Starting phenix.real_space_refine on Fri Nov 15 20:43:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5f_44210/11_2024/9b5f_44210.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5f_44210/11_2024/9b5f_44210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5f_44210/11_2024/9b5f_44210.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5f_44210/11_2024/9b5f_44210.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5f_44210/11_2024/9b5f_44210.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5f_44210/11_2024/9b5f_44210.cif" } resolution = 2.78 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= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 2 5.21 5 S 42 5.16 5 C 6078 2.51 5 N 1575 2.21 5 O 1836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 9536 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'A1AIV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.64, per 1000 atoms: 0.70 Number of scatterers: 9536 At special positions: 0 Unit cell: (87.248, 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 42 16.00 P 3 15.00 Mg 2 11.99 O 1836 8.00 N 1575 7.00 C 6078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS C 85 " distance=2.90 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.1 seconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 10 sheets defined 47.5% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.782A 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: 3.672A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.933A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.369A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LYS A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 123 Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.734A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYS A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.181A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 304 removed outlier: 3.663A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.562A 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: 4.524A 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: 3.557A pdb=" N ASN A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 474 " --> pdb=" O ASN A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'A' and resid 486 through 499 Processing helix chain 'A' and resid 500 through 503 Processing helix chain 'A' and resid 514 through 518 removed outlier: 4.041A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 528 removed outlier: 3.953A pdb=" N LYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.616A pdb=" N ARG A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.517A pdb=" N SER A 581 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.850A 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 630 Processing helix chain 'A' and resid 632 through 641 removed outlier: 3.876A 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: 3.779A 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: 3.952A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 3.858A 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: 3.732A pdb=" N THR A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.688A pdb=" N GLU A 882 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.670A 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 removed outlier: 3.672A pdb=" N ASP C 16 " --> pdb=" O ASP C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.507A pdb=" N LEU C 89 " --> pdb=" O LEU C 86 " (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 sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.714A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N THR A 129 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ILE A 43 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.312A 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: 4.025A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.249A 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: 4.025A 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: 6.572A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.180A 