Starting phenix.real_space_refine on Thu Mar 13 15:58:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5r_44222/03_2025/9b5r_44222.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5r_44222/03_2025/9b5r_44222.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b5r_44222/03_2025/9b5r_44222.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5r_44222/03_2025/9b5r_44222.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5r_44222/03_2025/9b5r_44222.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5r_44222/03_2025/9b5r_44222.cif" } resolution = 2.95 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= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 2 5.21 5 S 41 5.16 5 C 5703 2.51 5 N 1470 2.21 5 O 1716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8935 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7734 Classifications: {'peptide': 985} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 928} Chain breaks: 1 Chain: "C" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1158 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'A1AIV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.40, per 1000 atoms: 0.72 Number of scatterers: 8935 At special positions: 0 Unit cell: (85.12, 100.016, 119.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 41 16.00 P 3 15.00 Mg 2 11.99 O 1716 8.00 N 1470 7.00 C 5703 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS C 85 " distance=2.90 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: 2.32 Conformation dependent library (CDL) restraints added in 987.5 milliseconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 9 sheets defined 47.5% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.714A 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: 3.694A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.973A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.641A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.496A 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: 3.810A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.210A 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: 4.420A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 304 removed outlier: 3.657A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN A 296 " --> pdb=" O HIS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 332 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 354 through 375 Processing helix chain 'A' and resid 389 through 392 Processing helix chain 'A' and resid 399 through 404 Processing helix chain 'A' and resid 410 through 418 removed outlier: 4.317A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.541A 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: 3.724A pdb=" N ASN A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A 474 " --> pdb=" O ASN A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'A' and resid 486 through 499 Processing helix chain 'A' and resid 500 through 503 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.773A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.602A pdb=" N ARG A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 597 Processing helix chain 'A' and resid 601 through 618 Processing helix chain 'A' and resid 618 through 630 Processing helix chain 'A' and resid 632 through 641 removed outlier: 3.577A 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 Processing helix chain 'A' and resid 679 through 689 removed outlier: 3.647A pdb=" N GLN A 683 " --> pdb=" O ASN A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 737 Processing helix chain 'A' and resid 743 through 753 removed outlier: 3.963A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 794 removed outlier: 3.661A pdb=" N GLN A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) 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: 3.531A pdb=" N THR A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.642A pdb=" N GLU A 882 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR A 883 " --> pdb=" O ILE A 880 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 879 through 883' Processing helix chain 