Starting phenix.real_space_refine on Sun Aug 4 09:17:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5k_44215/08_2024/9b5k_44215.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5k_44215/08_2024/9b5k_44215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5k_44215/08_2024/9b5k_44215.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5k_44215/08_2024/9b5k_44215.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5k_44215/08_2024/9b5k_44215.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5k_44215/08_2024/9b5k_44215.cif" } resolution = 3.16 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= 0.065 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 43 5.16 5 C 6449 2.51 5 N 1678 2.21 5 O 1953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10128 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7734 Classifications: {'peptide': 985} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 928} Chain breaks: 1 Chain: "B" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "C" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1158 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131} Chain: "D" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 596 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'A1AIV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.59, per 1000 atoms: 0.65 Number of scatterers: 10128 At special positions: 0 Unit cell: (101.08, 103.208, 120.232, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 43 16.00 P 3 15.00 Mg 2 11.99 O 1953 8.00 N 1678 7.00 C 6449 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=2.95 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 4.02 Conformation dependent library (CDL) restraints added in 1.9 seconds 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2404 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 11 sheets defined 45.4% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.926A 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: 3.680A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.973A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.233A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LYS A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 123 Processing helix chain 'A' and resid 132 through 144 removed outlier: 3.793A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.217A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 304 removed outlier: 3.683A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A 296 " --> pdb=" O HIS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 332 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 354 through 375 Processing helix chain 'A' and resid 389 through 392 Processing helix chain 'A' and resid 410 through 418 removed outlier: 4.625A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 Processing helix chain 'A' and resid 436 through 450 Processing helix chain 'A' and resid 468 through 474 removed outlier: 3.704A pdb=" N ASN A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'A' and resid 486 through 499 Processing helix chain 'A' and resid 500 through 503 Processing helix chain 'A' and resid 514 through 518 removed outlier: 4.086A 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 removed outlier: 3.534A pdb=" N ARG A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.854A pdb=" N SER A 582 " --> pdb=" O TYR A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 597 Processing helix chain 'A' and resid 601 through 618 Processing helix chain 'A' and resid 618 through 630 Processing helix chain 'A' and resid 632 through 641 removed outlier: 3.909A pdb=" N THR A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 656 Processing helix chain 'A' and resid 662 through 679 removed outlier: 3.687A pdb=" N CYS A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 689 removed outlier: 3.576A 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: 3.991A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 794 Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 818 through 835 Processing helix chain 'A' and resid 840 through 849 Processing helix chain 'A' and resid 855 through 876 removed outlier: 3.723A pdb=" N THR A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 937 Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 969 through 979 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'C' and