Starting phenix.real_space_refine on Sat Nov 16 02:03:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5d_44208/11_2024/9b5d_44208.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5d_44208/11_2024/9b5d_44208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5d_44208/11_2024/9b5d_44208.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5d_44208/11_2024/9b5d_44208.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5d_44208/11_2024/9b5d_44208.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5d_44208/11_2024/9b5d_44208.cif" } resolution = 2.8 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= 0.071 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. Time to flip 7 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: 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: 7.60, per 1000 atoms: 0.75 Number of scatterers: 10128 At special positions: 0 Unit cell: (100.016, 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 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=2.91 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: 2.75 Conformation dependent library (CDL) restraints added in 1.2 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: 54 helices and 11 sheets defined 45.9% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.750A 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 73 through 79 removed outlier: 3.681A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 4.014A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.326A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYS A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 123 removed outlier: 3.607A pdb=" N ASN A 122 " --> pdb=" O TYR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.711A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 3.691A pdb=" N ASP A 223 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.291A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.652A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.613A 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: 4.406A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.555A 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: 3.619A 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: 3.847A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 528 removed outlier: 3.839A pdb=" N LYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.568A pdb=" N ARG A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.538A pdb=" N SER A 581 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.859A 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 Processing helix chain 'A' and resid 618 through 628 Processing helix chain 'A' and resid 632 through 641 removed outlier: 3.674A 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: 3.564A pdb=" N CYS A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 689 Processing helix chain 'A' and resid 718 through 737 Processing helix chain 'A' and resid 743 through 753 removed outlier: 3.982A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 794 removed outlier: 4.015A pdb=" N GLN A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 794 " --> pdb=" O ILE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 834 Processing helix chain 'A' and resid 840 through 849 Processing helix chain 'A' and resid 855 through 876 removed outlier: 3.521A pdb=" N THR A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.691A pdb=" N GLU A 882 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.736A 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 '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 Processing helix chain 'C' and resid 86 through 90 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 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: 6.806A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.235A 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: 4.242A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.226A 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: 4.242A 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: 6.447A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.279A 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: 6.352A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL A 990 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N SER A 947 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLU A 992 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.343A 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: 6.759A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.393A 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: 6.352A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.308A 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: 3.889A 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: 3.631A pdb=" N GLY C 24 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N HIS C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 12 through 16 487 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: 3.67 Time building geometry restraints manager: 3.08 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: 6015 1.54 - 1.67: 130 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 1.525 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.78e+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 1.17e+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 9.05e-01 ... (remaining 10339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 13908 1.90 - 3.79: 88 3.79 - 5.69: 8 5.69 - 7.58: 4 7.58 - 9.48: 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 121.70 128.14 -6.44 1.80e+00 3.09e-01 1.28e+01 angle pdb=" C03 A1AIV D 101 " pdb=" C02 A1AIV D 101 " pdb=" N01 A1AIV D 101 " ideal model delta sigma weight residual 111.06 101.58 9.48 3.00e+00 1.11e-01 9.98e+00 angle pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 106.53 103.30 3.23 1.18e+00 7.24e-01 7.56e+00 angle pdb=" C2' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O3' ATP A1103 " ideal model delta sigma weight residual 111.83 104.51 7.32 2.67e+00 1.40e-01 7.52e+00 angle pdb=" C3' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" C5' ATP A1103 " ideal model delta sigma weight residual 115.19 110.48 4.71 1.76e+00 3.23e-01 7.18e+00 ... (remaining 14004 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 6051 17.32 - 34.64: 200 34.64 - 51.95: 44 51.95 - 69.27: 9 69.27 - 86.59: 4 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 -147.30 61.30 1 1.00e+01 1.00e-02 4.99e+01 dihedral pdb=" CA LYS A 884 " pdb=" C LYS A 884 " pdb=" N ASN A 885 " pdb=" CA ASN A 885 " ideal model delta harmonic sigma weight residual 180.00 163.19 16.81 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" N CYS C 85 " pdb=" CA CYS C 85 " pdb=" CB CYS C 85 " pdb=" SG CYS C 85 " ideal model delta sinusoidal sigma weight residual -180.00 -122.72 -57.28 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 6305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1384 0.060 - 0.120: 162 0.120 - 0.179: 19 0.179 - 0.239: 1 0.239 - 0.299: 2 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 -2.98 0.30 2.00e-01 2.50e+01 2.24e+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 -2.92 0.29 2.00e-01 2.50e+01 2.06e+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 1.36e+00 ... (remaining 1565 not shown) Planarity restraints: 1812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 118 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.63e+00 pdb=" C GLU A 118 " 0.033 2.00e-02 2.50e+03 pdb=" O GLU A 118 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR A 119 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 75 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.80e+00 pdb=" N PRO C 76 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 76 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 76 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 94 " 0.021 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO C 95 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.018 5.00e-02 4.00e+02 ... (remaining 1809 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 69 2.59 - 3.17: 8500 3.17 - 3.74: 14717 3.74 - 4.32: 22137 4.32 - 4.90: 37575 Nonbonded interactions: 82998 Sorted by model distance: nonbonded pdb="MG MG A1101 " pdb=" O2B ATP A1103 " model vdw 2.012 2.170 nonbonded pdb=" OD2 ASP A 465 " pdb="MG MG A1102 " model vdw 2.044 2.170 nonbonded pdb=" OD2 ASP A 537 " pdb="MG MG A1101 " model vdw 2.052 2.170 nonbonded