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: 6.426A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N VAL A 990 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N SER A 947 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLU A 992 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU A 945 " --> pdb=" O GLU A 992 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N CYS A 994 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 6.837A 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: 6.426A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.376A 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: 3.862A 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: 6.229A pdb=" N HIS C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1275 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: 3.86 Time building geometry restraints manager: 2.95 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: 1619 1.27 - 1.40: 2292 1.40 - 1.54: 5646 1.54 - 1.67: 125 1.67 - 1.81: 64 Bond restraints: 9746 Sorted by residual: bond pdb=" C04 A1AIV D 201 " pdb=" C05 A1AIV D 201 " 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 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 2.65e+00 bond pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " ideal model delta sigma weight residual 1.531 1.518 0.013 1.20e-02 6.94e+03 1.13e+00 bond pdb=" C05 A1AIV D 201 " pdb=" N06 A1AIV D 201 " ideal model delta sigma weight residual 1.151 1.131 0.020 2.00e-02 2.50e+03 9.78e-01 bond pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 1.416 1.407 0.009 1.30e-02 5.92e+03 4.79e-01 ... (remaining 9741 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 13022 1.40 - 2.79: 103 2.79 - 4.19: 71 4.19 - 5.59: 4 5.59 - 6.99: 4 Bond angle restraints: 13204 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 121.70 128.58 -6.88 1.80e+00 3.09e-01 1.46e+01 angle pdb=" N ILE A 239 " pdb=" CA ILE A 239 " pdb=" C ILE A 239 " ideal model delta sigma weight residual 113.47 110.38 3.09 1.01e+00 9.80e-01 9.38e+00 angle pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 106.53 103.20 3.33 1.18e+00 7.24e-01 8.02e+00 angle pdb=" C3' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" C5' ATP A1103 " ideal model delta sigma weight residual 115.19 110.55 4.64 1.76e+00 3.23e-01 6.95e+00 angle pdb=" C2' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O3' ATP A1103 " ideal model delta sigma weight residual 111.83 104.84 6.99 2.67e+00 1.40e-01 6.85e+00 ... (remaining 13199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 5640 16.14 - 32.27: 221 32.27 - 48.41: 52 48.41 - 64.54: 15 64.54 - 80.68: 3 Dihedral angle restraints: 5931 sinusoidal: 2425 harmonic: 3506 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 -135.47 49.47 1 1.00e+01 1.00e-02 3.36e+01 dihedral pdb=" N GLN A 80 " pdb=" CA GLN A 80 " pdb=" CB GLN A 80 " pdb=" CG GLN A 80 " ideal model delta sinusoidal sigma weight residual -60.00 -118.52 58.52 3 1.50e+01 4.44e-03 9.47e+00 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 -122.28 -57.72 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 5928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1286 0.057 - 0.115: 153 0.115 - 0.172: 29 0.172 - 0.230: 0 0.230 - 0.287: 3 Chirality restraints: 1471 Sorted by residual: 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=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O2' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.68 -2.96 0.28 2.00e-01 2.50e+01 2.01e+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 1.37e+00 ... (remaining 1468 not shown) Planarity restraints: 1709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 288 " 0.019 5.00e-02 4.00e+02 2.81e-02 1.26e+00 pdb=" N PRO A 289 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 289 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 289 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 107 " 0.017 5.00e-02 4.00e+02 2.50e-02 9.99e-01 pdb=" N PRO A 108 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 108 