resid 3 through 16 removed outlier: 3.608A pdb=" N ASP C 16 " --> pdb=" O ASP C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 112 Processing helix chain 'C' and resid 120 through 130 Processing helix chain 'C' and resid 130 through 146 Processing helix chain 'D' and resid 22 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.549A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N THR A 129 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ILE A 43 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR A 385 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 172 Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 228 removed outlier: 4.088A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.274A 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: 4.088A 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: 6.579A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 460 " --> pdb=" O THR A 430 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER A 559 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 905 through 908 Processing sheet with id=AA7, first strand: chain 'A' and resid 920 through 923 removed outlier: 6.449A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N VAL A 990 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N SER A 947 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU A 992 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU A 945 " --> pdb=" O GLU A 992 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N CYS A 994 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU A 951 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 920 through 923 removed outlier: 6.449A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N CYS A 995 " --> pdb=" O VAL A1003 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 12 through 16 removed outlier: 3.847A pdb=" N ARG B 42 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 21 through 26 removed outlier: 10.644A pdb=" N SER C 22 " --> pdb=" O TRP C 33 " (cutoff:3.500A) removed outlier: 9.501A pdb=" N TRP C 33 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 10.408A pdb=" N GLY C 24 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N PHE C 31 " --> pdb=" O GLY C 24 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL C 26 " --> pdb=" O ASP C 29 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 12 through 16 490 hydrogen bonds defined for protein. 1323 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: 3.80 Time building geometry restraints manager: 4.36 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: 1723 1.27 - 1.40: 2410 1.40 - 1.54: 6020 1.54 - 1.67: 125 1.67 - 1.81: 66 Bond restraints: 10344 Sorted by residual: bond pdb=" C04 A1AIV D 101 " pdb=" C05 A1AIV D 101 " ideal model delta sigma weight residual 1.453 1.526 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.71e+00 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.66e+00 bond pdb=" C05 A1AIV D 101 " pdb=" N06 A1AIV D 101 " ideal model delta sigma weight residual 1.151 1.132 0.019 2.00e-02 2.50e+03 9.10e-01 bond pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " ideal model delta sigma weight residual 1.531 1.520 0.011 1.20e-02 6.94e+03 8.21e-01 ... (remaining 10339 not shown) Histogram of bond angle deviations from ideal: 99.70 - 115.66: 6754 115.66 - 131.62: 7243 131.62 - 147.58: 11 147.58 - 163.54: 0 163.54 - 179.50: 1 Bond angle restraints: 14009 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 121.70 128.17 -6.47 1.80e+00 3.09e-01 1.29e+01 angle pdb=" C03 A1AIV D 101 " pdb=" C02 A1AIV D 101 " pdb=" N01 A1AIV D 101 " ideal model delta sigma weight residual 111.06 103.09 7.97 3.00e+00 1.11e-01 7.05e+00 angle pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 106.53 103.57 2.96 1.18e+00 7.24e-01 6.36e+00 angle pdb=" C3' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" C5' ATP A1103 " ideal model delta sigma weight residual 115.19 110.79 4.40 1.76e+00 3.23e-01 6.26e+00 angle pdb=" C2' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O3' ATP A1103 " ideal model delta sigma weight residual 111.83 105.82 6.01 2.67e+00 1.40e-01 5.07e+00 ... (remaining 14004 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.88: 5984 14.88 - 29.76: 249 29.76 - 44.65: 53 44.65 - 59.53: 17 59.53 - 74.41: 5 Dihedral angle restraints: 6308 sinusoidal: 