pdb=" OD2 ASP A 463 " pdb=" O3' ATP A1103 " model vdw 2.098 3.040 nonbonded pdb=" OD1 ASN D 25 " pdb=" NZ LYS D 29 " model vdw 2.116 3.120 ... (remaining 82993 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: 2.370 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: 0.060 Set scattering table: 0.080 Process input model: 28.230 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 10344 Z= 0.225 Angle : 0.466 9.478 14009 Z= 0.237 Chirality : 0.043 0.299 1568 Planarity : 0.003 0.034 1812 Dihedral : 9.737 86.589 3901 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.06 % Allowed : 3.10 % Favored : 95.84 % 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: 1.46 (0.24), residues: 1273 helix: 1.66 (0.24), residues: 506 sheet: 0.78 (0.35), residues: 208 loop : 0.55 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 669 HIS 0.003 0.001 HIS C 75 PHE 0.011 0.001 PHE A 237 TYR 0.008 0.001 TYR A 544 ARG 0.003 0.000 ARG A 409 *********************** 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 166 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7419 (tp30) cc_final: 0.7011 (tp30) REVERT: A 32 MET cc_start: 0.8377 (mtp) cc_final: 0.8091 (mtp) REVERT: A 33 LYS cc_start: 0.7993 (ttpt) cc_final: 0.7714 (ttmm) REVERT: A 184 MET cc_start: 0.8383 (mtp) cc_final: 0.8111 (mtt) REVERT: A 196 MET cc_start: 0.8952 (mmp) cc_final: 0.8701 (mmp) REVERT: A 216 LYS cc_start: 0.7147 (mtmm) cc_final: 0.6817 (pttp) REVERT: A 262 LYS cc_start: 0.8936 (ttpp) cc_final: 0.8735 (tmtt) REVERT: A 286 MET cc_start: 0.8394 (mmm) cc_final: 0.7830 (pmt) REVERT: A 448 MET cc_start: 0.8910 (mmp) cc_final: 0.8620 (mmp) REVERT: A 596 LYS cc_start: 0.8578 (tmtt) cc_final: 0.8374 (mmmm) REVERT: A 611 ASP cc_start: 0.7233 (m-30) cc_final: 0.7033 (m-30) REVERT: A 652 ARG cc_start: 0.8187 (ttp80) cc_final: 0.7941 (tmm-80) REVERT: A 832 MET cc_start: 0.8503 (mtp) cc_final: 0.8250 (mtp) REVERT: A 869 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: A 879 LYS cc_start: 0.8723 (mmmm) cc_final: 0.8350 (mmtt) REVERT: A 1011 LYS cc_start: 0.8666 (ttmm) cc_final: 0.8343 (ttmm) REVERT: B 51 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8235 (mt-10) REVERT: B 58 ASP cc_start: 0.8146 (m-30) cc_final: 0.7552 (m-30) REVERT: C 8 ARG cc_start: 0.7996 (mtt-85) cc_final: 0.7687 (ttp-170) REVERT: C 136 LEU cc_start: 0.8285 (mm) cc_final: 0.7947 (tp) REVERT: C 143 ARG cc_start: 0.8444 (ttp80) cc_final: 0.8168 (mtm110) outliers start: 12 outliers final: 5 residues processed: 164 average time/residue: 1.5315 time to fit residues: 267.1195 Evaluate side-chains 119 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 91 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 0.3980 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 0.0770 chunk 60 optimal weight: 0.8980 chunk 73 optimal weight: 0.0470 chunk 114 optimal weight: 0.4980 overall best weight: 0.3436 ------------------------------------------------------------------------------- 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: 0.7609 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10344 Z= 0.170 Angle : 0.473 6.698 14009 Z= 0.246 Chirality : 0.042 0.153 1568 Planarity : 0.004 0.039 1812 Dihedral : 6.085 80.920 1416 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.59 % Allowed : 8.23 % Favored : 90.18 % 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: 1.78 (0.24), residues: 511 sheet: 0.97 (0.35), residues: 206 loop : 0.60 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 669 HIS 0.002 0.001 HIS A 458 PHE 0.010 0.001 PHE A 842 TYR 0.009 0.001 TYR A 736 ARG 0.006 0.000 ARG C 5 *********************** 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 141 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 1.324 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7551 (tp30) cc_final: 0.7150 (tp30) REVERT: A 32 MET cc_start: 0.8394 (mtp) cc_final: 0.8190 (mtp) REVERT: A 33 LYS cc_start: 0.8113 (ttpt) cc_final: 0.7777 (ttmm) REVERT: A 184 MET cc_start: 0.8297 (mtp) cc_final: 0.7997 (mtt) REVERT: A 196 MET cc_start: 0.8960 (mmp) cc_final: 0.8642 (mmp) REVERT: A 216 LYS cc_start: 0.7326 (mtmm) cc_final: 0.6972 (pttp) REVERT: A 286 MET cc_start: 0.8395 (mmm) cc_final: 0.7862 (pmt) REVERT: A 543 MET cc_start: 0.8674 (mmt) cc_final: 0.8353 (mmt) REVERT: A 611 ASP cc_start: 0.7287 (m-30) cc_final: 0.7086 (m-30) REVERT: A 832 MET cc_start: 0.8608 (mtp) cc_final: 0.8387 (mtp) REVERT: A 841 ARG cc_start: 0.7777 (ttm170) cc_final: 0.7240 (mtp180) REVERT: A 869 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: A 879 LYS cc_start: 0.8709 (mmmm) cc_final: 0.8133 (mmtt) REVERT: A 981 LYS cc_start: 0.8549 (mtpp) cc_final: 0.8142 (mptm) REVERT: B 11 LYS cc_start: 0.8465 (tttt) cc_final: 0.8074 (tttm) REVERT: B 58 ASP cc_start: 0.8142 (m-30) cc_final: 0.7444 (m-30) REVERT: C 8 ARG cc_start: 0.8081 (mtt-85) cc_final: 0.7828 (ttp-170) REVERT: C 136 LEU cc_start: 0.8303 (mm) cc_final: 0.7950 (tp) REVERT: C 143 ARG cc_start: 0.8404 (ttp80) cc_final: 0.8137 (mtm110) REVERT: C 144 LYS cc_start: 0.8427 (ttmt) cc_final: 0.8111 (ttmt) outliers start: 18 outliers final: 7 residues processed: 132 average time/residue: 1.4153 time to fit residues: 200.0483 Evaluate side-chains 113 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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: 0.7644 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10344 Z= 0.324 Angle : 0.499 6.574 14009 Z= 0.260 Chirality : 0.044 0.164 1568 Planarity : 0.004 0.047 1812 Dihedral : 6.211 85.223 1412 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.30 % Allowed : 9.03 % Favored : 88.67 % 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: 1.52 (0.24), residues: 1273 helix: 1.66 (0.24), residues: 511 sheet: 0.98 (0.34), residues: 209 loop : 0.54 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS C 75 PHE 0.012 0.001 PHE A 237 TYR 0.009 0.001 TYR A 81 ARG 0.011 0.001 ARG A 645 *********************** 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 134 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7619 (tp30) cc_final: 0.7071 (tp30) REVERT: A 32 MET cc_start: 0.8462 (mtp) cc_final: 0.8231 (mtp) REVERT: A 33 LYS cc_start: 0.8195 (ttpt) cc_final: 0.7757 (ttmm) REVERT: A 184 MET cc_start: 0.8345 (mtp) cc_final: 0.8073 (mtt) REVERT: A 196 MET cc_start: 0.9001 (mmp) cc_final: 0.8733 (mmp) REVERT: A 216 LYS cc_start: 0.7371 (mtmm) cc_final: 0.7054 (pttp) REVERT: A 286 MET cc_start: 0.8388 (mmm) cc_final: 0.7830 (pmt) REVERT: A 611 ASP cc_start: 0.7324 (m-30) cc_final: 0.7059 (m-30) REVERT: A 869 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: A 879 LYS cc_start: 0.8733 (mmmm) cc_final: 0.8192 (mmtt) REVERT: A 980 LYS cc_start: 0.7970 (ptmt) cc_final: 0.7394 (ptpt) REVERT: A 981 LYS cc_start: 0.8554 (mtpp) cc_final: 0.8162 (mptm) REVERT: A 1011 LYS cc_start: 0.8774 (ttmm) cc_final: 0.8455 (ttmm) REVERT: B 11 LYS cc_start: 0.8391 (tttt) cc_final: 0.8078 (tttm) REVERT: B 58 ASP cc_start: 0.8213 (m-30) cc_final: 0.7536 (m-30) REVERT: B 71 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8979 (pp) REVERT: C 8 ARG cc_start: 0.8125 (mtt-85) cc_final: 0.7876 (ttp-170) REVERT: C 136 LEU cc_start: 0.8266 (mm) cc_final: 0.7894 (tp) REVERT: C 143 ARG cc_start: 0.8279 (ttp80) cc_final: 0.7976 (mtm110) outliers start: 26 outliers final: 14 residues processed: 127 average time/residue: 1.5197 time to fit residues: 206.5474 Evaluate side-chains 117 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 121 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 109 optimal weight: 0.0770 chunk 32 optimal weight: 0.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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: 0.7631 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10344 Z= 0.228 Angle : 0.465 6.024 14009 Z= 0.243 Chirality : 0.042 0.160 1568 Planarity : 0.004 0.051 1812 Dihedral : 6.144 85.578 1412 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.48 % Allowed : 9.29 % 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: 1.53 (0.24), residues: 1273 helix: 1.65 (0.24), residues: 511 sheet: 1.00 (0.35), residues: 203 loop : 0.57 (0.28), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS C 75 PHE 0.011 0.001 PHE A 237 TYR 0.007 0.001 TYR A 736 ARG 0.009 0.000 ARG A 645 *********************** 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 135 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7623 (tp30) cc_final: 0.7071 (tp30) REVERT: A 32 MET cc_start: 0.8385 (mtp) cc_final: 0.8096 (mtp) REVERT: A 33 LYS cc_start: 0.8208 (ttpt) cc_final: 0.7745 (ttmm) REVERT: A 184 MET cc_start: 0.8375 (mtp) cc_final: 0.8111 (mtt) REVERT: A 196 MET cc_start: 0.8975 (mmp) cc_final: 0.8685 (mmp) REVERT: A 216 LYS cc_start: 0.7362 (mtmm) cc_final: 0.7035 (pttp) REVERT: A 250 TYR cc_start: 0.7822 (m-10) cc_final: 0.7582 (m-10) REVERT: A 286 MET cc_start: 0.8339 (mmm) cc_final: 0.7790 (pmt) REVERT: A 611 ASP cc_start: 0.7307 (m-30) cc_final: 0.7054 (m-30) REVERT: A 869 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7730 (mp0) REVERT: A 879 LYS cc_start: 0.8712 (mmmm) cc_final: 0.8164 (mmtt) REVERT: A 980 LYS cc_start: 0.7993 (ptmt) cc_final: 0.7429 (ptpt) REVERT: B 11 LYS cc_start: 0.8420 (tttt) cc_final: 0.8123 (tttm) REVERT: B 58 ASP cc_start: 0.8228 (m-30) cc_final: 0.7500 (m-30) REVERT: B 71 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8991 (pp) REVERT: C 8 ARG cc_start: 0.8193 (mtt-85) cc_final: 0.7932 (ttp-170) REVERT: C 135 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7216 (mp0) REVERT: C 136 LEU cc_start: 0.8252 (mm) cc_final: 0.7886 (tp) REVERT: C 143 ARG cc_start: 0.8260 (ttp80) cc_final: 0.7990 (mtm110) REVERT: C 144 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8104 (ttmt) REVERT: D 1 MET cc_start: 0.4561 (OUTLIER) cc_final: 0.4277 (mtm) outliers start: 28 outliers final: 14 residues processed: 123 average time/residue: 1.4606 time to fit residues: 192.7266 Evaluate side-chains 130 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain D residue 1 MET 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: 0.9980 chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 103 optimal weight: 0.1980 chunk 84 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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: 0.7651 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10344 Z= 0.331 Angle : 0.511 8.788 14009 Z= 0.264 Chirality : 0.045 0.357 1568 Planarity : 0.004 0.050 1812 Dihedral : 6.173 84.328 1411 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.48 % Allowed : 10.00 % Favored : 87.52 % 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: 1.41 (0.24), residues: 1273 helix: 1.56 (0.24), residues: 510 sheet: 0.89 (0.34), residues: 219 loop : 0.51 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 669 HIS 0.003 0.001 HIS C 75 PHE 0.013 0.001 PHE A 237 TYR 0.010 0.001 TYR A 544 ARG 0.006 0.000 ARG C 5 *********************** 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 140 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7655 (tp30) cc_final: 0.7138 (tp30) REVERT: A 32 MET cc_start: 0.8411 (mtp) cc_final: 0.8165 (mtp) REVERT: A 33 LYS cc_start: 0.8211 (ttpt) cc_final: 0.7747 (ttmm) REVERT: A 184 MET cc_start: 0.8399 (mtp) cc_final: 0.8160 (mtt) REVERT: A 196 MET cc_start: 0.8975 (mmp) cc_final: 0.8688 (mmp) REVERT: A 216 LYS cc_start: 0.7392 (mtmm) cc_final: 0.7057 (pttp) REVERT: A 286 MET cc_start: 0.8394 (mmm) cc_final: 0.7835 (pmt) REVERT: A 543 MET cc_start: 0.8788 (mmt) cc_final: 0.8559 (mmt) REVERT: A 611 ASP cc_start: 0.7334 (m-30) cc_final: 0.7134 (m-30) REVERT: A 869 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7730 (mp0) REVERT: A 879 LYS cc_start: 0.8725 (mmmm) cc_final: 0.8181 (mmtt) REVERT: A 919 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8468 (pmm-80) REVERT: A 980 LYS cc_start: 0.8056 (ptmt) cc_final: 0.7469 (ptpt) REVERT: A 981 LYS cc_start: 0.8541 (mtpp) cc_final: 0.8219 (mptm) REVERT: B 11 LYS cc_start: 0.8379 (tttt) cc_final: 0.8133 (tttm) REVERT: B 58 ASP cc_start: 0.8261 (m-30) cc_final: 0.7558 (m-30) REVERT: B 71 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8994 (pp) REVERT: C 8 ARG cc_start: 0.8217 (mtt-85) cc_final: 0.7894 (ttp80) REVERT: C 136 LEU cc_start: 0.8235 (mm) cc_final: 0.7882 (tp) REVERT: C 143 ARG cc_start: 0.8253 (ttp80) cc_final: 0.7973 (mtm110) REVERT: D 1 MET cc_start: 0.4598 (OUTLIER) cc_final: 0.4317 (mtm) outliers start: 28 outliers final: 13 residues processed: 131 average time/residue: 1.3709 time to fit residues: 192.6743 Evaluate side-chains 129 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain D residue 1 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.2980 