'A' and resid 926 through 937 Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 969 through 979 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 98 through 112 Processing helix chain 'C' and resid 120 through 130 Processing helix chain 'C' and resid 130 through 145 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.897A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.280A 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: 4.137A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.451A 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: 4.137A 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: 6.491A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 460 " --> pdb=" O THR A 430 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.107A 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 919 through 922 removed outlier: 6.452A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL A 990 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N SER A 947 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLU A 992 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU A 945 " --> pdb=" O GLU A 992 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N CYS A 994 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LEU A 951 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 919 through 922 removed outlier: 6.452A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N CYS A 995 " --> pdb=" O VAL A1003 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A1003 " --> pdb=" O CYS A 995 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 21 through 26 removed outlier: 3.657A pdb=" N GLY C 24 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N HIS C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) 436 hydrogen bonds defined for protein. 1209 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: 3.43 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1512 1.27 - 1.40: 2173 1.40 - 1.54: 5284 1.54 - 1.67: 109 1.67 - 1.81: 62 Bond restraints: 9140 Sorted by residual: bond pdb=" C04 A1AIV D 201 " pdb=" C05 A1AIV D 201 " ideal model delta sigma weight residual 1.453 1.525 -0.072 2.00e-02 2.50e+03 1.31e+01 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 1.20e+00 bond pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 1.416 1.404 0.012 1.30e-02 5.92e+03 9.14e-01 bond pdb=" C05 A1AIV D 201 " pdb=" N06 A1AIV D 201 " ideal model delta sigma weight residual 1.151 1.132 0.019 2.00e-02 2.50e+03 9.02e-01 bond pdb=" C PHE A 360 " pdb=" O PHE A 360 " ideal model delta sigma weight residual 1.236 1.242 -0.006 1.15e-02 7.56e+03 2.70e-01 ... (remaining 9135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 12251 1.42 - 2.85: 68 2.85 - 4.27: 62 4.27 - 5.69: 5 5.69 - 7.12: 4 Bond angle restraints: 12390 Sorted by residual: angle pdb=" C LYS A 381 " pdb=" N GLN A 382 " pdb=" CA GLN A 382 " ideal model delta sigma weight residual 121.70 128.82 -7.12 1.80e+00 3.09e-01 1.56e+01 angle pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 106.53 103.12 3.41 1.18e+00 7.24e-01 8.44e+00 angle pdb=" C3' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" C5' ATP A1103 " ideal model delta sigma weight residual 115.19 110.61 4.58 1.76e+00 3.23e-01 6.78e+00 angle pdb=" C2' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O3' ATP A1103 " ideal model delta sigma weight residual 111.83 105.39 6.44 2.67e+00 1.40e-01 5.83e+00 angle pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" O2' ATP A1103 " ideal model delta sigma weight residual 110.58 104.22 6.36 2.79e+00 1.28e-01 5.18e+00 ... (remaining 12385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 5334 17.55 - 35.09: 170 35.09 - 52.64: 37 52.64 - 70.19: 8 70.19 - 87.73: 3 Dihedral angle restraints: 5552 sinusoidal: 2262 harmonic: 3290 Sorted by residual: dihedral pdb=" CB CYS A 593 " pdb=" SG CYS A 593 " pdb=" SG CYS C 85 " pdb=" CB CYS C 85 " ideal model delta sinusoidal sigma weight residual -86.00 -142.26 56.26 1 1.00e+01 1.00e-02 4.27e+01 dihedral pdb=" CA LYS A 884 " pdb=" C LYS A 884 " pdb=" N ASN A 885 " pdb=" CA ASN A 885 " ideal