2587 harmonic: 3721 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 -136.22 50.22 1 1.00e+01 1.00e-02 3.46e+01 dihedral pdb=" N THR C 111 " pdb=" CA THR C 111 " pdb=" CB THR C 111 " pdb=" OG1 THR C 111 " ideal model delta sinusoidal sigma weight residual -180.00 -120.22 -59.78 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N GLU A 869 " pdb=" CA GLU A 869 " pdb=" CB GLU A 869 " pdb=" CG GLU A 869 " ideal model delta sinusoidal sigma weight residual -180.00 -121.52 -58.48 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 6305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1357 0.054 - 0.108: 162 0.108 - 0.162: 46 0.162 - 0.216: 0 0.216 - 0.270: 3 Chirality restraints: 1568 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 -2.95 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C3' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" O3' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.63 -2.89 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" C4' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" C5' ATP A1103 " pdb=" O4' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.49 -2.73 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1565 not shown) Planarity restraints: 1812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 94 " 0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO C 95 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 922 " 0.015 5.00e-02 4.00e+02 2.30e-02 8.47e-01 pdb=" N PRO A 923 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 923 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 923 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 63 " -0.014 5.00e-02 4.00e+02 2.16e-02 7.44e-01 pdb=" N PRO C 64 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " -0.012 5.00e-02 4.00e+02 ... (remaining 1809 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 81 2.61 - 3.18: 8822 3.18 - 3.76: 14723 3.76 - 4.33: 21346 4.33 - 4.90: 36639 Nonbonded interactions: 81611 Sorted by model distance: nonbonded pdb=" OD2 ASP A 465 " pdb="MG MG A1102 " model vdw 2.039 2.170 nonbonded pdb="MG MG A1101 " pdb=" O2B ATP A1103 " model vdw 2.119 2.170 nonbonded pdb=" OD2 ASP A 537 " pdb="MG MG A1101 " model vdw 2.122 2.170 nonbonded pdb=" OD2 ASP A 463 " pdb=" O3' ATP A1103 " model vdw 2.180 3.040 nonbonded pdb="MG MG A1101 " pdb=" O2A ATP A1103 " model vdw 2.212 2.170 ... (remaining 81606 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 Found NCS groups: ncs_group { reference = (chain 'B' and resid 1 through 75) selection = (chain 'D' and resid 1 through 75) } 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: 4.950 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: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.740 Find NCS groups from input model: 0.170 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: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 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 0.073 10344 Z= 0.182 Angle : 0.451 7.967 14009 Z= 0.226 Chirality : 0.042 0.270 1568 Planarity : 0.003 0.032 1812 Dihedral : 9.403 74.412 3901 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.33 % Allowed : 2.74 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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: 1.73 (0.24), residues: 1273 helix: 2.21 (0.24), residues: 491 sheet: 0.79 (0.35), residues: 209 loop : 0.45 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 93 HIS 0.002 0.000 HIS C 75 PHE 0.008 0.001 PHE A 842 TYR 0.007 0.001 TYR A 509 ARG 0.002 0.000 ARG A 965 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 220 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8684 (tp30) cc_final: 0.8315 (tp30) REVERT: A 184 MET cc_start: 0.8545 (mtm) cc_final: 0.8088 (mtt) REVERT: A 196 MET cc_start: 0.8288 (mmp) cc_final: 0.7785 (mmm) REVERT: A 229 VAL cc_start: 0.8916 (t) cc_final: 0.8267 (p) REVERT: A 413 GLN cc_start: 0.8596 (tt0) cc_final: 0.8371 (tt0) REVERT: A 465 ASP cc_start: 0.8127 (t0) cc_final: 0.7926 (t0) REVERT: A 543 MET cc_start: 0.8243 (mmt) cc_final: 0.7934 (mmt) REVERT: A 645 ARG cc_start: 0.9096 (ptm-80) cc_final: 0.8809 (tpp80) REVERT: A 915 LYS cc_start: 0.8798 (tppt) cc_final: 0.8589 (ttpp) REVERT: A 925 CYS cc_start: 0.8079 (p) cc_final: 0.7831 (p) REVERT: A 944 MET cc_start: 0.8046 (tmt) cc_final: 0.7325 (tmm) REVERT: A 987 LYS