chunk 109 optimal weight: 0.0010 chunk 24 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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: 0.7629 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10344 Z= 0.199 Angle : 0.470 8.246 14009 Z= 0.245 Chirality : 0.042 0.191 1568 Planarity : 0.004 0.050 1812 Dihedral : 6.028 81.413 1411 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.30 % Allowed : 10.71 % Favored : 86.99 % 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: 1.51 (0.24), residues: 1273 helix: 1.66 (0.24), residues: 509 sheet: 0.89 (0.34), residues: 217 loop : 0.57 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS C 75 PHE 0.010 0.001 PHE A 237 TYR 0.007 0.001 TYR C 74 ARG 0.005 0.000 ARG A 645 *********************** 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 135 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7691 (tp30) cc_final: 0.7155 (tp30) REVERT: A 32 MET cc_start: 0.8377 (mtp) cc_final: 0.8148 (mtp) REVERT: A 33 LYS cc_start: 0.8200 (ttpt) cc_final: 0.7745 (ttmm) REVERT: A 184 MET cc_start: 0.8326 (mtp) cc_final: 0.8045 (mtt) REVERT: A 216 LYS cc_start: 0.7414 (mtmm) cc_final: 0.7084 (pttp) REVERT: A 286 MET cc_start: 0.8310 (mmm) cc_final: 0.7782 (pmt) REVERT: A 543 MET cc_start: 0.8731 (mmt) cc_final: 0.8493 (mmt) REVERT: A 611 ASP cc_start: 0.7322 (m-30) cc_final: 0.7080 (m-30) REVERT: A 869 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: A 879 LYS cc_start: 0.8696 (mmmm) cc_final: 0.8139 (mmtt) REVERT: A 980 LYS cc_start: 0.8029 (ptmt) cc_final: 0.7447 (ptpt) REVERT: A 981 LYS cc_start: 0.8557 (mtpp) cc_final: 0.8204 (mptm) REVERT: B 58 ASP cc_start: 0.8248 (m-30) cc_final: 0.7531 (m-30) REVERT: B 71 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8985 (pp) REVERT: C 136 LEU cc_start: 0.8222 (mm) cc_final: 0.7875 (tp) REVERT: C 143 ARG cc_start: 0.8261 (ttp80) cc_final: 0.7972 (mtm110) outliers start: 26 outliers final: 14 residues processed: 124 average time/residue: 1.4141 time to fit residues: 187.7569 Evaluate side-chains 122 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 144 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 68 optimal weight: 0.0970 chunk 102 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 74 optimal weight: 0.0870 chunk 56 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.5156 ------------------------------------------------------------------------------- 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: 0.7627 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10344 Z= 0.195 Angle : 0.465 10.390 14009 Z= 0.241 Chirality : 0.043 0.281 1568 Planarity : 0.004 0.049 1812 Dihedral : 5.962 79.224 1411 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.95 % Allowed : 11.59 % Favored : 86.46 % 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: 1.53 (0.24), residues: 1273 helix: 1.68 (0.24), residues: 510 sheet: 0.91 (0.34), residues: 217 loop : 0.57 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS C 32 PHE 0.013 0.001 PHE A 237 TYR 0.007 0.001 TYR C 74 ARG 0.007 0.000 ARG C 5 *********************** 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 132 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7699 (tp30) cc_final: 0.7144 (tp30) REVERT: A 32 MET cc_start: 0.8385 (mtp) cc_final: 0.8116 (mtp) REVERT: A 33 LYS cc_start: 0.8210 (ttpt) cc_final: 0.7748 (ttmm) REVERT: A 184 MET cc_start: 0.8198 (mtp) cc_final: 0.7986 (mtt) REVERT: A 196 MET cc_start: 0.8794 (tpp) cc_final: 0.8562 (mmp) REVERT: A 216 LYS cc_start: 0.7437 (mtmm) cc_final: 0.7109 (pttp) REVERT: A 286 MET cc_start: 0.8306 (mmm) cc_final: 0.7789 (pmt) REVERT: A 611 ASP cc_start: 0.7319 (m-30) cc_final: 0.7100 (m-30) REVERT: A 869 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: A 879 LYS cc_start: 0.8694 (mmmm) cc_final: 0.8132 (mmtt) REVERT: A 980 LYS cc_start: 0.8059 (ptmt) cc_final: 0.7467 (ptpt) REVERT: A 981 LYS cc_start: 0.8563 (mtpp) cc_final: 0.8217 (mptm) REVERT: B 71 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8990 (pp) REVERT: C 136 LEU cc_start: 0.8230 (mm) cc_final: 0.7863 (tp) REVERT: C 143 ARG cc_start: 0.8277 (ttp80) cc_final: 0.7997 (mtm110) outliers start: 22 outliers final: 13 