Starting phenix.real_space_refine on Fri Nov 15 14:06:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5s_44223/11_2024/9b5s_44223.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5s_44223/11_2024/9b5s_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5s_44223/11_2024/9b5s_44223.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5s_44223/11_2024/9b5s_44223.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5s_44223/11_2024/9b5s_44223.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5s_44223/11_2024/9b5s_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-5513/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: 2.42 Conformation dependent library (CDL) restraints added in 1.1 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: 1.19 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: 3.29 Time building geometry restraints manager: 2.75 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: 4.170 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: 0.080 Process input model: 24.360 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:14.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.320 ------------------------------------------------------------------------------- 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 : 1.040 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: 1.4848 time to fit residues: 225.3260 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 : 0.991 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 : 7.060 74.955 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 : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.7913 (mtp) cc_final: 0.7482 (mtp) REVERT: A 196 MET cc_start: 0.8370 (mmp) cc_final: 0.7975 (mmp) REVERT: A 527 GLU cc_start: 0.7869 (mt-10) cc_final: 0.6846 (mt-10) REVERT: A 543 MET cc_start: 0.8516 (mmt) cc_final: 0.8111 (mmt) REVERT: A 879 LYS cc_start: 0.8501 (mmmm) cc_final: 0.8134 (mmmt) REVERT: C 32 HIS cc_start: 0.7545 (t-170) cc_final: 0.7003 (t70) REVERT: C 38 MET cc_start: 0.8787 (mtm) cc_final: 0.8415 (mtm) REVERT: C 59 ASP cc_start: 0.7893 (m-30) cc_final: 0.7301 (t0) REVERT: C 66 LYS cc_start: 0.8002 (mtpt) cc_final: 0.7747 (mttp) REVERT: C 72 ARG cc_start: 0.8401 (mmm-85) cc_final: 0.8159 (mmm-85) REVERT: C 80 SER cc_start: 0.8878 (m) cc_final: 0.8603 (p) REVERT: C 140 GLU cc_start: 0.7831 (tp30) cc_final: 0.7239 (tm-30) outliers start: 18 outliers final: 12 residues processed: 96 average time/residue: 1.3799 time to fit residues: 142.0046 Evaluate side-chains 97 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 56 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 84 optimal weight: 0.2980 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 101 optimal weight: 0.0670 chunk 110 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 100 optimal weight: 0.3980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9140 Z= 0.184 Angle : 0.478 6.945 12390 Z= 0.248 Chirality : 0.041 0.141 1374 Planarity : 0.004 0.045 1604 Dihedral : 6.530 77.934 1253 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.92 % Allowed : 9.68 % Favored : 88.41 % 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: 1.51 (0.24), residues: 491 sheet: 0.21 (0.40), residues: 174 loop : 0.21 (0.30), residues: 461 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 A 334 TYR 0.008 0.001 TYR A 834 ARG 0.003 0.000 ARG A 645 *********************** 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 107 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8404 (mmm) REVERT: A 184 MET cc_start: 0.7843 (mtp) cc_final: 0.7279 (mtm) REVERT: A 196 MET cc_start: 0.8345 (mmp) cc_final: 0.7941 (mmp) REVERT: A 498 MET cc_start: 0.8423 (mtt) cc_final: 0.8184 (mtt) REVERT: A 543 MET cc_start: 0.8441 (mmt) cc_final: 0.8038 (mmt) REVERT: A 879 LYS cc_start: 0.8495 (mmmm) cc_final: 0.8171 (mmmt) REVERT: C 32 HIS cc_start: 0.7498 (t-170) cc_final: 0.6963 (t70) REVERT: C 34 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8135 (tp-100) REVERT: C 38 MET cc_start: 0.8765 (mtm) cc_final: 0.8345 (mtm) REVERT: C 59 ASP cc_start: 0.7766 (m-30) cc_final: 0.7183 (t0) REVERT: C 66 LYS cc_start: 0.7981 (mtpt) cc_final: 0.7715 (mttp) REVERT: C 72 ARG cc_start: 0.8397 (mmm-85) cc_final: 0.8059 (mmm-85) REVERT: C 80 SER cc_start: 0.8844 (m) cc_final: 0.8576 (p) REVERT: C 111 THR cc_start: 0.7500 (m) cc_final: 0.7241 (p) REVERT: C 135 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6143 (mp0) REVERT: C 140 GLU cc_start: 0.7856 (tp30) cc_final: 0.7278 (tm-30) outliers start: 19 outliers final: 6 residues processed: 99 average time/residue: 1.2543 time to fit residues: 133.2925 Evaluate side-chains 83 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 53 optimal weight: 0.0170 chunk 96 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9140 Z= 0.236 Angle : 0.483 6.395 12390 Z= 0.249 Chirality : 0.042 0.138 1374 Planarity : 0.004 0.046 1604 Dihedral : 6.497 74.357 1253 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.12 % Allowed : 9.78 % 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: 1.12 (0.26), residues: 1126 helix: 1.52 (0.24), residues: 491 sheet: 0.34 (0.40), residues: 177 loop : 0.20 (0.30), residues: 458 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 0.010 0.001 PHE A 321 TYR 0.009 0.001 TYR A 81 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: 21 poor density : 82 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8352 (mmm) REVERT: A 184 MET cc_start: 0.7855 (mtp) cc_final: 0.7288 (mtm) REVERT: A 196 MET cc_start: 0.8341 (mmp) cc_final: 0.7950 (mmp) REVERT: A 498 MET cc_start: 0.8412 (mtt) cc_final: 0.8193 (mtt) REVERT: A 543 MET cc_start: 0.8438 (mmt) cc_final: 0.8050 (mmt) REVERT: A 879 LYS cc_start: 0.8517 (mmmm) cc_final: 0.8144 (mmmt) REVERT: C 32 HIS cc_start: 0.7511 (t-170) cc_final: 0.6959 (t70) REVERT: C 34 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8130 (tp-100) REVERT: C 38 MET cc_start: 0.8781 (mtm) cc_final: 0.8432 (mtm) REVERT: C 59 ASP cc_start: 0.7880 (m-30) cc_final: 0.7350 (t0) REVERT: C 66 LYS cc_start: 0.8021 (mtpt) cc_final: 0.7726 (mttp) REVERT: C 72 ARG cc_start: 0.8409 (mmm-85) cc_final: 0.7984 (mmm-85) REVERT: C 80 SER cc_start: 0.8846 (m) cc_final: 0.8548 (p) REVERT: C 135 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6053 (mp0) REVERT: C 140 GLU cc_start: 0.7818 (tp30) cc_final: 0.7259 (tm-30) outliers start: 21 outliers final: 12 residues processed: 97 average time/residue: 1.3732 time to fit residues: 142.1102 Evaluate side-chains 90 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 271 SER 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 104 LEU 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 61 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 97 optimal weight: 0.0060 chunk 27 optimal weight: 0.0270 chunk 36 optimal weight: 0.2980 overall best weight: 0.3454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9140 Z= 0.169 Angle : 0.467 6.232 12390 Z= 0.240 Chirality : 0.041 0.141 1374 Planarity : 0.004 0.046 1604 Dihedral : 6.362 74.307 1253 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.22 % Allowed : 9.48 % Favored : 88.31 % 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: 1.21 (0.26), residues: 1126 helix: 1.62 (0.24), residues: 491 sheet: 0.34 (0.40), residues: 177 loop : 0.23 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.001 0.000 HIS A 29 PHE 0.007 0.001 PHE A 321 TYR 0.008 0.001 TYR C 127 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 104 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8354 (mmm) REVERT: A 184 MET cc_start: 0.7841 (mtp) cc_final: 0.7262 (mtm) REVERT: A 196 MET cc_start: 0.8317 (mmp) cc_final: 0.7912 (mmp) REVERT: A 543 MET cc_start: 0.8424 (mmt) cc_final: 0.8038 (mmt) REVERT: A 879 LYS cc_start: 0.8503 (mmmm) cc_final: 0.8170 (mmmt) REVERT: C 32 HIS cc_start: 0.7485 (t-170) cc_final: 0.6920 (t70) REVERT: C 34 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7928 (tp40) REVERT: C 38 MET cc_start: 0.8772 (mtm) cc_final: 0.8436 (mtm) REVERT: C 59 ASP cc_start: 0.7867 (m-30) cc_final: 0.7433 (t0) REVERT: C 