cc_start: 0.8929 (mtpt) cc_final: 0.8405 (mmtt) REVERT: B 11 LYS cc_start: 0.8509 (tttt) cc_final: 0.8196 (ttpt) REVERT: C 59 ASP cc_start: 0.8905 (t0) cc_final: 0.8597 (t0) REVERT: C 93 TRP cc_start: 0.5841 (OUTLIER) cc_final: 0.3147 (t-100) REVERT: C 116 ASP cc_start: 0.8003 (m-30) cc_final: 0.7520 (m-30) REVERT: C 117 ASP cc_start: 0.8184 (t0) cc_final: 0.7838 (m-30) REVERT: C 127 TYR cc_start: 0.8293 (t80) cc_final: 0.8090 (t80) outliers start: 15 outliers final: 7 residues processed: 230 average time/residue: 0.2963 time to fit residues: 88.4399 Evaluate side-chains 135 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 127 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 93 TRP Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 52 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 60 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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: 0.7885 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 10344 Z= 0.203 Angle : 0.530 8.455 14009 Z= 0.271 Chirality : 0.043 0.175 1568 Planarity : 0.004 0.045 1812 Dihedral : 6.694 89.447 1421 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.68 % Allowed : 6.37 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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: 1.63 (0.24), residues: 1273 helix: 1.94 (0.24), residues: 510 sheet: 0.92 (0.35), residues: 213 loop : 0.45 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 93 HIS 0.002 0.001 HIS A 458 PHE 0.010 0.001 PHE A 842 TYR 0.013 0.001 TYR C 74 ARG 0.006 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8653 (tp30) cc_final: 0.8267 (tp30) REVERT: A 184 MET cc_start: 0.8592 (mtm) cc_final: 0.8280 (mtt) REVERT: A 185 ILE cc_start: 0.8714 (mt) cc_final: 0.8478 (mp) REVERT: A 205 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7564 (mt-10) REVERT: A 229 VAL cc_start: 0.8947 (t) cc_final: 0.8597 (p) REVERT: A 465 ASP cc_start: 0.8449 (t0) cc_final: 0.8127 (t0) REVERT: A 626 MET cc_start: 0.8689 (tpp) cc_final: 0.8307 (tpt) REVERT: A 645 ARG cc_start: 0.9107 (ptm-80) cc_final: 0.8782 (tpt-90) REVERT: A 915 LYS cc_start: 0.8839 (tppt) cc_final: 0.8570 (ttpp) REVERT: A 925 CYS cc_start: 0.8131 (p) cc_final: 0.7898 (p) REVERT: A 987 LYS cc_start: 0.8897 (mtpt) cc_final: 0.8355 (mmtt) REVERT: B 11 LYS cc_start: 0.8541 (tttt) cc_final: 0.8313 (ttpp) REVERT: B 60 ASN cc_start: 0.8318 (t0) cc_final: 0.7830 (t0) REVERT: B 64 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8608 (mm-30) REVERT: C 59 ASP cc_start: 0.8827 (t0) cc_final: 0.8512 (t0) REVERT: C 127 TYR cc_start: 0.8411 (t80) cc_final: 0.7977 (t80) REVERT: C 143 ARG cc_start: 0.8662 (ttp80) cc_final: 0.8351 (mtm110) outliers start: 19 outliers final: 14 residues processed: 153 average time/residue: 0.2565 time to fit residues: 53.9436 Evaluate side-chains 135 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 56 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 95 optimal weight: 0.2980 chunk 77 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 123 optimal weight: 10.0000 chunk 102 optimal weight: 0.2980 chunk 113 optimal weight: 0.9990 chunk 39 optimal weight: 0.0000 chunk 91 optimal weight: 0.8980 overall best weight: 0.4184 ------------------------------------------------------------------------------- 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: 0.7876 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10344 Z= 0.147 Angle : 0.470 8.053 14009 Z= 0.241 Chirality : 0.041 0.139 1568 Planarity : 0.003 0.044 1812 Dihedral : 6.347 74.920 1416 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.77 % Allowed : 7.79 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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: 1.63 (0.24), residues: 1273 helix: 1.89 (0.23), residues: 515 sheet: 1.05 (0.36), residues: 211 loop : 0.41 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 93 HIS 0.001 0.000 HIS C 75 PHE 0.009 0.001 PHE A 254 TYR 0.014 0.001 TYR C 60 ARG 0.004 0.000 ARG A 841 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8620 (tp30) cc_final: 0.8237 (tp30) REVERT: A 229 VAL cc_start: 0.8974 (t) cc_final: 0.8614 (p) REVERT: A 250 TYR cc_start: 0.8460 (m-80) cc_final: 0.8119 (m-10) REVERT: A 465 ASP cc_start: 0.8524 (t0) cc_final: 0.8181 (t0) REVERT: A 626 MET cc_start: 0.8747 (tpp) cc_final: 0.8444 (tpt) REVERT: A 645 ARG cc_start: 0.9111 (ptm-80) cc_final: 0.8852 (tpt-90) REVERT: A 719 ARG cc_start: 0.8051 (mmm160) cc_final: 0.7784 (mmm160) REVERT: A 915 LYS cc_start: 0.8873 (tppt) cc_final: 0.8579 (ttpp) REVERT: A 925 CYS cc_start: 0.8164 (p) cc_final: 0.7931 (p) REVERT: A 987 LYS cc_start: 0.8907 (mtpt) cc_final: 0.8368 (mmtt) REVERT: B 60 ASN cc_start: 0.8365 (t0) cc_final: 0.7746 (t0) REVERT: B 64 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8618 (mm-30) REVERT: C 59 ASP cc_start: 0.8877 (t0) cc_final: 0.8432 (t0) REVERT: C 93 TRP cc_start: 0.6144 (OUTLIER) cc_final: 0.3627 (t-100) REVERT: C 143 ARG cc_start: 0.8653 (ttp80) cc_final: 0.8273 (ttp-110) outliers start: 20 outliers final: 17 residues processed: 142 average time/residue: 0.2505 time to fit residues: 49.2366 Evaluate side-chains 140 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 93 TRP Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 70 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.9990 chunk 86 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 0.0970 chunk 76 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 121 optimal weight: 9.9990 chunk 60 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10344 Z= 0.176 Angle : 0.471 7.789 14009 Z= 0.241 Chirality : 0.042 0.159 1568 Planarity : 0.004 0.044 1812 Dihedral : 6.167 80.445 1414 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.12 % Allowed : 8.76 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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: 1.63 (0.24), residues: 1273 helix: 1.91 (0.23), residues: 515 sheet: 1.10 (0.35), residues: 210 loop : 0.37 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 93 HIS 0.002 0.000 HIS A 818 PHE 0.023 0.001 PHE C 62 TYR 0.010 0.001 TYR D 59 ARG 0.006 0.000 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 126 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8634 (tp30) cc_final: 0.8062 (tp30) REVERT: A 185 ILE cc_start: 0.8879 (mt) cc_final: 0.8660 (mp) REVERT: A 229 VAL cc_start: 0.9017 (t) cc_final: 0.8636 (p) REVERT: A 465 ASP cc_start: 0.8533 (t0) cc_final: 0.8127 (t0) REVERT: A 645 ARG cc_start: 0.9099 (ptm-80) cc_final: 0.8861 (tpt-90) REVERT: A 855 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8169 (mtp) REVERT: A 915 LYS cc_start: 0.8890 (tppt) cc_final: 0.8613 (ttpp) REVERT: A 987 LYS cc_start: 0.8940 (mtpt) cc_final: 0.8358 (mmtt) REVERT: B 60 ASN cc_start: 0.8411 (t0) cc_final: 0.7728 (t0) REVERT: C 59 ASP cc_start: 0.8917 (t0) cc_final: 0.8531 (t0) REVERT: C 93 TRP cc_start: 0.6211 (OUTLIER) cc_final: 0.3875 (t-100) REVERT: C 143 ARG cc_start: 0.8672 (ttp80) cc_final: 0.8322 (ttp-110) outliers start: 24 outliers final: 17 residues processed: 143 average time/residue: 0.2537 time to fit residues: 49.6434 Evaluate side-chains 134 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 93 TRP Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 70 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 1 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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: 0.7907 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10344 Z= 0.200 Angle : 0.468 6.664 14009 Z= 0.241 Chirality : 0.042 0.158 1568 Planarity : 0.004 0.044 1812 Dihedral : 6.215 80.719 1414 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.57 % Allowed : 9.20 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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: 1.54 (0.24), residues: 1273 helix: 1.83 (0.23), residues: 516 sheet: 1.07 (0.35), residues: 218 loop : 0.31 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 93 HIS 0.002 0.000 HIS A 818 PHE 0.020 0.001 PHE C 62 TYR 0.019 0.001 TYR C 127 ARG 0.006 0.000 ARG A 841 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 126 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8641 (tp30) cc_final: 0.8074 (tp30) REVERT: A 185 ILE cc_start: 0.8879 (mt) cc_final: 0.8619 (mp) REVERT: A 250 TYR cc_start: 0.8474 (m-10) cc_final: 0.8161 (m-10) REVERT: A 465 ASP cc_start: 0.8532 (t0) cc_final: 0.8059 (t0) REVERT: A 546 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8323 (t0) REVERT: A 567 ASN cc_start: 0.8967 (OUTLIER) cc_final: 0.8740 (p0) REVERT: A 645 ARG cc_start: 0.9102 (ptm-80) cc_final: 0.8873 (tpt-90) REVERT: A 719 ARG cc_start: 0.8202 (mmm160) cc_final: 