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 108 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 75 " -0.016 5.00e-02 4.00e+02 2.42e-02 9.40e-01 pdb=" N PRO C 76 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO C 76 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 76 " -0.014 5.00e-02 4.00e+02 ... (remaining 1706 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 67 2.60 - 3.18: 8126 3.18 - 3.75: 13977 3.75 - 4.33: 20919 4.33 - 4.90: 35359 Nonbonded interactions: 78448 Sorted by model distance: nonbonded pdb=" OD2 ASP A 465 " pdb="MG MG A1102 " model vdw 2.027 2.170 nonbonded pdb="MG MG A1101 " pdb=" O2B ATP A1103 " model vdw 2.046 2.170 nonbonded pdb="MG MG A1101 " pdb=" O2A ATP A1103 " model vdw 2.082 2.170 nonbonded pdb=" OD2 ASP A 537 " pdb="MG MG A1101 " model vdw 2.106 2.170 nonbonded pdb=" O PRO C 18 " pdb=" OG SER C 19 " model vdw 2.127 3.040 ... (remaining 78443 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.480 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.180 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 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 9746 Z= 0.249 Angle : 0.474 6.986 13204 Z= 0.245 Chirality : 0.043 0.287 1471 Planarity : 0.003 0.033 1709 Dihedral : 9.870 80.677 3664 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.94 % Allowed : 2.73 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.25), residues: 1200 helix: 1.99 (0.25), residues: 482 sheet: 0.99 (0.35), residues: 183 loop : 0.13 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 608 HIS 0.003 0.001 HIS C 75 PHE 0.011 0.001 PHE A 360 TYR 0.009 0.001 TYR A 20 ARG 0.003 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8387 (t) cc_final: 0.8029 (p) REVERT: A 114 GLU cc_start: 0.7628 (tt0) cc_final: 0.7358 (tm-30) REVERT: A 190 ASP cc_start: 0.7434 (t0) cc_final: 0.7146 (t0) REVERT: A 196 MET cc_start: 0.8568 (mmp) cc_final: 0.8342 (mmm) REVERT: A 214 GLU cc_start: 0.7687 (mt-10) cc_final: 0.6883 (tt0) REVERT: A 216 LYS cc_start: 0.6259 (mtmm) cc_final: 0.5839 (pttp) REVERT: A 218 MET cc_start: 0.7748 (mtt) cc_final: 0.7496 (mtt) REVERT: A 286 MET cc_start: 0.7625 (mmm) cc_final: 0.6608 (pmt) REVERT: A 306 GLU cc_start: 0.8286 (mp0) cc_final: 0.7803 (mp0) REVERT: A 387 ASP cc_start: 0.8676 (p0) cc_final: 0.8462 (p0) REVERT: A 397 THR cc_start: 0.8241 (m) cc_final: 0.7934 (t) REVERT: A 524 GLU cc_start: 0.7530 (mp0) cc_final: 0.7235 (mp0) REVERT: A 583 GLN cc_start: 0.7813 (mt0) cc_final: 0.7094 (mp10) REVERT: A 878 LYS cc_start: 0.8261 (mmtp) cc_final: 0.8037 (mmtp) REVERT: A 879 LYS cc_start: 0.7917 (mttm) cc_final: 0.7486 (mttm) REVERT: A 919 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7927 (pmm-80) REVERT: A 1004 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7791 (mt-10) REVERT: A 1011 LYS cc_start: 0.7948 (ttmm) cc_final: 0.7682 (ttmt) outliers start: 10 outliers final: 4 residues processed: 144 average time/residue: 1.5228 time to fit residues: 233.1798 Evaluate side-chains 121 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 97 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 93 optimal weight: 0.0070 chunk 36 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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: 0.7482 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9746 Z= 0.238 Angle : 0.499 6.580 13204 Z= 0.261 Chirality : 0.043 0.152 1471 Planarity : 0.004 0.041 1709 Dihedral : 6.412 85.689 1336 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.89 % Allowed : 6.88 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.24), residues: 1200 helix: 1.82 (0.24), residues: 490 sheet: 1.11 (0.35), residues: 187 loop : 0.19 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 608 HIS 0.003 0.001 HIS C 75 PHE 0.012 0.001 PHE A 360 TYR 0.009 0.001 TYR C 74 ARG 0.007 0.000 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 1.020 Fit side-chains REVERT: A 110 SER cc_start: 0.8533 (t) cc_final: 0.8132 (p) REVERT: A 114 GLU cc_start: 0.7646 (tt0) cc_final: 0.7376 (tm-30) REVERT: A 184 