66 LYS cc_start: 0.8002 (mtpt) cc_final: 0.7718 (mttp) REVERT: C 72 ARG cc_start: 0.8407 (mmm-85) cc_final: 0.7990 (mmm-85) REVERT: C 80 SER cc_start: 0.8846 (m) cc_final: 0.8580 (p) REVERT: C 135 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6051 (mp0) REVERT: C 140 GLU cc_start: 0.7872 (tp30) cc_final: 0.7326 (tm-30) outliers start: 22 outliers final: 14 residues processed: 97 average time/residue: 1.3207 time to fit residues: 137.3451 Evaluate side-chains 101 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 1.148 ------------------------------------------------------------------------------- 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 835 ASP 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 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 97 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 50 optimal weight: 0.0970 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 104 optimal weight: 0.1980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1786 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= 0.193 Angle : 0.475 8.579 12390 Z= 0.244 Chirality : 0.041 0.146 1374 Planarity : 0.004 0.046 1604 Dihedral : 6.313 73.294 1253 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.92 % Allowed : 10.79 % Favored : 87.30 % 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: 1.21 (0.26), residues: 1126 helix: 1.64 (0.24), residues: 489 sheet: 0.23 (0.38), residues: 193 loop : 0.26 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.000 HIS A 202 PHE 0.008 0.001 PHE A 321 TYR 0.008 0.001 TYR C 127 ARG 0.002 0.000 ARG A 645 *********************** 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: 19 poor density : 85 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8355 (mmm) REVERT: A 184 MET cc_start: 0.7852 (mtp) cc_final: 0.7275 (mtm) REVERT: A 196 MET cc_start: 0.8304 (mmp) cc_final: 0.7889 (mmp) REVERT: A 543 MET cc_start: 0.8429 (mmt) cc_final: 0.8006 (mmt) REVERT: A 879 LYS cc_start: 0.8514 (mmmm) cc_final: 0.8178 (mmmt) REVERT: C 32 HIS cc_start: 0.7484 (t-170) cc_final: 0.6921 (t70) REVERT: C 34 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7943 (tp40) REVERT: C 38 MET cc_start: 0.8754 (mtm) cc_final: 0.8422 (mtm) REVERT: C 59 ASP cc_start: 0.7880 (m-30) cc_final: 0.7452 (t0) REVERT: C 66 LYS cc_start: 0.8005 (mtpt) cc_final: 0.7714 (mttp) REVERT: C 72 ARG cc_start: 0.8373 (mmm-85) cc_final: 0.7985 (mmm-85) REVERT: C 80 SER cc_start: 0.8845 (m) cc_final: 0.8575 (p) REVERT: C 135 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6054 (mp0) REVERT: C 140 GLU cc_start: 0.7874 (tp30) cc_final: 0.7333 (tm-30) outliers start: 19 outliers final: 13 residues processed: 98 average time/residue: 1.3377 time to fit residues: 139.9825 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 : 1.029 ------------------------------------------------------------------------------- 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 710 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1822 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= 0.266 Angle : 0.501 9.425 12390 Z= 0.258 Chirality : 0.042 0.162 1374 Planarity : 0.004 0.047 1604 Dihedral : 6.375 70.407 1253 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.52 % Allowed : 10.99 % Favored : 86.49 % 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: 1.57 (0.24), residues: 489 sheet: 0.13 (0.38), residues: 193 loop : 0.23 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 669 HIS 0.002 0.001 HIS A 202 PHE 0.010 0.001 PHE A 321 TYR 0.009 0.001 TYR A 81 ARG 0.002 0.000 ARG A 311 *********************** 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 100 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8333 (mmm) REVERT: A 184 MET cc_start: 0.7875 (mtp) cc_final: 0.7299 (mtm) REVERT: A 196 MET cc_start: 0.8306 (mmp) cc_final: 0.7920 (mmp) REVERT: A 543 MET cc_start: 0.8478 (mmt) cc_final: 0.8073 (mmt) REVERT: A 879 LYS cc_start: 0.8519 (mmmm) cc_final: 0.8304 (mttp) REVERT: C 32 HIS cc_start: 0.7492 (t-170) cc_final: 0.6952 (t70) REVERT: C 34 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7944 (tp40) REVERT: C 38 MET cc_start: 0.8760 (mtm) cc_final: 0.8420 (mtm) REVERT: C 59 ASP cc_start: 0.7920 (m-30) cc_final: 0.7476 (t0) REVERT: C 66 LYS cc_start: 0.8019 (mtpt) cc_final: 0.7724 (mttp) REVERT: C 72 ARG cc_start: 0.8381 (mmm-85) cc_final: 0.8000 (mmm-85) REVERT: C 80 SER cc_start: 0.8844 (m) cc_final: 0.8571 (p) REVERT: C 135 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6068 (mp0) REVERT: C 140 GLU cc_start: 0.7880 (tp30) cc_final: 0.7329 (tm-30) outliers start: 25 outliers final: 15 residues processed: 94 average time/residue: 1.3189 time to fit residues: 132.6853 Evaluate side-chains 99 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 1.229 ------------------------------------------------------------------------------- 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 594 THR Chi-restraints excluded: chain A residue 710 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9140 Z= 0.237 Angle : 0.498 8.815 12390 Z= 0.256 Chirality : 0.042 0.158 1374 Planarity : 0.004 0.046 1604 Dihedral : 6.372 68.710 1253 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.32 % Allowed : 11.29 % 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: 1.04 (0.26), residues: 1126 helix: 1.55 (0.24), residues: 489 sheet: 0.00 (0.39), residues: 185 loop : 0.18 (0.30), residues: 452 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 321 TYR 0.009 0.001 TYR A 81 ARG 0.001 0.000 ARG A 311 *********************** 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 105 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8340 (mmm) REVERT: A 184 MET cc_start: 0.7871 (mtp) cc_final: 0.7267 (mtm) REVERT: A 196 MET cc_start: 0.8352 (mmp) cc_final: 0.7957 (mmp) REVERT: A 543 MET cc_start: 0.8473 (mmt) cc_final: 0.8070 (mmt) REVERT: A 879 LYS cc_start: 0.8514 (mmmm) cc_final: 0.8302 (mttp) REVERT: C 32 HIS cc_start: 0.7501 (t-170) cc_final: 0.6929 (t70) REVERT: C 34 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.7947 (tp40) REVERT: C 38 MET cc_start: 0.8768 (mtm) cc_final: 0.8430 (mtm) REVERT: C 59 ASP cc_start: 0.7860 (m-30) cc_final: 0.7379 (t0) REVERT: C 66 LYS cc_start: 0.7994 (mtpt) cc_final: 0.7711 (mttp) REVERT: C 72 ARG cc_start: 0.8382 (mmm-85) cc_final: 0.8001 (mmm-85) REVERT: C 80 SER cc_start: 0.8839 (m) cc_final: 0.8565 (p) REVERT: C 135 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6065 (mp0) REVERT: C 140 GLU cc_start: 0.7866 (tp30) cc_final: 0.7316 (tm-30) outliers start: 23 outliers final: 15 residues processed: 98 average time/residue: 1.2404 time to fit residues: 130.7971 Evaluate side-chains 91 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 710 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 103 optimal weight: 0.2980 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 78 optimal weight: 0.0570 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 66 optimal weight: 0.0570 chunk 106 optimal weight: 0.6980 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1911 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= 0.181 Angle : 0.487 8.980 12390 Z= 0.252 Chirality : 0.041 0.156 1374 Planarity : 0.004 0.053 1604 Dihedral : 6.323 70.158 1253 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.92 % Allowed : 11.39 % Favored : 86.69 % 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: 1.14 (0.26), residues: 1126 helix: 1.66 (0.24), residues: 482 sheet: 0.01 (0.38), residues: 185 loop : 0.24 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.001 0.000 HIS C 125 PHE 0.011 0.001 PHE C 62 TYR 0.008 0.001 TYR C 127 ARG 0.002 0.000 ARG A 73 *********************** 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 95 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.976 Fit side-chains REVERT: A 32 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8327 (mmm) REVERT: A 184 MET cc_start: 0.7830 (mtp) cc_final: 0.7239 (mtm) REVERT: A 196 MET cc_start: 0.8252 (mmp) cc_final: 0.7718 (mmp) REVERT: A 543 MET cc_start: 0.8421 (mmt) cc_final: 