0.7752 (mmm160) REVERT: A 915 LYS cc_start: 0.8922 (tppt) cc_final: 0.8625 (ttpp) REVERT: A 944 MET cc_start: 0.8363 (tmm) cc_final: 0.8157 (tmm) REVERT: A 987 LYS cc_start: 0.8954 (mtpt) cc_final: 0.8348 (mmtt) REVERT: B 60 ASN cc_start: 0.8460 (t0) cc_final: 0.7849 (t0) REVERT: C 59 ASP cc_start: 0.8920 (t0) cc_final: 0.8632 (t0) REVERT: C 93 TRP cc_start: 0.6270 (OUTLIER) cc_final: 0.3970 (t-100) REVERT: C 116 ASP cc_start: 0.7825 (m-30) cc_final: 0.7218 (t0) REVERT: C 131 ARG cc_start: 0.8749 (mmm-85) cc_final: 0.8482 (mmm-85) outliers start: 29 outliers final: 20 residues processed: 146 average time/residue: 0.2506 time to fit residues: 50.5718 Evaluate side-chains 144 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 93 TRP Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 56 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.6980 chunk 109 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 101 optimal weight: 0.0070 chunk 56 optimal weight: 0.0980 chunk 10 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- 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: 0.7889 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10344 Z= 0.140 Angle : 0.467 6.756 14009 Z= 0.240 Chirality : 0.041 0.175 1568 Planarity : 0.004 0.046 1812 Dihedral : 6.045 83.903 1411 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.30 % Allowed : 9.91 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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: 1.62 (0.24), residues: 1273 helix: 1.88 (0.23), residues: 516 sheet: 1.23 (0.36), residues: 206 loop : 0.34 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 33 HIS 0.001 0.000 HIS A 818 PHE 0.017 0.001 PHE C 62 TYR 0.025 0.001 TYR C 60 ARG 0.007 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 123 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8609 (tp30) cc_final: 0.8048 (tp30) REVERT: A 185 ILE cc_start: 0.8821 (mt) cc_final: 0.8569 (mp) REVERT: A 465 ASP cc_start: 0.8556 (t0) cc_final: 0.8073 (t0) REVERT: A 546 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8303 (t0) REVERT: A 645 ARG cc_start: 0.9082 (ptm-80) cc_final: 0.8853 (tpt-90) REVERT: A 719 ARG cc_start: 0.8136 (mmm160) cc_final: 0.7676 (mmm160) REVERT: A 915 LYS cc_start: 0.8914 (ttpt) cc_final: 0.8614 (ttpp) REVERT: A 987 LYS cc_start: 0.8952 (mtpt) cc_final: 0.8348 (mmtt) REVERT: B 60 ASN cc_start: 0.8508 (t0) cc_final: 0.7870 (t0) REVERT: C 5 ARG cc_start: 0.8675 (tpt90) cc_final: 0.8398 (tpt-90) REVERT: C 59 ASP cc_start: 0.8749 (t0) cc_final: 0.7964 (t70) REVERT: C 116 ASP cc_start: 0.7801 (m-30) cc_final: 0.7154 (t0) REVERT: C 131 ARG cc_start: 0.8702 (mmm-85) cc_final: 0.8374 (mmm-85) outliers start: 26 outliers final: 18 residues processed: 139 average time/residue: 0.2762 time to fit residues: 52.9393 Evaluate side-chains 140 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 56 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 121 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 74 optimal weight: 0.1980 chunk 56 optimal weight: 0.0970 chunk 75 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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: 0.7890 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10344 Z= 0.152 Angle : 0.465 6.281 14009 Z= 0.238 Chirality : 0.041 0.151 1568 Planarity : 0.004 0.044 1812 Dihedral : 6.020 85.822 1411 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.04 % Allowed : 9.56 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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: 1.63 (0.24), residues: 1273 helix: 1.88 (0.23), residues: 516 sheet: 1.27 (0.36), residues: 205 loop : 0.32 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 93 HIS 0.001 0.000 HIS A 818 PHE 0.010 0.001 PHE C 62 TYR 0.028 0.001 TYR C 60 ARG 0.011 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8609 (tp30) cc_final: 0.8037 (tp30) REVERT: A 185 ILE cc_start: 0.8839 (mt) cc_final: 0.8588 (mp) REVERT: A 465 ASP cc_start: 0.8493 (t0) cc_final: 0.8015 (t0) REVERT: A 546 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.8307 (t0) REVERT: A 567 ASN cc_start: 0.8942 (OUTLIER) cc_final: 0.8717 (p0) REVERT: A 645 ARG cc_start: 0.9082 (ptm-80) cc_final: 0.8858 (tpt-90) REVERT: A 719 ARG cc_start: 0.8155 (mmm160) cc_final: 0.7687 (mmm160) REVERT: A 915 LYS cc_start: 0.8920 (ttpt) cc_final: 