residues processed: 123 average time/residue: 1.4412 time to fit residues: 189.7863 Evaluate side-chains 120 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 144 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 82 optimal weight: 0.4980 chunk 60 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10344 Z= 0.270 Angle : 0.497 8.812 14009 Z= 0.258 Chirality : 0.043 0.174 1568 Planarity : 0.004 0.048 1812 Dihedral : 6.008 77.651 1411 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.95 % Allowed : 11.68 % Favored : 86.37 % 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: 1.42 (0.24), residues: 1273 helix: 1.56 (0.23), residues: 510 sheet: 0.86 (0.34), residues: 217 loop : 0.54 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 669 HIS 0.002 0.001 HIS C 75 PHE 0.013 0.001 PHE A 237 TYR 0.009 0.001 TYR A 544 ARG 0.011 0.001 ARG C 8 *********************** 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 127 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7740 (tp30) cc_final: 0.7163 (tp30) REVERT: A 32 MET cc_start: 0.8411 (mtp) cc_final: 0.8149 (mtp) REVERT: A 33 LYS cc_start: 0.8234 (ttpt) cc_final: 0.7755 (ttmm) REVERT: A 196 MET cc_start: 0.8830 (tpp) cc_final: 0.8542 (mmp) REVERT: A 216 LYS cc_start: 0.7456 (mtmm) cc_final: 0.7129 (pttp) REVERT: A 286 MET cc_start: 0.8335 (mmm) cc_final: 0.7801 (pmt) REVERT: A 543 MET cc_start: 0.8730 (mmt) cc_final: 0.8422 (mmp) REVERT: A 611 ASP cc_start: 0.7330 (m-30) cc_final: 0.7074 (m-30) REVERT: A 869 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: A 879 LYS cc_start: 0.8714 (mmmm) cc_final: 0.8164 (mmtt) REVERT: A 980 LYS cc_start: 0.8124 (ptmt) cc_final: 0.7516 (ptpt) REVERT: A 981 LYS cc_start: 0.8563 (mtpp) cc_final: 0.8204 (mptm) REVERT: B 71 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8994 (pp) REVERT: C 136 LEU cc_start: 0.8221 (mm) cc_final: 0.7869 (tp) REVERT: C 143 ARG cc_start: 0.8233 (ttp80) cc_final: 0.7943 (mtm110) outliers start: 22 outliers final: 14 residues processed: 120 average time/residue: 1.4968 time to fit residues: 192.8650 Evaluate side-chains 111 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 144 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.9980 chunk 116 optimal weight: 0.0670 chunk 68 optimal weight: 0.2980 chunk 49 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 74 optimal weight: 0.0010 chunk 119 optimal weight: 2.9990 overall best weight: 0.3924 ------------------------------------------------------------------------------- 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: 0.7620 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10344 Z= 0.166 Angle : 0.466 11.564 14009 Z= 0.241 Chirality : 0.042 0.293 1568 Planarity : 0.004 0.065 1812 Dihedral : 5.929 76.259 1411 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.50 % Allowed : 12.30 % Favored : 86.19 % 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: 1.55 (0.24), residues: 1273 helix: 1.65 (0.24), residues: 509 sheet: 0.99 (0.34), residues: 222 loop : 0.60 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.000 HIS C 32 PHE 0.013 0.001 PHE C 62 TYR 0.007 0.001 TYR C 74 ARG 0.009 0.000 ARG A 645 *********************** 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 112 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7694 (tp30) cc_final: 0.7152 (tp30) REVERT: A 32 MET cc_start: 0.8372 (mtp) cc_final: 0.8098 (mtp) REVERT: A 33 LYS cc_start: 0.8193 (ttpt) cc_final: 0.7719 (ttmm) REVERT: A 193 VAL cc_start: 0.8645 (t) cc_final: 0.8281 (p) REVERT: A 196 MET cc_start: 0.8796 (tpp) cc_final: 0.8528 (mmp) REVERT: A 216 LYS cc_start: 0.7409 (mtmm) cc_final: 0.7110 (pttp) REVERT: A 286 MET cc_start: 0.8283 (mmm) cc_final: 0.7769 (pmt) REVERT: A 543 MET cc_start: 0.8723 (mmt) cc_final: 0.8385 (mmp) REVERT: A 611 ASP cc_start: 0.7315 (m-30) cc_final: 0.7057 (m-30) REVERT: A 869 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: A 879 LYS cc_start: 0.8692 (mmmm) cc_final: 0.8116 (mmtt) REVERT: A 980 LYS cc_start: 0.8085 (ptmt) cc_final: 0.7499 (ptpt) REVERT: A 981 LYS cc_start: 0.8555 (mtpp) cc_final: 0.8199 (mptm) REVERT: B 71 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8992 (pp) REVERT: C 136 LEU cc_start: 0.8219 (mm) cc_final: 0.7873 (tp) REVERT: C 143 ARG cc_start: 0.8270 (ttp80) cc_final: 0.7987 (mtm110) outliers start: 17 outliers final: 11 residues processed: 106 average time/residue: 1.4407 time to fit residues: 163.8486 Evaluate side-chains 115 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 656 VAL 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 B residue 21 ASP Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 144 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.0770 chunk 56 optimal weight: 0.1980 chunk 83 optimal weight: 0.9980 chunk 125 optimal weight: 10.0000 chunk 115 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 10 optimal weight: 0.0270 chunk 77 optimal weight: 4.9990 chunk 61 optimal weight: 0.4980 chunk 79 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 overall best weight: 0.3196 ------------------------------------------------------------------------------- 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: 0.7608 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10344 Z= 0.151 Angle : 0.480 11.374 14009 Z= 0.247 Chirality : 0.042 0.221 1568 Planarity : 0.004 0.057 1812 Dihedral : 5.631 72.583 1410 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.24 % Allowed : 12.57 % Favored : 86.19 % 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: 1.58 (0.24), residues: 1273 helix: 1.65 (0.24), residues: 513 sheet: 1.02 (0.34), residues: 223 loop : 0.62 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS C 32 PHE 0.011 0.001 PHE C 62 TYR 0.007 0.001 TYR C 74 ARG 0.009 0.000 ARG C 8 ********************** 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 121 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7713 (tp30) cc_final: 0.7113 (tp30) REVERT: A 32 MET cc_start: 0.8365 (mtp) cc_final: 0.8109 (mtp) REVERT: A 33 LYS cc_start: 0.8018 (ttpt) cc_final: 0.7538 (ttmm) REVERT: A 193 VAL cc_start: 0.8608 (t) cc_final: 0.8235 (p) REVERT: A 196 MET cc_start: 0.8785 (tpp) cc_final: 0.8519 (mmp) REVERT: A 216 LYS cc_start: 0.7423 (mtmm) cc_final: 0.7126 (pttp) REVERT: A 286 MET cc_start: 0.8273 (mmm) cc_final: 0.7797 (pmt) REVERT: A 543 MET cc_start: 0.8694 (mmt) cc_final: 0.8372 (mmp) REVERT: A 611 ASP cc_start: 0.7305 (m-30) cc_final: 0.7044 (m-30) REVERT: A 869 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7680 (mp0) REVERT: A 879 LYS cc_start: 0.8692 (mmmm) cc_final: 0.8111 (mmtt) REVERT: A 980 LYS cc_start: 0.8093 (ptmt) cc_final: 0.7516 (ptpt) REVERT: A 981 LYS cc_start: 0.8558 (mtpp) cc_final: 0.8208 (mptm) REVERT: B 11 LYS cc_start: 0.8387 (tttt) cc_final: 0.8120 (tttm) REVERT: B 71 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8970 (pp) REVERT: C 130 ASP cc_start: 0.8200 (t0) cc_final: 0.7786 (t0) REVERT: C 136 LEU cc_start: 0.8246 (mm) cc_final: 0.7887 (tp) REVERT: C 143 ARG cc_start: 0.8282 (ttp80) cc_final: 0.7998 (mtm110) outliers start: 14 outliers final: 10 residues processed: 117 average time/residue: 1.4052 time to fit residues: 176.4780 Evaluate side-chains 110 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 656 VAL 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 B residue 71 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 144 LYS 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: 0.5980 chunk 27 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.140244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.097017 restraints weight = 12084.020| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.63 r_work: 0.2857 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10344 Z= 0.216 Angle : 0.493 10.767 14009 Z= 0.255 Chirality : 0.043 0.221 1568 Planarity : 0.004 0.061 1812 Dihedral : 5.714 73.465 1410 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.15 % Allowed : 12.74 % Favored : 86.11 % 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: 1.50 (0.24), residues: 1273 helix: 1.57 (0.23), residues: 513 sheet: 0.99 (0.34), residues: 223 loop : 0.59 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 669 HIS 0.002 0.001 HIS C 75 PHE 0.011 0.001 PHE A 237 TYR 0.008 0.001 TYR A 544 ARG 0.010 0.000 ARG C 8 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 3991.05 seconds wall clock time: 71 minutes 46.76 seconds (4306.76 seconds total)