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7973 (mtm) REVERT: A 190 ASP cc_start: 0.7402 (t0) cc_final: 0.7195 (t0) REVERT: A 214 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7009 (tt0) REVERT: A 216 LYS cc_start: 0.6448 (mtmm) cc_final: 0.6006 (pttp) REVERT: A 286 MET cc_start: 0.7690 (mmm) cc_final: 0.6670 (pmt) REVERT: A 306 GLU cc_start: 0.8333 (mp0) cc_final: 0.7856 (mp0) REVERT: A 397 THR cc_start: 0.8269 (m) cc_final: 0.7975 (t) REVERT: A 524 GLU cc_start: 0.7704 (mp0) cc_final: 0.7328 (mp0) REVERT: A 583 GLN cc_start: 0.7877 (mt0) cc_final: 0.7041 (mp10) REVERT: A 601 ARG cc_start: 0.7053 (mtp180) cc_final: 0.6476 (mtm-85) REVERT: A 652 ARG cc_start: 0.7365 (tmm-80) cc_final: 0.7138 (ttp80) REVERT: A 878 LYS cc_start: 0.8293 (mmtp) cc_final: 0.8077 (mmtp) REVERT: A 879 LYS cc_start: 0.7903 (mttm) cc_final: 0.7473 (mttm) REVERT: A 1004 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7735 (mt-10) REVERT: A 1011 LYS cc_start: 0.7967 (ttmm) cc_final: 0.7649 (ttmt) REVERT: B 31 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8191 (tt0) outliers start: 20 outliers final: 9 residues processed: 122 average time/residue: 1.5039 time to fit residues: 195.0642 Evaluate side-chains 121 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 108 optimal weight: 0.0060 chunk 116 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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: 0.7475 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9746 Z= 0.201 Angle : 0.474 6.160 13204 Z= 0.247 Chirality : 0.042 0.159 1471 Planarity : 0.004 0.044 1709 Dihedral : 6.224 82.752 1332 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.98 % Allowed : 7.16 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.24), residues: 1200 helix: 1.75 (0.24), residues: 491 sheet: 1.11 (0.36), residues: 186 loop : 0.22 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 608 HIS 0.002 0.001 HIS C 75 PHE 0.012 0.001 PHE A 360 TYR 0.008 0.001 TYR C 74 ARG 0.007 0.000 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 1.146 Fit side-chains REVERT: A 110 SER cc_start: 0.8463 (t) cc_final: 0.8042 (p) REVERT: A 114 GLU cc_start: 0.7633 (tt0) cc_final: 0.7360 (tm-30) REVERT: A 214 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7017 (tt0) REVERT: A 216 LYS cc_start: 0.6304 (mtmm) cc_final: 0.5882 (pttp) REVERT: A 274 ASP cc_start: 0.8014 (p0) cc_final: 0.7803 (p0) REVERT: A 286 MET cc_start: 0.7655 (mmm) cc_final: 0.6688 (pmt) REVERT: A 306 GLU cc_start: 0.8337 (mp0) cc_final: 0.7923 (mp0) REVERT: A 353 ASP cc_start: 0.8370 (t70) cc_final: 0.7869 (t0) REVERT: A 397 THR cc_start: 0.8272 (m) cc_final: 0.7984 (t) REVERT: A 524 GLU cc_start: 0.7738 (mp0) cc_final: 0.7332 (mp0) REVERT: A 583 GLN cc_start: 0.7876 (mt0) cc_final: 0.7037 (mp10) REVERT: A 601 ARG cc_start: 0.7085 (mtp180) cc_final: 0.6535 (mtm-85) REVERT: A 652 ARG cc_start: 0.7373 (tmm-80) cc_final: 0.7136 (ttp80) REVERT: A 878 LYS cc_start: 0.8283 (mmtp) cc_final: 0.8066 (mmtp) REVERT: A 879 LYS cc_start: 0.7917 (mttm) cc_final: 0.7485 (mttm) REVERT: A 1004 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7759 (mt-10) REVERT: A 1011 LYS cc_start: 0.7983 (ttmm) cc_final: 0.7654 (ttmt) REVERT: B 31 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8332 (tt0) REVERT: C 5 ARG cc_start: 0.6869 (ttt90) cc_final: 0.6502 (ttt-90) outliers start: 21 outliers final: 12 residues processed: 124 average time/residue: 1.4725 time to fit residues: 194.4627 Evaluate side-chains 125 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 992 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 4.9990 chunk 81 optimal weight: 0.0470 chunk 56 optimal weight: 0.0470 chunk 11 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 95 optimal weight: 0.0970 overall best weight: 0.3574 ------------------------------------------------------------------------------- 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: 0.7463 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9746 Z= 0.158 Angle : 0.456 6.063 13204 Z= 0.238 Chirality : 0.041 0.156 1471 