model delta harmonic sigma weight residual 180.00 162.99 17.01 0 5.00e+00 4.00e-02 1.16e+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 -122.79 -57.21 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 5549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1213 0.057 - 0.114: 134 0.114 - 0.171: 24 0.171 - 0.229: 1 0.229 - 0.286: 2 Chirality restraints: 1374 Sorted by residual: chirality pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O2' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.04e+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 -2.90 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C4' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" C5' ATP A1103 " pdb=" O4' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.49 -2.72 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1371 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 94 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO C 95 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 17 " 0.018 5.00e-02 4.00e+02 2.65e-02 1.13e+00 pdb=" N PRO C 18 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO C 18 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 18 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 120 " -0.017 5.00e-02 4.00e+02 2.53e-02 1.03e+00 pdb=" N PRO C 121 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO C 121 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 121 " -0.014 5.00e-02 4.00e+02 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 57 2.58 - 3.16: 7398 3.16 - 3.74: 12983 3.74 - 4.32: 19327 4.32 - 4.90: 32792 Nonbonded interactions: 72557 Sorted by model distance: nonbonded pdb=" OD2 ASP A 465 " pdb="MG MG A1102 " model vdw 2.006 2.170 nonbonded pdb="MG MG A1101 " pdb=" O2B ATP A1103 " model vdw 2.040 2.170 nonbonded pdb=" OD2 ASP A 463 " pdb=" O3' ATP A1103 " model vdw 2.186 3.040 nonbonded pdb=" OD2 ASP A 537 " pdb="MG MG A1101 " model vdw 2.189 2.170 nonbonded pdb=" N GLU A 489 " pdb=" OE1 GLU A 489 " model vdw 2.236 3.120 ... (remaining 72552 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: 340.080 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.190 Find NCS groups from input model: 0.130 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:13.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 378.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9140 Z= 0.192 Angle : 0.453 7.119 12390 Z= 0.227 Chirality : 0.042 0.286 1374 Planarity : 0.003 0.030 1604 Dihedral : 9.740 87.732 3425 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.31 % Allowed : 2.52 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.26), residues: 1126 helix: 1.50 (0.25), residues: 476 sheet: 0.44 (0.39), residues: 174 loop : 0.04 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 608 HIS 0.002 0.000 HIS A 818 PHE 0.010 0.001 PHE A 842 TYR 0.008 0.001 TYR A 732 ARG 0.002 0.000 ARG A 919 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ILE cc_start: 0.8643 (mt) cc_final: 0.8431 (mm) REVERT: A 218 MET cc_start: 0.7338 (mtt) cc_final: 0.7065 (mtt) REVERT: A 262 LYS cc_start: 0.8587 (ttpp) cc_final: 0.8376 (mtpm) REVERT: A 270 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7954 (mt-10) REVERT: A 273 LYS cc_start: 0.7776 (mttt) cc_final: 0.7536 (mtmt) REVERT: A 353 ASP cc_start: 0.8389 (t0) cc_final: 0.8108 (t0) REVERT: A 368 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8275 (mm-30) REVERT: A 526 PHE cc_start: 0.9317 (OUTLIER) cc_final: 0.8878 (m-80) REVERT: A 562 LEU cc_start: 0.8323 (tp) cc_final: 0.8062 (tt) REVERT: A 596 LYS cc_start: 0.8533 (tmtt) cc_final: 0.8206 (tttt) REVERT: A 755 ASN cc_start: 0.8783 (m-40) cc_final: 0.8144 (p0) REVERT: A 832 MET cc_start: 0.8213 (mtp) cc_final: 0.7949 (mtp) REVERT: A 879 LYS cc_start: 0.8449 (mmmm) cc_final: 0.7704 (mtmm) REVERT: A 909 ASN cc_start: 0.7453 (t0) cc_final: 0.7123 (t0) REVERT: A 937 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: A 979 LYS cc_start: 0.7940 (mmtp) cc_final: 0.7733 (mmmt) REVERT: A 980 LYS cc_start: 0.8176 (ttpp) cc_final: 0.7490 (ttpp) REVERT: A 1011 LYS cc_start: 0.7983 (ttmm) cc_final: 0.7629 (tppt) outliers start: 13 outliers final: 3 residues processed: 159 average time/residue: 1.6779 time to fit residues: 281.0467 Evaluate side-chains 103 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.130441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.095702 restraints weight = 11669.518| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.96 r_work: 0.2946 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9140 Z= 0.337 Angle : 0.537 6.139 12390 Z= 0.282 Chirality : 0.044 0.150 1374 Planarity : 0.005 0.046 1604 Dihedral : 6.968 75.644 1256 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.92 % Allowed : 9.38 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1126 helix: 1.40 (0.25), residues: 486 sheet: 0.46 (0.39), residues: 173 loop : -0.10 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS A 147 PHE 0.012 0.001 PHE A 237 TYR 0.011 0.001 TYR A 81 ARG 0.007 0.001 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 1.859 Fit side-chains REVERT: A 32 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8695 (mmm) REVERT: A 85 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8130 (mt-10) REVERT: A 182 THR cc_start: 0.8792 (t) cc_final: 0.8535 (m) REVERT: A 185 ILE cc_start: 0.8792 (mt) cc_final: 0.8521 (mm) REVERT: A 228 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8329 (tppt) REVERT: A 353 ASP cc_start: 0.8363 (t0) cc_final: 0.8135 (t0) REVERT: A 562 LEU cc_start: 0.8677 (tp) cc_final: 0.8440 (tt) REVERT: A 596 LYS cc_start: 0.8516 (tmtt) cc_final: 0.8311 (tttt) REVERT: A 668 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8175 (mmt) REVERT: A 699 GLN cc_start: 0.8604 (mp10) cc_final: 0.8342 (mp10) REVERT: A 755 ASN cc_start: 0.8773 (m-40) cc_final: 0.8216 (p0) REVERT: A 879 LYS cc_start: 0.8706 (mmmm) cc_final: 0.8450 (mtmm) REVERT: A 909 ASN cc_start: 0.7485 (t0) cc_final: 0.7152 (t0) REVERT: A 980 LYS cc_start: 0.8251 (ttpp) cc_final: 0.7752 (ttpp) REVERT: A 1011 LYS cc_start: 0.8276 (ttmm) cc_final: 0.8072 (tppt) REVERT: C 32 HIS cc_start: 0.8218 (t-170) cc_final: 0.7916 (t70) REVERT: C 38 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.8111 (mtm) REVERT: C 143 ARG cc_start: 0.8113 (ttp80) cc_final: 0.7714 (tmm-80) outliers start: 19 outliers final: 6 residues processed: 111 average time/residue: 1.7545 time to fit residues: 205.4418 Evaluate side-chains 108 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 38 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 18 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 20 optimal weight: 0.0370 chunk 85 optimal weight: 0.5980 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.130726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.095606 restraints weight = 11885.343| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.02 r_work: 0.2967 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9140 Z= 0.216 Angle : 0.512 10.850 12390 Z= 0.265 Chirality : 0.042 0.173 1374 Planarity : 0.004 0.045 1604 Dihedral : 6.327 80.810 1250 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.32 % Allowed : 10.58 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.25), residues: 1126 helix: 1.48 (0.25), residues: 486 sheet: 0.34 (0.37), residues: 181 loop : -0.14 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 669 HIS 0.001 0.000 HIS A 818 PHE 0.009 0.001 PHE A 237 TYR 0.013 0.001 TYR C 145 ARG 0.007 0.001 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 1.066 Fit side-chains REVERT: A 32 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8700 (mmm) REVERT: A 85 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8075 (mt-10) REVERT: A 182 THR cc_start: 0.8818 (t) cc_final: 0.8586 (m) REVERT: A 185 ILE cc_start: 0.8801 (mt) cc_final: 0.8558 (mm) REVERT: A 228 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8371 (mmmt) REVERT: A 353 ASP cc_start: 0.8393 (t0) cc_final: 0.8145 (t0) REVERT: A 526 PHE cc_start: 0.9475 (OUTLIER) cc_final: 0.9107 (m-80) REVERT: A 562 LEU cc_start: 0.8698 (tp) cc_final: 0.8457 (tt) REVERT: A 699 GLN cc_start: 0.8608 (mp10) cc_final: 0.8347 (mp10) REVERT: A 755 ASN cc_start: 0.8768 (m-40) cc_final: 0.8221 (p0) REVERT: A 879 LYS cc_start: 0.8733 (mmmm) cc_final: 0.8485 (mtmm) REVERT: A 909 ASN cc_start: 0.7491 (t0) cc_final: 0.7164 (t0) REVERT: A 980 LYS cc_start: 0.8312 (ttpp) cc_final: 0.7791 (ttpp) REVERT: C 32 HIS cc_start: 0.8206 (t-170) cc_final: 0.7914 (t70) REVERT: C 38 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.8129 (mtm) outliers start: 23 outliers final: 7 residues processed: 108 average time/residue: 1.6175 time to fit residues: 184.5473 Evaluate side-chains 104 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 72 optimal weight: 0.0770 chunk 65 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 81 optimal weight: 0.0060 chunk 14 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.130792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.096976 restraints weight = 11815.398| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.02 r_work: 0.2981 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9140 Z= 0.211 Angle : 0.492 10.410 12390 Z= 0.255 Chirality : 0.042 0.166 1374 Planarity : 0.004 0.046 1604 Dihedral : 6.308 85.950 1250 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.42 % Allowed : 11.09 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.26), residues: 1126 helix: 1.52 (0.25), residues: 486 sheet: 0.34 (0.37), residues: 181 loop : -0.12 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 669 HIS 0.002 0.000 HIS A 818 PHE 0.009 0.001 PHE A 237 TYR 0.011 0.001 TYR C 145 ARG 0.008 0.001 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 1.025 Fit side-chains REVERT: A 32 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8626 (mmm) REVERT: A 85 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8077 (mt-10) REVERT: A 218 MET cc_start: 0.7041 (mtt) cc_final: 0.6269 (mmt) REVERT: A 228 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8386 (mmmt) REVERT: A 353 ASP cc_start: 0.8431 (t0) cc_final: 0.8194 (t0) REVERT: A 526 PHE cc_start: 0.9470 (OUTLIER) cc_final: 0.9102 (m-80) REVERT: A 562 LEU cc_start: 0.8699 (tp) cc_final: 0.8458 (tt) REVERT: A 699 GLN cc_start: 0.8633 (mp10) cc_final: 0.8369 (mp10) REVERT: A 755 ASN cc_start: 0.8795 (m-40) cc_final: 0.8206 (p0) REVERT: A 879 LYS cc_start: 0.8732 (mmmm) cc_final: 0.8468 (mtmm) REVERT: A 909 ASN cc_start: 0.7473 (t0) cc_final: 0.7145 (t0) REVERT: A 980 LYS cc_start: 0.8392 (ttpp) cc_final: 0.7728 (ttpp) REVERT: C 32 HIS cc_start: 0.8168 (t-170) cc_final: 0.7842 (t70) REVERT: C 72 ARG cc_start: 0.8430 (tpp80) cc_final: 0.8199 (ttm-80) REVERT: C 143 ARG cc_start: 0.8104 (ttp80) cc_final: 0.7804 (tmm-80) outliers start: 24 outliers final: 10 residues processed: 111 average time/residue: 1.4352 time to fit residues: 169.1399 Evaluate side-chains 106 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 9 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 82 optimal weight: 0.0020 chunk 19 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 93 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.129209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.090753 restraints weight = 11569.654| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.29 r_work: 0.2904 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9140 Z= 0.233 Angle : 0.498 9.508 12390 Z= 0.259 Chirality : 0.042 0.156 1374 Planarity : 0.004 0.047 1604 Dihedral : 6.256 81.404 1250 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.12 % Allowed : 11.79 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.26), residues: 1126 helix: 1.51 (0.25), residues: 486 sheet: 0.02 (0.37), residues: 189 loop : -0.10 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 669 HIS 0.002 0.000 HIS A 818 PHE 0.009 0.001 PHE A 677 TYR 0.009 0.001 TYR A 81 ARG 0.010 0.001 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8091 (mmm) REVERT: A 85 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8118 (mt-10) REVERT: A 184 MET cc_start: 0.7204 (ptp) cc_final: 0.6850 (ptm) REVERT: A 218 MET cc_start: 0.6457 (mtt) cc_final: 0.5771 (mmt) REVERT: A 353 ASP cc_start: 0.8475 (t0) cc_final: 0.8058 (t0) REVERT: A 526 PHE cc_start: 0.9242 (OUTLIER) cc_final: 0.8798 (m-80) REVERT: A 562 LEU cc_start: 0.8213 (tp) cc_final: 0.7998 (tt) REVERT: A 699 GLN cc_start: 0.8498 (mp10) cc_final: 0.8139 (mp10) REVERT: A 755 ASN cc_start: 0.8852 (m-40) cc_final: 0.8035 (p0) REVERT: A 804 ARG cc_start: 0.8109 (mmt90) cc_final: 0.7803 (mmm-85) REVERT: A 879 LYS cc_start: 0.8442 (mmmm) cc_final: 0.7880 (mtmm) REVERT: A 909 ASN cc_start: 0.7395 (t0) cc_final: 0.7063 (t0) REVERT: A 980 LYS cc_start: 0.8189 (ttpp) cc_final: 0.7378 (ttpp) REVERT: C 32 HIS cc_start: 0.7921 (t-170) cc_final: 0.7299 (t70) REVERT: C 72 ARG cc_start: 0.8495 (tpp80) cc_final: 0.8078 (ttm-80) REVERT: C 117 ASP cc_start: 0.8322 (t0) cc_final: 0.7892 (t0) outliers start: 21 outliers final: 10 residues processed: 109 average time/residue: 1.8117 time to fit residues: 209.2775 Evaluate side-chains 104 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 21 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 101 optimal weight: 0.0670 chunk 62 optimal weight: 0.8980 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.129042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.090722 restraints weight = 11678.650| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.29 r_work: 0.2902 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9140 Z= 0.242 Angle : 0.507 10.547 12390 Z= 0.261 Chirality : 0.042 0.166 1374 Planarity : 0.004 0.049 1604 Dihedral : 6.281 82.471 1250 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.22 % Allowed : 12.50 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.26), residues: 1126 helix: 1.47 (0.24), residues: 486 sheet: -0.01 (0.37), residues: 190 loop : -0.10 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS A 818 PHE 0.009 0.001 PHE A 677 TYR 0.010 0.001 TYR A 81 ARG 0.009 0.001 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8105 (mmm) REVERT: A 85 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8135 (mt-10) REVERT: A 184 MET cc_start: 0.7232 (ptp) cc_final: 0.6889 (ptm) REVERT: A 218 MET cc_start: 0.6497 (mtt) cc_final: 0.5835 (mmt) REVERT: A 353 ASP cc_start: 0.8493 (t0) cc_final: 0.8071 (t0) REVERT: A 526 PHE cc_start: 0.9254 (OUTLIER) cc_final: 0.8812 (m-80) REVERT: A 562 LEU cc_start: 0.8228 (tp) cc_final: 0.8009 (tt) REVERT: A 699 GLN cc_start: 0.8510 (mp10) cc_final: 0.8238 (mp10) REVERT: A 755 ASN cc_start: 0.8860 (m-40) cc_final: 0.8049 (p0) REVERT: A 804 ARG cc_start: 0.8119 (mmt90) cc_final: 0.7798 (mmm-85) REVERT: A 879 LYS cc_start: 0.8441 (mmmm) cc_final: 0.7903 (mtmm) REVERT: A 909 ASN cc_start: 0.7401 (t0) cc_final: 0.7069 (t0) REVERT: A 980 LYS cc_start: 0.8193 (ttpp) cc_final: 0.7407 (ttpp) REVERT: C 32 HIS cc_start: 0.7933 (t-170) cc_final: 0.7357 (t70) REVERT: C 72 ARG cc_start: 0.8502 (tpp80) cc_final: 0.8090 (ttm-80) REVERT: C 117 ASP cc_start: 0.8338 (t0) cc_final: 0.7965 (t0) outliers start: 22 outliers final: 14 residues processed: 108 average time/residue: 1.5603 time to fit residues: 178.9271 Evaluate side-chains 109 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 7 optimal weight: 0.3980 chunk 18 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.128941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.092113 restraints weight = 11675.792| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.33 r_work: 0.2904 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9140 Z= 0.240 Angle : 0.507 9.587 12390 Z= 0.261 Chirality : 0.042 0.153 1374 Planarity : 0.004 0.047 1604 Dihedral : 6.177 74.209 1250 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.22 % Allowed : 12.70 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.26), residues: 1126 helix: 1.45 (0.24), residues: 486 sheet: -0.00 (0.37), residues: 190 loop : -0.11 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.001 0.000 HIS A 818 PHE 0.009 0.001 PHE A 677 TYR 0.010 0.001 TYR A 81 ARG 0.010 0.001 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8199 (mmm) REVERT: A 85 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8131 (mt-10) REVERT: A 184 MET cc_start: 0.7270 (ptp) cc_final: 0.6948 (ptm) REVERT: A 353 ASP cc_start: 0.8473 (t0) cc_final: 0.8049 (t0) REVERT: A 526 PHE cc_start: 0.9281 (OUTLIER) cc_final: 0.8843 (m-80) REVERT: A 562 LEU cc_start: 0.8267 (tp) cc_final: 0.8045 (tt) REVERT: A 699 GLN cc_start: 0.8511 (mp10) cc_final: 0.8239 (mp10) REVERT: A 755 ASN cc_start: 0.8866 (m-40) cc_final: 0.8057 (p0) REVERT: A 804 ARG cc_start: 0.8119 (mmt90) cc_final: 0.7789 (mmm-85) REVERT: A 879 LYS cc_start: 0.8464 (mmmm) cc_final: 0.7931 (mtmm) REVERT: A 909 ASN cc_start: 0.7418 (t0) cc_final: 0.7085 (t0) REVERT: A 980 LYS cc_start: 0.8206 (ttpp) cc_final: 0.7417 (ttpp) REVERT: C 32 HIS cc_start: 0.7947 (t-170) cc_final: 0.7382 (t70) REVERT: C 72 ARG cc_start: 0.8528 (tpp80) cc_final: 0.8112 (ttm-80) outliers start: 22 outliers final: 14 residues processed: 107 average time/residue: 1.4863 time to fit residues: 168.6586 Evaluate side-chains 110 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 64 optimal weight: 0.0970 chunk 54 optimal weight: 0.8980 chunk 50 optimal weight: 0.0030 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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 = 0.3570 r_free = 0.3570 target = 0.129902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.093397 restraints weight = 11844.259| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.20 r_work: 0.2908 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9140 Z= 0.195 Angle : 0.493 10.795 12390 Z= 0.253 Chirality : 0.041 0.151 1374 Planarity : 0.004 0.047 1604 Dihedral : 6.032 67.951 1250 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.92 % Allowed : 13.00 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.26), residues: 1126 helix: 1.52 (0.25), residues: 480 sheet: 0.05 (0.38), residues: 190 loop : -0.06 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 669 HIS 0.001 0.000 HIS A 818 PHE 0.008 0.001 PHE A1007 TYR 0.008 0.001 TYR A 736 ARG 0.009 0.001 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.914 Fit side-chains REVERT: A 32 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8197 (mmm) REVERT: A 85 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8145 (mt-10) REVERT: A 184 MET cc_start: 0.7258 (ptp) cc_final: 0.6937 (ptm) REVERT: A 353 ASP cc_start: 0.8467 (t0) cc_final: 0.8076 (t0) REVERT: A 562 LEU cc_start: 0.8236 (tp) cc_final: 0.8032 (tt) REVERT: A 699 GLN cc_start: 0.8539 (mp10) cc_final: 0.8265 (mp10) REVERT: A 755 ASN cc_start: 0.8875 (m-40) cc_final: 0.8060 (p0) REVERT: A 804 ARG cc_start: 0.8113 (mmt90) cc_final: 0.7782 (mmm-85) REVERT: A 879 LYS cc_start: 0.8467 (mmmm) cc_final: 0.7937 (mtmm) REVERT: A 909 ASN cc_start: 0.7424 (t0) cc_final: 0.7096 (t0) REVERT: A 962 LEU cc_start: 0.6210 (mp) cc_final: 0.5964 (mp) REVERT: A 980 LYS cc_start: 0.8204 (ttpp) cc_final: 0.7418 (ttpp) REVERT: C 32 HIS cc_start: 0.7939 (t-170) cc_final: 0.7527 (t-90) REVERT: C 72 ARG cc_start: 0.8498 (tpp80) cc_final: 0.8073 (ttm-80) outliers start: 19 outliers final: 12 residues processed: 111 average time/residue: 1.5023 time to fit residues: 176.2664 Evaluate side-chains 108 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 44 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 82 optimal weight: 0.0570 chunk 4 optimal weight: 0.6980 chunk 50 optimal weight: 0.3980 chunk 6 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 = 0.3570 r_free = 0.3570 target = 0.130145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.093261 restraints weight = 11659.551| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.35 r_work: 0.2919 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9140 Z= 0.197 Angle : 0.509 11.991 12390 Z= 0.260 Chirality : 0.042 0.158 1374 Planarity : 0.004 0.048 1604 Dihedral : 5.905 59.087 1250 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.71 % Allowed : 13.81 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1126 helix: 1.50 (0.24), residues: 487 sheet: 0.08 (0.38), residues: 190 loop : -0.05 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 669 HIS 0.001 0.000 HIS A 818 PHE 0.008 0.001 PHE A1007 TYR 0.010 0.001 TYR C 145 ARG 0.011 0.001 