A 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: 4.365A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.546A pdb=" N SER A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 450 Processing helix chain 'A' and resid 468 through 474 removed outlier: 3.856A pdb=" N ASN A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG A 474 " --> pdb=" O ASN A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'A' and resid 486 through 499 Processing helix chain 'A' and resid 500 through 503 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.720A 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 removed outlier: 3.675A pdb=" N SER A 581 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 582 " --> pdb=" O TYR A 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 578 through 582' Processing helix chain 'A' and resid 591 through 597 Processing helix chain 'A' and resid 601 through 618 removed outlier: 3.536A 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: 3.534A 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: 3.548A pdb=" N CYS A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 689 removed outlier: 3.596A 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: 3.988A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 794 removed outlier: 3.766A pdb=" N GLN A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 794 " --> pdb=" O ILE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 818 through 835 Processing helix chain 'A' and resid 840 through 849 Processing helix chain 'A' and resid 855 through 876 removed outlier: 3.504A pdb=" N THR A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.523A pdb=" N GLU A 882 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR A 883 " --> pdb=" O ILE A 880 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 879 through 883' Processing helix chain 'A' and resid 926 through 937 Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 969 through 979 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 98 through 112 Processing helix chain 'C' and resid 120 through 130 Processing helix chain 'C' and resid 130 through 145 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.850A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N THR A 129 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE A 43 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.311A 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: 4.099A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.412A 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: 4.099A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 506 through 509 removed outlier: 6.500A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A 460 " --> pdb=" O THR A 430 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.137A 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: 6.400A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N VAL A 990 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N SER A 947 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLU A 992 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU A 945 " --> pdb=" O GLU A 992 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N CYS A 994 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.476A 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: 6.400A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N CYS A 995 " --> pdb=" O VAL A1003 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 21 through 22 removed outlier: 6.260A pdb=" N HIS C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 21 through 22 438 hydrogen bonds defined for protein. 