Planarity : 0.004 0.045 1709 Dihedral : 6.176 88.451 1332 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.51 % Allowed : 8.11 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.24), residues: 1200 helix: 1.82 (0.24), residues: 491 sheet: 1.16 (0.36), residues: 186 loop : 0.25 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 669 HIS 0.002 0.000 HIS C 75 PHE 0.011 0.001 PHE A 360 TYR 0.008 0.001 TYR C 74 ARG 0.008 0.000 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8307 (t) cc_final: 0.7883 (p) REVERT: A 114 GLU cc_start: 0.7627 (tt0) cc_final: 0.7357 (tm-30) REVERT: A 214 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7124 (tt0) REVERT: A 216 LYS cc_start: 0.6191 (mtmm) cc_final: 0.5812 (pttp) REVERT: A 218 MET cc_start: 0.7633 (mtp) cc_final: 0.7419 (mtp) REVERT: A 286 MET cc_start: 0.7750 (mmm) cc_final: 0.6787 (pmt) REVERT: A 306 GLU cc_start: 0.8337 (mp0) cc_final: 0.7930 (mp0) REVERT: A 387 ASP cc_start: 0.8679 (p0) cc_final: 0.8420 (p0) REVERT: A 397 THR cc_start: 0.8278 (m) cc_final: 0.8017 (t) REVERT: A 524 GLU cc_start: 0.7736 (mp0) cc_final: 0.7344 (mp0) REVERT: A 583 GLN cc_start: 0.7811 (mt0) cc_final: 0.6987 (mp10) REVERT: A 601 ARG cc_start: 0.7046 (mtp180) cc_final: 0.6561 (mtm-85) REVERT: A 652 ARG cc_start: 0.7198 (tmm-80) cc_final: 0.6997 (ttp80) REVERT: A 878 LYS cc_start: 0.8285 (mmtp) cc_final: 0.8072 (mmtp) REVERT: A 879 LYS cc_start: 0.7901 (mttm) cc_final: 0.7444 (mttm) REVERT: A 1004 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7749 (mt-10) REVERT: A 1011 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7643 (ttmt) REVERT: B 34 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8169 (mm-30) REVERT: C 5 ARG cc_start: 0.6905 (ttt90) cc_final: 0.6653 (ttt-90) outliers start: 16 outliers final: 11 residues processed: 123 average time/residue: 1.4862 time to fit residues: 194.4598 Evaluate side-chains 120 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 992 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 79 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 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: 0.7477 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9746 Z= 0.229 Angle : 0.479 5.935 13204 Z= 0.250 Chirality : 0.042 0.141 1471 Planarity : 0.004 0.045 1709 Dihedral : 6.253 87.857 1332 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.70 % Allowed : 8.58 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.24), residues: 1200 helix: 1.76 (0.24), residues: 491 sheet: 1.15 (0.36), residues: 186 loop : 0.24 (0.28), residues: 523 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 0.012 0.001 PHE A 360 TYR 0.008 0.001 TYR A 20 ARG 0.009 0.000 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8427 (t) cc_final: 0.7994 (p) REVERT: A 114 GLU cc_start: 0.7630 (tt0) cc_final: 0.7355 (tm-30) REVERT: A 214 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7124 (tt0) REVERT: A 216 LYS cc_start: 0.6042 (mtmm) cc_final: 0.5608 (pttp) REVERT: A 286 MET cc_start: 0.7725 (mmm) cc_final: 0.6797 (pmt) REVERT: A 306 GLU cc_start: 0.8340 (mp0) cc_final: 0.7928 (mp0) REVERT: A 353 ASP cc_start: 0.8445 (t70) cc_final: 0.8044 (t0) REVERT: A 387 ASP cc_start: 0.8777 (p0) cc_final: 0.8509 (p0) REVERT: A 397 THR cc_start: 0.8284 (m) cc_final: 0.8014 (t) REVERT: A 524 GLU cc_start: 0.7739 (mp0) cc_final: 0.7417 (mp0) REVERT: A 583 GLN cc_start: 0.7826 (mt0) cc_final: 0.6993 (mp10) REVERT: A 601 ARG cc_start: 0.7111 (mtp180) cc_final: 0.6620 (mtm-85) REVERT: A 657 THR cc_start: 0.8309 (m) cc_final: 0.8021 (m) REVERT: A 878 LYS cc_start: 0.8292 (mmtp) cc_final: 0.8071 (mmtp) REVERT: A 879 LYS cc_start: 0.7928 (mttm) cc_final: 0.7465 (mttm) REVERT: A 1004 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7766 (mt-10) REVERT: A 1011 LYS cc_start: 0.7992 (ttmm) cc_final: 0.7658 (ttmt) REVERT: B 34 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8004 (mm-30) REVERT: C 5 ARG cc_start: 0.6925 (ttt90) cc_final: 0.6719 (ttt-90) outliers start: 18 outliers final: 16 residues processed: 121 average time/residue: 