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.976 Fit side-chains REVERT: A 32 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8175 (mmm) REVERT: A 85 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: A 184 MET cc_start: 0.7229 (ptp) cc_final: 0.6931 (ptm) REVERT: A 353 ASP cc_start: 0.8453 (t0) cc_final: 0.8060 (t0) REVERT: A 562 LEU cc_start: 0.8223 (tp) cc_final: 0.8020 (tt) REVERT: A 699 GLN cc_start: 0.8531 (mp10) cc_final: 0.8255 (mp10) REVERT: A 755 ASN cc_start: 0.8871 (m-40) cc_final: 0.8053 (p0) REVERT: A 879 LYS cc_start: 0.8460 (mmmm) cc_final: 0.7924 (mtmm) REVERT: A 909 ASN cc_start: 0.7412 (t0) cc_final: 0.7096 (t0) REVERT: A 980 LYS cc_start: 0.8195 (ttpp) cc_final: 0.7413 (ttpp) REVERT: C 32 HIS cc_start: 0.7898 (t-170) cc_final: 0.7320 (t70) REVERT: C 72 ARG cc_start: 0.8471 (tpp80) cc_final: 0.8030 (ttm-80) outliers start: 17 outliers final: 14 residues processed: 109 average time/residue: 1.4826 time to fit residues: 171.6411 Evaluate side-chains 108 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 21 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 101 optimal weight: 0.1980 chunk 105 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 57 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3565 r_free = 0.3565 target = 0.129538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.093850 restraints weight = 11672.138| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.17 r_work: 0.2905 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9140 Z= 0.233 Angle : 0.523 12.358 12390 Z= 0.267 Chirality : 0.042 0.154 1374 Planarity : 0.004 0.048 1604 Dihedral : 5.876 59.693 1250 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.61 % Allowed : 14.01 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.26), residues: 1126 helix: 1.48 (0.24), residues: 487 sheet: 0.09 (0.38), residues: 190 loop : -0.06 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 669 HIS 0.001 0.000 HIS A 818 PHE 0.009 0.001 PHE A 677 TYR 0.013 0.001 TYR C 74 ARG 0.012 0.001 ARG C 139 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 1.016 Fit side-chains REVERT: A 32 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8190 (mmm) REVERT: A 85 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8121 (mt-10) REVERT: A 184 MET cc_start: 0.7204 (ptp) cc_final: 0.6908 (ptm) REVERT: A 353 ASP cc_start: 0.8460 (t0) cc_final: 0.8060 (t0) REVERT: A 562 LEU cc_start: 0.8274 (tp) cc_final: 0.8062 (tt) REVERT: A 699 GLN cc_start: 0.8537 (mp10) cc_final: 0.8263 (mp10) REVERT: A 755 ASN cc_start: 0.8880 (m-40) cc_final: 0.8054 (p0) REVERT: A 879 LYS cc_start: 0.8465 (mmmm) cc_final: 0.7928 (mtmm) REVERT: A 909 ASN cc_start: 0.7430 (t0) cc_final: 0.7117 (t0) REVERT: A 980 LYS cc_start: 0.8213 (ttpp) cc_final: 0.7428 (ttpp) REVERT: C 32 HIS cc_start: 0.7924 (t-170) cc_final: 0.7537 (t-90) REVERT: C 72 ARG cc_start: 0.8490 (tpp80) cc_final: 0.8054 (ttm-80) outliers start: 16 outliers final: 13 residues processed: 102 average time/residue: 1.5067 time to fit residues: 163.0483 Evaluate side-chains 104 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 10 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 76 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.129267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.093631 restraints weight = 11748.820| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.17 r_work: 0.2898 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9140 Z= 0.260 Angle : 0.532 12.835 12390 Z= 0.272 Chirality : 0.043 0.151 1374 Planarity : 0.005 0.049 1604 Dihedral : 5.877 60.438 1250 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.71 % Allowed : 14.11 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.26), residues: 1126 helix: 1.42 (0.24), residues: 487 sheet: 0.09 (0.38), residues: 190 loop : -0.07 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS A 818 PHE 0.009 0.001 PHE A 677 TYR 0.014 0.001 TYR A 627 ARG 0.012 0.001 ARG C 139 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 7081.25 seconds wall clock time: 123 minutes 31.67 seconds (7411.67 seconds total)