1203 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: 3.16 Time building geometry restraints manager: 3.10 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: 1512 1.27 - 1.40: 2173 1.40 - 1.54: 5261 1.54 - 1.67: 132 1.67 - 1.81: 62 Bond restraints: 9140 Sorted by residual: bond pdb=" C04 A1AIV D 201 " pdb=" C05 A1AIV D 201 " ideal model delta sigma weight residual 1.453 1.524 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 1.416 1.402 0.014 1.30e-02 5.92e+03 1.16e+00 bond pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " ideal model delta sigma weight residual 1.531 1.518 0.013 1.20e-02 6.94e+03 1.13e+00 bond pdb=" C05 A1AIV D 201 " pdb=" N06 A1AIV D 201 " ideal model delta sigma weight residual 1.151 1.131 0.020 2.00e-02 2.50e+03 9.51e-01 bond pdb=" CG PRO A 312 " pdb=" CD PRO A 312 " ideal model delta sigma weight residual 1.503 1.484 0.019 3.40e-02 8.65e+02 3.26e-01 ... (remaining 9135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 12250 1.39 - 2.79: 68 2.79 - 4.18: 64 4.18 - 5.58: 4 5.58 - 6.97: 4 Bond angle restraints: 12390 Sorted by residual: angle pdb=" C LYS A 381 " pdb=" N GLN A 382 " pdb=" CA GLN A 382 " ideal model delta sigma weight residual 121.70 128.15 -6.45 1.80e+00 3.09e-01 1.28e+01 angle pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 106.53 103.12 3.41 1.18e+00 7.24e-01 8.44e+00 angle pdb=" C3' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" C5' ATP A1103 " ideal model delta sigma weight residual 115.19 110.53 4.66 1.76e+00 3.23e-01 7.02e+00 angle pdb=" C2' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O3' ATP A1103 " ideal model delta sigma weight residual 111.83 104.86 6.97 2.67e+00 1.40e-01 6.82e+00 angle pdb=" C3' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" O2' ATP A1103 " ideal model delta sigma weight residual 111.83 104.91 6.92 2.67e+00 1.40e-01 6.72e+00 ... (remaining 12385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 5337 17.53 - 35.07: 157 35.07 - 52.60: 47 52.60 - 70.14: 9 70.14 - 87.67: 2 Dihedral angle restraints: 5552 sinusoidal: 2262 harmonic: 3290 Sorted by residual: dihedral pdb=" CB CYS A 593 " pdb=" SG CYS A 593 " pdb=" SG CYS C 85 " pdb=" CB CYS C 85 " ideal model delta sinusoidal sigma weight residual -86.00 -143.34 57.34 1 1.00e+01 1.00e-02 4.42e+01 dihedral pdb=" CA LYS A 884 " pdb=" C LYS A 884 " pdb=" N ASN A 885 " pdb=" CA ASN A 885 " ideal model delta harmonic sigma weight residual 180.00 162.74 17.26 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" N GLN A 80 " pdb=" CA GLN A 80 " pdb=" CB GLN A 80 " pdb=" CG GLN A 80 " ideal model delta sinusoidal sigma weight residual -60.00 -117.00 57.00 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 5549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1222 0.060 - 0.119: 137 0.119 - 0.179: 12 0.179 - 0.239: 1 0.239 - 0.298: 2 Chirality restraints: 1374 Sorted by residual: chirality pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O2' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C3' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" O3' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.63 -2.91 0.27 2.00e-01 2.50e+01 1.83e+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 -2.72 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1371 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 94 " 0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO C 95 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 499 " 0.018 5.00e-02 4.00e+02 2.68e-02 1.15e+00 pdb=" N PRO A 500 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 500 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 500 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 120 " 0.016 5.00e-02 4.00e+02 2.43e-02 9.43e-01 pdb=" N PRO C 121 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO C 121 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 121 " 0.014 5.00e-02 4.00e+02 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 53 2.57 - 3.15: 7217 3.15 - 3.73: 13100 3.73 - 4.32: 19171 4.32 - 4.90: 33011 Nonbonded interactions: 72552 Sorted by model distance: nonbonded pdb=" OD2 ASP A 465 " pdb="MG MG A1102 " model vdw 1.986 2.170 nonbonded pdb="MG MG A1101 " pdb=" O2B ATP A1103 " model vdw 2.015 2.170 nonbonded pdb=" OD2 ASP A 537 " pdb="MG MG A1101 " model vdw 2.093 2.170 nonbonded pdb=" N GLU A 489 " pdb=" OE1 GLU A 489 " model vdw 2.198 3.120 nonbonded pdb="MG MG A1102 " pdb=" O1B ATP A1103 " model vdw 2.218 2.170 ... (remaining 72547 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.020 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.490 Find NCS groups from input model: 0.080 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:11.