0.8005 (mmt) REVERT: A 879 LYS cc_start: 0.8507 (mmmm) cc_final: 0.8187 (mmmt) REVERT: C 32 HIS cc_start: 0.7490 (t-170) cc_final: 0.6931 (t70) REVERT: C 34 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7933 (tp40) REVERT: C 38 MET cc_start: 0.8760 (mtm) cc_final: 0.8416 (mtm) REVERT: C 59 ASP cc_start: 0.7734 (m-30) cc_final: 0.7230 (t0) REVERT: C 66 LYS cc_start: 0.7991 (mtpt) cc_final: 0.7699 (mttp) REVERT: C 72 ARG cc_start: 0.8378 (mmm-85) cc_final: 0.8002 (mmm-85) REVERT: C 80 SER cc_start: 0.8829 (m) cc_final: 0.8560 (p) REVERT: C 135 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6037 (mp0) REVERT: C 140 GLU cc_start: 0.7865 (tp30) cc_final: 0.7322 (tm-30) outliers start: 19 outliers final: 13 residues processed: 89 average time/residue: 1.3503 time to fit residues: 129.1740 Evaluate side-chains 87 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 594 THR Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 34 GLN 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 64 optimal weight: 0.5980 chunk 50 optimal weight: 0.0970 chunk 73 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 88 optimal weight: 0.1980 chunk 9 optimal weight: 0.0980 chunk 68 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1983 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= 0.171 Angle : 0.503 11.094 12390 Z= 0.258 Chirality : 0.041 0.170 1374 Planarity : 0.004 0.052 1604 Dihedral : 6.118 68.347 1252 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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: 1.20 (0.26), residues: 1126 helix: 1.74 (0.24), residues: 482 sheet: -0.07 (0.42), residues: 160 loop : 0.26 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.001 0.000 HIS C 125 PHE 0.007 0.001 PHE A 321 TYR 0.007 0.001 TYR C 127 ARG 0.001 0.000 ARG A 73 ********************** 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 95 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 1.013 Fit side-chains REVERT: A 255 THR cc_start: 0.8987 (m) cc_final: 0.8622 (p) REVERT: A 543 MET cc_start: 0.8421 (mmt) cc_final: 0.8001 (mmt) REVERT: A 879 LYS cc_start: 0.8507 (mmmm) cc_final: 0.8169 (mmmt) REVERT: C 32 HIS cc_start: 0.7490 (t-170) cc_final: 0.6909 (t70) REVERT: C 34 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7924 (tp40) REVERT: C 38 MET cc_start: 0.8739 (mtm) cc_final: 0.8391 (mtm) REVERT: C 59 ASP cc_start: 0.7796 (m-30) cc_final: 0.7348 (t0) REVERT: C 66 LYS cc_start: 0.7991 (mtpt) cc_final: 0.7705 (mttp) REVERT: C 72 ARG cc_start: 0.8375 (mmm-85) cc_final: 0.7993 (mmm-85) REVERT: C 80 SER cc_start: 0.8812 (m) cc_final: 0.8546 (p) REVERT: C 135 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6067 (mp0) REVERT: C 140 GLU cc_start: 0.7871 (tp30) cc_final: 0.7342 (tm-30) outliers start: 19 outliers final: 13 residues processed: 89 average time/residue: 1.3448 time to fit residues: 128.2350 Evaluate side-chains 87 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 461 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 34 GLN 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 27 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.127444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.095233 restraints weight = 11552.161| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.02 r_work: 0.3003 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9140 Z= 0.263 Angle : 0.542 10.730 12390 Z= 0.278 Chirality : 0.043 0.164 1374 Planarity : 0.004 0.054 1604 Dihedral : 6.214 63.216 1252 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.92 % Allowed : 12.20 % Favored : 85.89 % 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: 1.08 (0.26), residues: 1126 helix: 1.61 (0.24), residues: 483 sheet: -0.07 (0.38), residues: 188 loop : 0.24 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 669 HIS 0.002 0.001 HIS A 818 PHE 0.010 0.001 PHE A 321 TYR 0.010 0.001 TYR A 81 ARG 0.004 0.000 ARG C 5 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 3177.60 seconds wall clock time: 57 minutes 26.20 seconds (3446.20 seconds total)