1.4908 time to fit residues: 191.7550 Evaluate side-chains 123 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 992 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7482 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9746 Z= 0.249 Angle : 0.489 5.958 13204 Z= 0.254 Chirality : 0.043 0.186 1471 Planarity : 0.004 0.046 1709 Dihedral : 6.281 86.890 1332 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.79 % Allowed : 9.24 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.24), residues: 1200 helix: 1.75 (0.24), residues: 491 sheet: 1.13 (0.36), residues: 186 loop : 0.24 (0.28), residues: 523 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 360 TYR 0.008 0.001 TYR A 20 ARG 0.011 0.001 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8432 (t) cc_final: 0.7989 (p) REVERT: A 114 GLU cc_start: 0.7634 (tt0) cc_final: 0.7357 (tm-30) REVERT: A 214 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7126 (tt0) REVERT: A 216 LYS cc_start: 0.6034 (mtmm) cc_final: 0.5594 (pttp) REVERT: A 218 MET cc_start: 0.7651 (mtp) cc_final: 0.7398 (mtp) REVERT: A 274 ASP cc_start: 0.8160 (p0) cc_final: 0.7870 (p0) REVERT: A 286 MET cc_start: 0.7628 (mmm) cc_final: 0.6671 (pmt) REVERT: A 306 GLU cc_start: 0.8338 (mp0) cc_final: 0.7922 (mp0) REVERT: A 387 ASP cc_start: 0.8796 (p0) cc_final: 0.8519 (p0) REVERT: A 397 THR cc_start: 0.8283 (m) cc_final: 0.8011 (t) REVERT: A 524 GLU cc_start: 0.7740 (mp0) cc_final: 0.7414 (mp0) REVERT: A 583 GLN cc_start: 0.7886 (mt0) cc_final: 0.7006 (mp10) REVERT: A 601 ARG cc_start: 0.7127 (mtp180) cc_final: 0.6629 (mtm-85) REVERT: A 878 LYS cc_start: 0.8308 (mmtp) cc_final: 0.8091 (mmtp) REVERT: A 879 LYS cc_start: 0.7949 (mttm) cc_final: 0.7474 (mttm) REVERT: A 1004 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7779 (mt-10) REVERT: A 1011 LYS cc_start: 0.7980 (ttmm) cc_final: 0.7637 (ttmt) REVERT: B 34 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8068 (mm-30) REVERT: C 5 ARG cc_start: 0.7132 (ttt90) cc_final: 0.6915 (ttt-90) outliers start: 19 outliers final: 17 residues processed: 122 average time/residue: 1.4749 time to fit residues: 191.3111 Evaluate side-chains 125 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 992 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 70 optimal weight: 0.0370 chunk 45 optimal weight: 1.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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: 0.7480 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9746 Z= 0.224 Angle : 0.484 5.959 13204 Z= 0.251 Chirality : 0.042 0.162 1471 Planarity : 0.004 0.046 1709 Dihedral : 6.277 87.329 1332 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.70 % Allowed : 9.33 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.24), residues: 1200 helix: 1.75 (0.24), residues: 491 sheet: 1.09 (0.36), residues: 186 loop : 0.25 (0.28), residues: 523 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 0.012 0.001 PHE A 360 TYR 0.008 0.001 TYR A 20 ARG 0.008 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 1.092 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8423 (t) cc_final: 0.7980 (p) REVERT: A 114 GLU cc_start: 0.7616 (tt0) cc_final: 0.7357 (tm-30) REVERT: A 214 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7125 (tt0) REVERT: A 216 LYS cc_start: 0.6044 (mtmm) cc_final: 0.5593 (pttp) REVERT: A 218 MET cc_start: 0.7663 (mtp) cc_final: 0.7401 (mtp) REVERT: A 274 ASP cc_start: 0.8049 (p0) cc_final: 0.7821 (p0) REVERT: A 286 MET cc_start: 0.7626 (mmm) cc_final: 0.6670 (pmt) REVERT: A 306 GLU cc_start: 0.8339 (mp0) cc_final: 0.7960 (mp0) REVERT: A 327 LYS cc_start: 0.6680 (ttmm) cc_final: 0.6357 (ttmm) REVERT: A 387 ASP cc_start: 0.8796 (p0) cc_final: 0.8513 (p0) REVERT: A 524 GLU cc_start: 0.7752 (mp0) cc_final: 0.7431 (mp0) REVERT: A 583 GLN cc_start: 0.7887 (mt0) cc_final: 0.7006 (mp10) REVERT: A 601 ARG cc_start: 0.7186 (mtp180) cc_final: 0.6650 (mtm-85) REVERT: A 878 LYS cc_start: 0.8300 (mmtp) cc_final: 0.8078 (mmtp) REVERT: A 879 LYS cc_start: 0.7961 (mttm) cc_final: 0.7488 (mttm) REVERT: A 1004 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7790 (mt-10) REVERT: A 1011 LYS cc_start: 0.8019 (ttmm) cc_final: 0.7659 (ttmt) REVERT: B 34 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8097 (mm-30) outliers start: 18 outliers final: 17 residues processed: 120 average time/residue: 1.4436 time to fit residues: 184.1862 Evaluate side-chains 122 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 236 THR 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 593 CYS Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 992 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 109 optimal weight: 0.0980 chunk 100 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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: 0.7486 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9746 Z= 0.249 Angle : 0.485 6.031 13204 Z= 0.252 Chirality : 0.042 0.147 1471 Planarity : 0.004 0.048 1709 Dihedral : 6.321 88.413 1332 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.79 % Allowed : 9.24 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.24), residues: 1200 helix: 1.71 (0.24), residues: 491 sheet: 1.05 (0.36), residues: 186 loop : 0.24 (0.27), residues: 523 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 360 TYR 0.009 0.001 TYR A 20 ARG 0.010 0.001 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8435 (t) cc_final: 0.7981 (p) REVERT: A 114 GLU cc_start: 0.7600 (tt0) cc_final: 0.7359 (tm-30) REVERT: A 190 ASP cc_start: 0.7462 (t70) cc_final: 0.7254 (t0) REVERT: A 214 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7119 (tt0) REVERT: A 216 LYS cc_start: 0.6037 (mtmm) cc_final: 0.5537 (tttm) REVERT: A 218 MET cc_start: 0.7646 (mtp) cc_final: 0.7390 (mtp) REVERT: A 286 MET cc_start: 0.7637 (mmm) cc_final: 0.6675 (pmt) REVERT: A 306 GLU cc_start: 0.8342 (mp0) cc_final: 0.7964 (mp0) REVERT: A 524 GLU cc_start: 0.7750 (mp0) cc_final: 0.7427 (mp0) REVERT: A 583 GLN cc_start: 0.7883 (mt0) cc_final: 0.6996 (mp10) REVERT: A 601 ARG cc_start: 0.7218 (mtp180) cc_final: 0.6680 (mtm-85) REVERT: A 879 LYS cc_start: 0.8007 (mttm) cc_final: 0.7527 (mttm) REVERT: A 1004 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7805 (mt-10) REVERT: A 1011 LYS cc_start: 0.8053 (ttmm) cc_final: 0.7683 (ttmt) REVERT: B 34 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8071 (mm-30) outliers start: 19 outliers final: 17 residues processed: 123 average time/residue: 1.4152 time to fit residues: 185.6244 Evaluate side-chains 124 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 236 THR 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 593 CYS Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 992 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 7.9990 chunk 109 optimal weight: 0.2980 chunk 64 optimal weight: 0.9980 chunk 46 optimal weight: 0.4980 chunk 83 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 0.0170 chunk 70 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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: 0.7475 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9746 Z= 0.185 Angle : 0.475 5.980 13204 Z= 0.247 Chirality : 0.042 0.247 1471 Planarity : 0.004 0.059 1709 Dihedral : 6.249 89.557 1332 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.41 % Allowed : 9.90 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.24), residues: 1200 helix: 1.77 (0.24), residues: 492 sheet: 1.11 (0.36), residues: 184 loop : 0.27 (0.28), residues: 524 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 0.012 0.001 PHE A 360 TYR 0.007 0.001 TYR C 74 ARG 0.012 0.001 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 1.147 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8341 (t) cc_final: 0.7898 (p) REVERT: A 114 GLU cc_start: 0.7584 (tt0) cc_final: 0.7345 (tm-30) REVERT: A 182 THR cc_start: 0.8508 (t) cc_final: 0.8305 (m) REVERT: A 214 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7131 (tt0) REVERT: A 216 LYS cc_start: 0.6066 (mtmm) cc_final: 0.5605 (pttp) REVERT: A 218 MET cc_start: 0.7663 (mtp) cc_final: 0.7416 (mtp) REVERT: A 286 MET cc_start: 0.7613 (mmm) cc_final: 0.6661 (pmt) REVERT: A 306 GLU cc_start: 0.8344 (mp0) cc_final: 0.7967 (mp0) REVERT: A 327 LYS cc_start: 0.6620 (ttmm) cc_final: 0.6322 (ttmm) REVERT: A 524 GLU cc_start: 0.7755 (mp0) cc_final: 0.7432 (mp0) REVERT: A 583 GLN cc_start: 0.7821 (mt0) cc_final: 0.6972 (mp10) REVERT: A 601 ARG cc_start: 0.7170 (mtp180) cc_final: 0.6633 (mtm-85) REVERT: A 879 LYS cc_start: 0.7974 (mttm) cc_final: 0.7505 (mttm) REVERT: A 1004 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7790 (mt-10) REVERT: A 1011 LYS cc_start: 0.8016 (ttmm) cc_final: 0.7646 (ttmt) outliers start: 15 outliers final: 14 residues processed: 118 average time/residue: 1.4541 time to fit residues: 183.3976 Evaluate side-chains 121 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 992 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 109 optimal weight: 0.0030 chunk 94 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 0.0670 chunk 74 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.4728 ------------------------------------------------------------------------------- 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: 0.7473 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9746 Z= 0.185 Angle : 0.480 7.390 13204 Z= 0.249 Chirality : 0.042 0.223 1471 Planarity : 0.004 0.049 1709 Dihedral : 6.178 89.986 1331 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.41 % Allowed : 9.99 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.24), residues: 1200 helix: 1.79 (0.24), residues: 492 sheet: 1.09 (0.36), residues: 184 loop : 0.28 (0.28), residues: 524 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 0.011 0.001 PHE A 360 TYR 0.007 0.001 TYR C 74 ARG 0.011 0.000 ARG C 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 1.186 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8363 (t) cc_final: 0.7937 (p) REVERT: A 114 GLU cc_start: 0.7583 (tt0) cc_final: 0.7345 (tm-30) REVERT: A 214 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7135 (tt0) REVERT: A 216 LYS cc_start: 0.6010 (mtmm) cc_final: 0.5553 (pttp) REVERT: A 218 MET cc_start: 0.7686 (mtp) cc_final: 0.7442 (mtp) REVERT: A 286 MET cc_start: 0.7622 (mmm) cc_final: 0.6670 (pmt) REVERT: A 306 GLU cc_start: 0.8346 (mp0) cc_final: 0.7961 (mp0) REVERT: A 327 LYS cc_start: 0.6641 (ttmm) cc_final: 0.6328 (ttmm) REVERT: A 387 ASP cc_start: 0.8784 (p0) cc_final: 0.8499 (p0) REVERT: A 524 GLU cc_start: 0.7752 (mp0) cc_final: 0.7429 (mp0) REVERT: A 583 GLN cc_start: 0.7819 (mt0) cc_final: 0.6967 (mp10) REVERT: A 601 ARG cc_start: 0.7167 (mtp180) cc_final: 0.6631 (mtm-85) REVERT: A 879 LYS cc_start: 0.7983 (mttm) cc_final: 0.7512 (mttm) REVERT: A 1004 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7790 (mt-10) outliers start: 15 outliers final: 15 residues processed: 115 average time/residue: 1.4529 time to fit residues: 177.9486 Evaluate side-chains 118 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 236 THR 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 746 ILE Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 992 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 0.1980 chunk 94 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.126750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.088881 restraints weight = 11694.546| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.33 r_work: 0.2890 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9746 Z= 0.236 Angle : 0.497 7.636 13204 Z= 0.257 Chirality : 0.043 0.242 1471 Planarity : 0.004 0.047 1709 Dihedral : 6.205 88.915 1331 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.51 % Allowed : 9.90 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.24), residues: 1200 helix: 1.75 (0.24), residues: 492 sheet: 1.04 (0.37), residues: 176 loop : 0.28 (0.27), residues: 532 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 360 TYR 0.008 0.001 TYR A 20 ARG 0.011 0.001 ARG C 72 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 3801.47 seconds wall clock time: 68 minutes 34.47 seconds (4114.47 seconds total)