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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 : 0.003 0.071 9140 Z= 0.226 Angle : 0.457 6.971 12390 Z= 0.229 Chirality : 0.042 0.298 1374 Planarity : 0.003 0.031 1604 Dihedral : 9.815 87.672 3425 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.21 % Allowed : 3.02 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.20 (0.26), residues: 1126 helix: 1.63 (0.25), residues: 476 sheet: 0.44 (0.38), residues: 185 loop : 0.19 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS A 818 PHE 0.009 0.001 PHE A 842 TYR 0.011 0.001 TYR A 732 ARG 0.003 0.000 ARG A 919 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: A 184 MET cc_start: 0.8034 (mtp) cc_final: 0.7424 (mtm) REVERT: A 196 MET cc_start: 0.8349 (mmp) cc_final: 0.7858 (mmp) REVERT: A 255 THR cc_start: 0.8923 (m) cc_final: 0.8662 (p) REVERT: A 527 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7638 (mt-10) REVERT: A 543 MET cc_start: 0.8576 (mmt) cc_final: 0.8165 (mmt) REVERT: A 668 MET cc_start: 0.7762 (mmm) cc_final: 0.7397 (mmm) REVERT: A 879 LYS cc_start: 0.8440 (mmmm) cc_final: 0.8130 (mmmt) REVERT: A 935 GLN cc_start: 0.8233 (tp40) cc_final: 0.7707 (tt0) REVERT: C 32 HIS cc_start: 0.7573 (t-170) cc_final: 0.6995 (t70) REVERT: C 49 VAL cc_start: 0.8406 (t) cc_final: 0.8159 (m) REVERT: C 59 ASP cc_start: 0.7925 (m-30) cc_final: 0.7201 (t70) REVERT: C 66 LYS cc_start: 0.8010 (mtpt) cc_final: 0.7717 (mttp) REVERT: C 72 ARG cc_start: 0.8307 (mmm-85) cc_final: 0.8040 (mmm-85) REVERT: C 80 SER cc_start: 0.8827 (m) cc_final: 0.8617 (p) outliers start: 12 outliers final: 4 residues processed: 143 average time/residue: 1.8342 time to fit residues: 278.3568 Evaluate side-chains 91 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 110 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3561 r_free = 0.3561 target = 0.127432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.094594 restraints weight = 11457.484| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.02 r_work: 0.2989 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9140 Z= 0.293 Angle : 0.534 7.384 12390 Z= 0.278 Chirality : 0.043 0.144 1374 Planarity : 0.004 0.042 1604 Dihedral : 7.064 75.366 1253 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.81 % Allowed : 9.27 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.04 (0.25), residues: 1126 helix: 1.42 (0.24), residues: 492 sheet: 0.52 (0.39), residues: 169 loop : 0.09 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 669 HIS 0.003 0.001 HIS A 202 PHE 0.012 0.001 PHE A 321 TYR 0.011 0.001 TYR A 732 ARG 0.003 0.000 ARG A 645 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.7970 (mtp) cc_final: 0.7539 (mtp) REVERT: A 196 MET cc_start: 0.8285 (mmp) cc_final: 0.7845 (mmp) REVERT: A 206 ASN cc_start: 0.8330 (m110) cc_final: 0.8009 (t0) REVERT: A 401 GLU cc_start: 0.8362 (tp30) cc_final: 0.8042 (mp0) REVERT: A 527 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7195 (mt-10) REVERT: A 543 MET cc_start: 0.8468 (mmt) cc_final: 0.8111 (mmt) REVERT: A 879 LYS cc_start: 0.8580 (mmmm) cc_final: 0.8008 (mmmt) REVERT: C 32 HIS cc_start: 0.7722 (t-170) cc_final: 0.7236 (t70) REVERT: C 38 MET cc_start: 0.8920 (mtm) cc_final: 0.8610 (mtm) REVERT: C 59 ASP cc_start: 0.8004 (m-30) cc_final: 0.7419 (t0) REVERT: C 66 LYS cc_start: 0.8159 (mtpt) cc_final: 0.7923 (mttp) REVERT: C 72 ARG cc_start: 0.8503 (mmm-85) cc_final: 0.8272 (mmm-85) REVERT: C 80 SER cc_start: 0.8911 (m) cc_final: 0.8650 (p) REVERT: C 140 GLU cc_start: 0.7947 (tp30) cc_final: 0.7364 (tm-30) outliers start: 18 outliers final: 12 residues processed: 96 average time/residue: 1.4023 time to fit residues: 143.6284 Evaluate side-chains 99 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 110 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 18 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 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 = 0.3558 r_free = 0.3558 target = 0.126752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.094065 restraints weight = 11695.087| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.04 r_work: 0.2985 