0.8613 (ttpp) REVERT: A 987 LYS cc_start: 0.8947 (mtpt) cc_final: 0.8358 (mmtt) REVERT: B 60 ASN cc_start: 0.8499 (t0) cc_final: 0.7878 (t0) REVERT: C 5 ARG cc_start: 0.8679 (tpt90) cc_final: 0.7810 (mmm-85) REVERT: C 59 ASP cc_start: 0.8917 (t0) cc_final: 0.8615 (t0) REVERT: C 116 ASP cc_start: 0.7769 (m-30) cc_final: 0.7117 (t0) REVERT: C 131 ARG cc_start: 0.8659 (mmm-85) cc_final: 0.8417 (mmm-85) REVERT: C 143 ARG cc_start: 0.8652 (ttp80) cc_final: 0.8375 (mtm110) outliers start: 23 outliers final: 21 residues processed: 135 average time/residue: 0.2625 time to fit residues: 48.3479 Evaluate side-chains 142 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 119 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 70 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 116 optimal weight: 0.3980 chunk 106 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.7892 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10344 Z= 0.156 Angle : 0.463 6.316 14009 Z= 0.237 Chirality : 0.041 0.152 1568 Planarity : 0.004 0.042 1812 Dihedral : 5.981 84.305 1411 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.21 % Allowed : 9.65 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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: 1.63 (0.24), residues: 1273 helix: 1.89 (0.23), residues: 516 sheet: 1.21 (0.36), residues: 206 loop : 0.35 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 93 HIS 0.001 0.000 HIS A 818 PHE 0.008 0.001 PHE D 45 TYR 0.016 0.001 TYR D 59 ARG 0.009 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 123 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8607 (tp30) cc_final: 0.8035 (tp30) REVERT: A 465 ASP cc_start: 0.8503 (t0) cc_final: 0.8002 (t0) REVERT: A 546 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8309 (t0) REVERT: A 567 ASN cc_start: 0.8966 (OUTLIER) cc_final: 0.8734 (p0) REVERT: A 645 ARG cc_start: 0.9095 (ptm-80) cc_final: 0.8882 (tpt-90) REVERT: A 719 ARG cc_start: 0.8171 (mmm160) cc_final: 0.7697 (mmm160) REVERT: A 915 LYS cc_start: 0.8924 (ttpt) cc_final: 0.8606 (ttpp) REVERT: A 944 MET cc_start: 0.8191 (tmm) cc_final: 0.7787 (tmm) REVERT: A 987 LYS cc_start: 0.8949 (mtpt) cc_final: 0.8356 (mmtt) REVERT: B 60 ASN cc_start: 0.8510 (t0) cc_final: 0.7913 (t0) REVERT: C 5 ARG cc_start: 0.8641 (tpt90) cc_final: 0.8326 (tpt-90) REVERT: C 59 ASP cc_start: 0.8885 (t0) cc_final: 0.8593 (t0) REVERT: C 116 ASP cc_start: 0.7758 (m-30) cc_final: 0.7110 (t0) REVERT: C 130 ASP cc_start: 0.7342 (t0) cc_final: 0.6889 (p0) REVERT: C 131 ARG cc_start: 0.8660 (mmm-85) cc_final: 0.8330 (mmm-85) REVERT: C 143 ARG cc_start: 0.8671 (ttp80) cc_final: 0.8198 (ttp-110) outliers start: 25 outliers final: 19 residues processed: 136 average time/residue: 0.2662 time to fit residues: 49.3557 Evaluate side-chains 139 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 70 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.7980 chunk 116 optimal weight: 0.1980 chunk 68 optimal weight: 0.0070 chunk 49 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 0.4980 chunk 102 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 112 optimal weight: 0.5980 chunk 74 optimal weight: 7.9990 chunk 119 optimal weight: 7.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- 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: 0.7886 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10344 Z= 0.145 Angle : 0.468 7.774 14009 Z= 0.238 Chirality : 0.041 0.153 1568 Planarity : 0.004 0.039 1812 Dihedral : 5.954 84.976 1411 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.86 % Allowed : 10.18 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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: 1.67 (0.24), residues: 1273 helix: 1.94 (0.23), residues: 516 sheet: 1.25 (0.35), residues: 205 loop : 0.35 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 33 HIS 0.001 0.000 HIS A 818 PHE 0.011 0.001 PHE C 62 TYR 0.053 0.001 TYR C 60 ARG 0.008 0.000 ARG A 841 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8595 (tp30) cc_final: 0.8023 (tp30) REVERT: A 185 ILE cc_start: 0.8910 (mt) cc_final: 0.8705 (mp) REVERT: A 442 MET cc_start: 0.8199 (tpp) cc_final: 0.7980 (mtp) REVERT: A 465 ASP cc_start: 0.8499 (t0) cc_final: 0.8002 (t0) REVERT: A 546 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8302 (t0) REVERT: A 567 ASN cc_start: 0.8960 (OUTLIER) cc_final: 0.8728 (p0) REVERT: A 645 ARG cc_start: 0.9077 (ptm-80) cc_final: 0.8850 (tpt-90) REVERT: A 719 ARG cc_start: 0.8169 (mmm160) cc_final: 0.7693 (mmm160) REVERT: A 915 LYS cc_start: 0.8926 (ttpt) cc_final: 0.8602 (ttpp) REVERT: A 944 MET cc_start: 0.8184 (tmm) cc_final: 0.7778 (tmm) REVERT: A 987 LYS cc_start: 0.8948 (mtpt) cc_final: 0.8447 (mttm) REVERT: B 60 ASN cc_start: 0.8529 (t0) cc_final: 0.7954 (t0) REVERT: C 5 ARG cc_start: 0.8663 (tpt90) cc_final: 0.7857 (mmm-85) REVERT: C 59 ASP cc_start: 0.8756 (t0) cc_final: 0.7965 (t70) REVERT: C 60 TYR cc_start: 0.8974 (t80) cc_final: 0.8683 (t80) REVERT: C 116 ASP cc_start: 0.7746 (m-30) cc_final: 0.7097 (t0) REVERT: C 131 ARG cc_start: 0.8639 (mmm-85) cc_final: 0.8374 (mmm-85) REVERT: C 143 ARG cc_start: 0.8671 (ttp80) cc_final: 0.8192 (ttp-110) outliers start: 21 outliers final: 19 residues processed: 134 average time/residue: 0.2738 time to fit residues: 49.7295 Evaluate side-chains 139 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.0020 chunk 56 optimal weight: 0.0370 chunk 83 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 106 optimal weight: 0.2980 overall best weight: 0.3066 ------------------------------------------------------------------------------- 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: 0.7878 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10344 Z= 0.134 Angle : 0.471 7.836 14009 Z= 0.239 Chirality : 0.041 0.148 1568 Planarity : 0.004 0.040 1812 Dihedral : 5.930 84.888 1411 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.77 % Allowed : 10.44 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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: 1.75 (0.24), residues: 1273 helix: 1.99 (0.23), residues: 516 sheet: 1.31 (0.36), residues: 208 loop : 0.40 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 33 HIS 0.001 0.000 HIS A 818 PHE 0.008 0.001 PHE A 360 TYR 0.042 0.001 TYR C 60 ARG 0.008 0.001 ARG A 841 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8595 (tp30) cc_final: 0.8020 (tp30) REVERT: A 80 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8267 (tp40) REVERT: A 465 ASP cc_start: 0.8497 (t0) cc_final: 0.8002 (t0) REVERT: A 546 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8291 (t0) REVERT: A 567 ASN cc_start: 0.8942 (OUTLIER) cc_final: 0.8714 (p0) REVERT: A 719 ARG cc_start: 0.8162 (mmm160) cc_final: 0.7688 (mmm160) REVERT: A 915 LYS cc_start: 0.8918 (ttpt) cc_final: 0.8587 (ttpp) REVERT: A 944 MET cc_start: 0.8146 (tmm) cc_final: 0.7742 (tmm) REVERT: A 987 LYS cc_start: 0.8944 (mtpt) cc_final: 0.8443 (mttm) REVERT: B 60 ASN cc_start: 0.8533 (t0) cc_final: 0.7976 (t0) REVERT: C 5 ARG cc_start: 0.8664 (tpt90) cc_final: 0.7864 (mmm-85) REVERT: C 59 ASP cc_start: 0.8797 (t0) cc_final: 0.8014 (t70) REVERT: C 60 TYR cc_start: 0.8954 (t80) cc_final: 0.8744 (t80) REVERT: C 116 ASP cc_start: 0.7730 (m-30) cc_final: 0.7084 (t0) REVERT: C 130 ASP cc_start: 0.7326 (t0) cc_final: 0.6932 (p0) REVERT: C 143 ARG cc_start: 0.8680 (ttp80) cc_final: 0.8204 (ttp-110) outliers start: 20 outliers final: 17 residues processed: 133 average time/residue: 0.2748 time to fit residues: 49.6763 Evaluate side-chains 134 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 114 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 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 = 0.3642 r_free = 0.3642 target = 0.115313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.082282 restraints weight = 17270.956| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.32 r_work: 0.2990 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10344 Z= 0.189 Angle : 0.487 8.008 14009 Z= 0.249 Chirality : 0.042 0.151 1568 Planarity : 0.004 0.040 1812 Dihedral : 5.977 85.431 1411 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.68 % Allowed : 10.62 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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: 1.66 (0.24), residues: 1273 helix: 1.95 (0.23), residues: 516 sheet: 1.18 (0.35), residues: 209 loop : 0.34 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 93 HIS 0.002 0.000 HIS A 818 PHE 0.010 0.001 PHE A 677 TYR 0.042 0.001 TYR C 60 ARG 0.009 0.000 ARG A 841 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2444.06 seconds wall clock time: 43 minutes 48.84 seconds (2628.84 seconds total)