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9140 Z= 0.278 Angle : 0.510 6.877 12390 Z= 0.265 Chirality : 0.043 0.142 1374 Planarity : 0.004 0.046 1604 Dihedral : 6.721 77.763 1253 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.22 % Allowed : 9.68 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 0.97 (0.25), residues: 1126 helix: 1.37 (0.24), residues: 492 sheet: 0.41 (0.39), residues: 169 loop : 0.07 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 669 HIS 0.003 0.001 HIS A 202 PHE 0.011 0.001 PHE A 321 TYR 0.009 0.001 TYR A 81 ARG 0.004 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8166 (mmm) REVERT: A 184 MET cc_start: 0.7922 (mtp) cc_final: 0.7328 (mtm) REVERT: A 196 MET cc_start: 0.8307 (mmp) cc_final: 0.7875 (mmp) REVERT: A 206 ASN cc_start: 0.8341 (m110) cc_final: 0.8028 (t0) REVERT: A 401 GLU cc_start: 0.8343 (tp30) cc_final: 0.8035 (mp0) REVERT: A 527 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7896 (tm-30) REVERT: A 543 MET cc_start: 0.8395 (mmt) cc_final: 0.8049 (mmt) REVERT: A 879 LYS cc_start: 0.8604 (mmmm) cc_final: 0.8025 (mmmt) REVERT: C 32 HIS cc_start: 0.7710 (t-170) cc_final: 0.7246 (t70) REVERT: C 34 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8382 (tp-100) REVERT: C 38 MET cc_start: 0.8927 (mtm) cc_final: 0.8560 (mtm) REVERT: C 59 ASP cc_start: 0.7957 (m-30) cc_final: 0.7358 (t0) REVERT: C 66 LYS cc_start: 0.8169 (mtpt) cc_final: 0.7905 (mttp) REVERT: C 72 ARG cc_start: 0.8526 (mmm-85) cc_final: 0.8312 (mmm-85) REVERT: C 80 SER cc_start: 0.8884 (m) cc_final: 0.8620 (p) REVERT: C 135 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6227 (mp0) REVERT: C 140 GLU cc_start: 0.7944 (tp30) cc_final: 0.7375 (tm-30) outliers start: 22 outliers final: 12 residues processed: 97 average time/residue: 1.3096 time to fit residues: 136.0858 Evaluate side-chains 92 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 34 GLN Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 135 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 20 optimal weight: 0.0070 chunk 105 optimal weight: 0.1980 chunk 81 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 overall best weight: 0.4398 ------------------------------------------------------------------------------- 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 = 0.3577 r_free = 0.3577 target = 0.128350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.095454 restraints weight = 11555.983| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.06 r_work: 0.3003 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9140 Z= 0.187 Angle : 0.471 6.569 12390 Z= 0.244 Chirality : 0.041 0.140 1374 Planarity : 0.004 0.047 1604 Dihedral : 6.543 77.181 1253 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.22 % Allowed : 9.58 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.09 (0.26), residues: 1126 helix: 1.52 (0.24), residues: 491 sheet: 0.28 (0.40), residues: 177 loop : 0.17 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.000 HIS C 125 PHE 0.008 0.001 PHE A 321 TYR 0.008 0.001 TYR A 834 ARG 0.002 0.000 ARG A 645 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 1.066 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8163 (mmm) REVERT: A 184 MET cc_start: 0.7891 (mtp) cc_final: 0.7302 (mtm) REVERT: A 196 MET cc_start: 0.8277 (mmp) cc_final: 0.7853 (mmp) REVERT: A 206 ASN cc_start: 0.8330 (m110) cc_final: 0.8018 (t0) REVERT: A 401 GLU cc_start: 0.8324 (tp30) cc_final: 0.8039 (mp0) REVERT: A 527 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7950 (tm-30) REVERT: A 543 MET cc_start: 0.8360 (mmt) cc_final: 0.8012 (mmt) REVERT: A 699 GLN cc_start: 0.7780 (mp10) cc_final: 0.7573 (mp10) REVERT: A 879 LYS cc_start: 0.8585 (mmmm) cc_final: 0.8001 (mmmt) REVERT: C 32 HIS cc_start: 0.7702 (t-170) cc_final: 0.7197 (t70) REVERT: C 34 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8379 (tp-100) REVERT: C 38 MET cc_start: 0.8934 (mtm) cc_final: 0.8649 (mtm) REVERT: C 59 ASP cc_start: 0.8002 (m-30) cc_final: 0.7403 (t0) REVERT: C 66 LYS cc_start: 0.8149 (mtpt) cc_final: 0.7898 (mttp) REVERT: C 72 ARG cc_start: 0.8520 (mmm-85) cc_final: 0.8114 (mmm-85) REVERT: C 80 SER cc_start: 0.8865 (m) cc_final: 0.8580 (p) REVERT: C 111 THR cc_start: 0.7421 (m) cc_final: 0.7178 (p) REVERT: C 135 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6156 (mp0) REVERT: C 140 GLU cc_start: 0.7932 (tp30) cc_final: 0.7382 (tm-30) outliers start: 22 outliers final: 10 residues processed: 94 average time/residue: 1.3886 time to fit residues: 138.9410 Evaluate side-chains 88 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 34 GLN Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 135 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 9 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 19 optimal weight: 0.2980 chunk 110 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 42 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.127940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.095286 restraints weight = 11459.500| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.06 r_work: 0.3006 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9140 Z= 0.202 Angle : 0.473 6.268 12390 Z= 0.244 Chirality : 0.041 0.135 1374 Planarity : 0.004 0.047 1604 Dihedral : 6.493 77.760 1253 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.12 % Allowed : 9.98 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.12 (0.26), residues: 1126 helix: 1.54 (0.24), residues: 491 sheet: 0.27 (0.39), residues: 177 loop : 0.19 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.000 HIS C 125 PHE 0.009 0.001 PHE A 321 TYR 0.008 0.001 TYR A 834 ARG 0.002 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8154 (mmm) REVERT: A 184 MET cc_start: 0.7919 (mtp) cc_final: 0.7327 (mtm) REVERT: A 196 MET cc_start: 0.8282 (mmp) cc_final: 0.7885 (mmp) REVERT: A 206 ASN cc_start: 0.8331 (m110) cc_final: 0.8011 (t0) REVERT: A 333 GLN cc_start: 0.7678 (tm-30) cc_final: 0.7429 (tm-30) REVERT: A 401 GLU cc_start: 0.8329 (tp30) cc_final: 0.8033 (mp0) REVERT: A 527 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7947 (tm-30) REVERT: A 543 MET cc_start: 0.8336 (mmt) cc_final: 0.7988 (mmt) REVERT: A 699 GLN cc_start: 0.7789 (mp10) cc_final: 0.7543 (mp10) REVERT: A 879 LYS cc_start: 0.8587 (mmmm) cc_final: 0.8000 (mmmt) REVERT: C 32 HIS cc_start: 0.7661 (t-170) cc_final: 0.7144 (t70) REVERT: C 34 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8385 (tp-100) REVERT: C 38 MET cc_start: 0.8902 (mtm) cc_final: 0.8612 (mtm) REVERT: C 59 ASP cc_start: 0.8093 (m-30) cc_final: 0.7484 (t0) REVERT: C 66 LYS cc_start: 0.8168 (mtpt) cc_final: 0.7915 (mttp) REVERT: C 72 ARG cc_start: 0.8523 (mmm-85) cc_final: 0.8126 (mmm-85) REVERT: C 80 SER cc_start: 0.8857 (m) cc_final: 0.8574 (p) REVERT: C 111 THR cc_start: 0.7416 (m) cc_final: 0.7189 (p) REVERT: C 135 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6181 (mp0) REVERT: C 140 GLU cc_start: 0.7982 (tp30) cc_final: 0.7441 (tm-30) outliers start: 21 outliers final: 12 residues processed: 93 average time/residue: 1.3307 time to fit residues: 132.5940 Evaluate side-chains 92 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 34 GLN Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 135 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 21 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3558 r_free = 0.3558 target = 0.126642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.094228 restraints weight = 11632.330| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.04 r_work: 0.2985 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9140 Z= 0.286 Angle : 0.500 7.944 12390 Z= 0.258 Chirality : 0.043 0.140 1374 Planarity : 0.004 0.048 1604 Dihedral : 6.571 74.054 1253 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.72 % Allowed : 9.48 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.03 (0.26), residues: 1126 helix: 1.46 (0.24), residues: 491 sheet: 0.18 (0.39), residues: 177 loop : 0.17 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 669 HIS 0.003 0.001 HIS A 202 PHE 0.011 0.001 PHE A 321 TYR 0.010 0.001 TYR A 81 ARG 0.002 0.000 ARG A 311 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8107 (mmm) REVERT: A 184 MET cc_start: 0.7920 (mtp) cc_final: 0.7343 (mtm) REVERT: A 196 MET cc_start: 0.8294 (mmp) cc_final: 0.7897 (mmp) REVERT: A 206 ASN cc_start: 0.8339 (m110) cc_final: 0.8038 (t0) REVERT: A 333 GLN cc_start: 0.7878 (tm-30) cc_final: 0.7636 (tm-30) REVERT: A 401 GLU cc_start: 0.8352 (tp30) cc_final: 0.8047 (mp0) REVERT: A 527 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7968 (tm-30) REVERT: A 543 MET cc_start: 0.8409 (mmt) cc_final: 0.8037 (mmt) REVERT: A 879 LYS cc_start: 0.8619 (mmmm) cc_final: 0.8219 (mttp) REVERT: C 32 HIS cc_start: 0.7687 (t-170) cc_final: 0.7197 (t70) REVERT: C 34 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8398 (tp-100) REVERT: C 38 MET cc_start: 0.8865 (mtm) cc_final: 0.8574 (mtm) REVERT: C 59 ASP cc_start: 0.8198 (m-30) cc_final: 0.7665 (t0) REVERT: C 66 LYS cc_start: 0.8161 (mtpt) cc_final: 0.7916 (mttp) REVERT: C 72 ARG cc_start: 0.8509 (mmm-85) cc_final: 0.8133 (mmm-85) REVERT: C 80 SER cc_start: 0.8859 (m) cc_final: 0.8574 (p) REVERT: C 135 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6162 (mp0) REVERT: C 140 GLU cc_start: 0.7990 (tp30) cc_final: 0.7440 (tm-30) outliers start: 27 outliers final: 19 residues processed: 95 average time/residue: 1.3010 time to fit residues: 132.4255 Evaluate side-chains 97 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 34 GLN Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 135 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 7 optimal weight: 0.0980 chunk 18 optimal weight: 0.0060 chunk 95 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 42 optimal weight: 0.4980 chunk 75 optimal weight: 9.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 = 0.3577 r_free = 0.3577 target = 0.128265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.096028 restraints weight = 11630.380| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.03 r_work: 0.3012 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9140 Z= 0.181 Angle : 0.467 9.175 12390 Z= 0.240 Chirality : 0.041 0.136 1374 Planarity : 0.004 0.047 1604 Dihedral : 6.432 75.366 1253 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.02 % Allowed : 10.48 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.11 (0.26), residues: 1126 helix: 1.59 (0.24), residues: 491 sheet: 0.10 (0.40), residues: 172 loop : 0.20 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.000 HIS C 125 PHE 0.008 0.001 PHE A 321 TYR 0.008 0.001 TYR C 127 ARG 0.001 0.000 ARG A 645 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8176 (mmm) REVERT: A 184 MET cc_start: 0.7882 (mtp) cc_final: 0.7332 (mtm) REVERT: A 196 MET cc_start: 0.8140 (mmp) cc_final: 0.7621 (mmp) REVERT: A 206 ASN cc_start: 0.8326 (m110) cc_final: 0.8026 (t0) REVERT: A 333 GLN cc_start: 0.7950 (tm-30) cc_final: 0.7677 (tm-30) REVERT: A 401 GLU cc_start: 0.8312 (tp30) cc_final: 0.8056 (mp0) REVERT: A 527 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7992 (tm-30) REVERT: A 543 MET cc_start: 0.8371 (mmt) cc_final: 0.7985 (mmt) REVERT: A 879 LYS cc_start: 0.8595 (mmmm) cc_final: 0.8108 (mmmt) REVERT: C 32 HIS cc_start: 0.7682 (t-170) cc_final: 0.7191 (t70) REVERT: C 34 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8195 (tp40) REVERT: C 38 MET cc_start: 0.8906 (mtm) cc_final: 0.8622 (mtm) REVERT: C 59 ASP cc_start: 0.8146 (m-30) cc_final: 0.7779 (t0) REVERT: C 66 LYS cc_start: 0.8186 (mtpt) cc_final: 0.7950 (mttp) REVERT: C 72 ARG cc_start: 0.8492 (mmm-85) cc_final: 0.8110 (mmm-85) REVERT: C 80 SER cc_start: 0.8859 (m) cc_final: 0.8610 (p) REVERT: C 135 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6166 (mp0) REVERT: C 140 GLU cc_start: 0.8019 (tp30) cc_final: 0.7487 (tm-30) outliers start: 20 outliers final: 12 residues processed: 95 average time/residue: 1.3795 time to fit residues: 139.8410 Evaluate side-chains 91 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 34 GLN Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 135 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 33 optimal weight: 0.6980 chunk 64 optimal weight: 0.3980 chunk 54 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3564 r_free = 0.3564 target = 0.127185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.094726 restraints weight = 11796.944| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.06 r_work: 0.2997 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9140 Z= 0.241 Angle : 0.488 8.630 12390 Z= 0.252 Chirality : 0.042 0.137 1374 Planarity : 0.004 0.047 1604 Dihedral : 6.433 73.071 1253 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.22 % Allowed : 10.79 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.05 (0.26), residues: 1126 helix: 1.54 (0.24), residues: 490 sheet: 0.04 (0.39), residues: 175 loop : 0.18 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS A 202 PHE 0.009 0.001 PHE A 321 TYR 0.009 0.001 TYR A 81 ARG 0.002 0.000 ARG A 645 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8256 (mmm) REVERT: A 184 MET cc_start: 0.7886 (mtp) cc_final: 0.7331 (mtm) REVERT: A 196 MET cc_start: 0.8148 (mmp) cc_final: 0.7628 (mmp) REVERT: A 206 ASN cc_start: 0.8336 (m110) cc_final: 0.8030 (t0) REVERT: A 333 GLN cc_start: 0.7953 (tm-30) cc_final: 0.7668 (tm-30) REVERT: A 401 GLU cc_start: 0.8332 (tp30) cc_final: 0.8060 (mp0) REVERT: A 527 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7991 (tm-30) REVERT: A 543 MET cc_start: 0.8401 (mmt) cc_final: 0.8034 (mmt) REVERT: A 601 ARG cc_start: 0.8191 (mtp85) cc_final: 0.7751 (ttm-80) REVERT: A 879 LYS cc_start: 0.8607 (mmmm) cc_final: 0.8208 (mttp) REVERT: C 32 HIS cc_start: 0.7680 (t-170) cc_final: 0.7174 (t70) REVERT: C 34 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8409 (tp-100) REVERT: C 38 MET cc_start: 0.8902 (mtm) cc_final: 0.8616 (mtm) REVERT: C 59 ASP cc_start: 0.8123 (m-30) cc_final: 0.7713 (t0) REVERT: C 66 LYS cc_start: 0.8170 (mtpt) cc_final: 0.7930 (mttp) REVERT: C 72 ARG cc_start: 0.8500 (mmm-85) cc_final: 0.8133 (mmm-85) REVERT: C 80 SER cc_start: 0.8861 (m) cc_final: 0.8594 (p) REVERT: C 135 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6170 (mp0) REVERT: C 140 GLU cc_start: 0.8011 (tp30) cc_final: 0.7447 (tm-30) outliers start: 22 outliers final: 14 residues processed: 95 average time/residue: 1.6969 time to fit residues: 172.6150 Evaluate side-chains 93 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 34 GLN Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 135 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 44 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 4 optimal weight: 0.2980 chunk 50 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 56 optimal weight: 0.0270 chunk 12 optimal weight: 0.8980 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.127949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.095851 restraints weight = 11643.576| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.02 r_work: 0.3009 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9140 Z= 0.203 Angle : 0.481 8.827 12390 Z= 0.247 Chirality : 0.041 0.135 1374 Planarity : 0.004 0.044 1604 Dihedral : 6.399 72.278 1253 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.81 % Allowed : 11.79 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.05 (0.26), residues: 1126 helix: 1.57 (0.24), residues: 490 sheet: 0.02 (0.39), residues: 172 loop : 0.14 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS C 125 PHE 0.009 0.001 PHE A 321 TYR 0.008 0.001 TYR C 127 ARG 0.003 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 1.067 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8260 (mmm) REVERT: A 184 MET cc_start: 0.7910 (mtp) cc_final: 0.7317 (mtm) REVERT: A 196 MET cc_start: 0.8178 (mmp) cc_final: 0.7638 (mmp) REVERT: A 206 ASN cc_start: 0.8337 (m110) cc_final: 0.8075 (t160) REVERT: A 401 GLU cc_start: 0.8316 (tp30) cc_final: 0.8057 (mp0) REVERT: A 527 GLU cc_start: 0.8241 (mt-10) cc_final: 0.8001 (tm-30) REVERT: A 543 MET cc_start: 0.8410 (mmt) cc_final: 0.8042 (mmt) REVERT: A 601 ARG cc_start: 0.8179 (mtp85) cc_final: 0.7744 (ttm-80) REVERT: A 879 LYS cc_start: 0.8602 (mmmm) cc_final: 0.8111 (mmmt) REVERT: C 32 HIS cc_start: 0.7686 (t-170) cc_final: 0.7168 (t70) REVERT: C 34 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8204 (tp40) REVERT: C 38 MET cc_start: 0.8927 (mtm) cc_final: 0.8640 (mtm) REVERT: C 59 ASP cc_start: 0.8061 (m-30) cc_final: 0.7611 (t0) REVERT: C 66 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7937 (mttp) REVERT: C 72 ARG cc_start: 0.8494 (mmm-85) cc_final: 0.8134 (mmm-85) REVERT: C 80 SER cc_start: 0.8839 (m) cc_final: 0.8584 (p) REVERT: C 135 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6157 (mp0) REVERT: C 140 GLU cc_start: 0.8024 (tp30) cc_final: 0.7464 (tm-30) outliers start: 18 outliers final: 13 residues processed: 94 average time/residue: 1.3357 time to fit residues: 134.3948 Evaluate side-chains 90 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 34 GLN Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 135 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 21 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 57 optimal weight: 0.0570 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.127183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.094980 restraints weight = 11644.883| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.01 r_work: 0.3000 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9140 Z= 0.241 Angle : 0.503 8.656 12390 Z= 0.260 Chirality : 0.042 0.164 1374 Planarity : 0.004 0.052 1604 Dihedral : 6.405 68.666 1253 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.92 % Allowed : 11.90 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.05 (0.26), residues: 1126 helix: 1.58 (0.24), residues: 483 sheet: -0.03 (0.39), residues: 175 loop : 0.18 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS A 818 PHE 0.010 0.001 PHE A 334 TYR 0.009 0.001 TYR A 81 ARG 0.001 0.000 ARG A 311 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 1.214 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8257 (mmm) REVERT: A 184 MET cc_start: 0.7904 (mtp) cc_final: 0.7316 (mtm) REVERT: A 196 MET cc_start: 0.8193 (mmp) cc_final: 0.7654 (mmp) REVERT: A 206 ASN cc_start: 0.8346 (m110) cc_final: 0.8079 (t160) REVERT: A 401 GLU cc_start: 0.8320 (tp30) cc_final: 0.8057 (mp0) REVERT: A 527 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7972 (tm-30) REVERT: A 543 MET cc_start: 0.8416 (mmt) cc_final: 0.8048 (mmt) REVERT: A 601 ARG cc_start: 0.8195 (mtp85) cc_final: 0.7760 (ttm-80) REVERT: A 879 LYS cc_start: 0.8609 (mmmm) cc_final: 0.8223 (mttp) REVERT: C 32 HIS cc_start: 0.7693 (t-170) cc_final: 0.7208 (t70) REVERT: C 34 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8214 (tp40) REVERT: C 38 MET cc_start: 0.8890 (mtm) cc_final: 0.8609 (mtm) REVERT: C 59 ASP cc_start: 0.8061 (m-30) cc_final: 0.7615 (t0) REVERT: C 66 LYS cc_start: 0.8182 (mtpt) cc_final: 0.7938 (mttp) REVERT: C 72 ARG cc_start: 0.8502 (mmm-85) cc_final: 0.8145 (mmm-85) REVERT: C 80 SER cc_start: 0.8838 (m) cc_final: 0.8578 (p) REVERT: C 135 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6168 (mp0) REVERT: C 140 GLU cc_start: 0.8001 (tp30) cc_final: 0.7462 (tm-30) outliers start: 19 outliers final: 15 residues processed: 88 average time/residue: 1.3558 time to fit residues: 127.8517 Evaluate side-chains 89 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 34 GLN Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 135 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 10 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 73 optimal weight: 0.3980 chunk 76 optimal weight: 7.9990 chunk 29 optimal weight: 0.1980 chunk 105 optimal weight: 0.0770 chunk 96 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.128064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.095954 restraints weight = 11740.433| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.01 r_work: 0.3014 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9140 Z= 0.186 Angle : 0.495 8.465 12390 Z= 0.255 Chirality : 0.041 0.159 1374 Planarity : 0.004 0.053 1604 Dihedral : 6.365 68.885 1253 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.92 % Allowed : 12.00 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.03 (0.26), residues: 1126 helix: 1.65 (0.24), residues: 483 sheet: -0.08 (0.39), residues: 175 loop : 0.09 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.001 0.000 HIS C 125 PHE 0.009 0.001 PHE C 62 TYR 0.008 0.001 TYR C 127 ARG 0.002 0.000 ARG A 73 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 6012.22 seconds wall clock time: 105 minutes 8.67 seconds (6308.67 seconds total)