Starting phenix.real_space_refine on Thu Jan 16 03:25:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5r_44222/01_2025/9b5r_44222.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5r_44222/01_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_44222/01_2025/9b5r_44222.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5r_44222/01_2025/9b5r_44222.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5r_44222/01_2025/9b5r_44222.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5r_44222/01_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-5571/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: 0.00, per 1000 atoms: 0.00 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: 2.59 Conformation dependent library (CDL) restraints added in 1.1 seconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 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: 1.11 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: 3.36 Time building geometry restraints manager: 2.57 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: 24.360 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 15.420 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.760 ------------------------------------------------------------------------------- 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 : 1.040 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: 1.7427 time to fit residues: 291.7150 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 : 0.964 ------------------------------------------------------------------------------- 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 = 0.3602 r_free = 0.3602 target = 0.130478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.095925 restraints weight = 11672.957| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.94 r_work: 0.2951 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1310 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 6.183 12390 Z= 0.282 Chirality : 0.044 0.151 1374 Planarity : 0.005 0.046 1604 Dihedral : 6.992 75.531 1256 Min Nonbonded Distance : 1.925 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: 1.39 (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 : 0.963 Fit side-chains REVERT: A 32 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8703 (mmm) REVERT: A 85 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8122 (mt-10) REVERT: A 182 THR cc_start: 0.8797 (t) cc_final: 0.8545 (m) REVERT: A 185 ILE cc_start: 0.8802 (mt) cc_final: 0.8533 (mm) REVERT: A 228 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8338 (tppt) REVERT: A 353 ASP cc_start: 0.8351 (t0) cc_final: 0.8130 (t0) REVERT: A 562 LEU cc_start: 0.8682 (tp) cc_final: 0.8446 (tt) REVERT: A 668 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8176 (mmt) REVERT: A 699 GLN cc_start: 0.8606 (mp10) cc_final: 0.8349 (mp10) REVERT: A 755 ASN cc_start: 0.8769 (m-40) cc_final: 0.8221 (p0) REVERT: A 879 LYS cc_start: 0.8707 (mmmm) cc_final: 0.8468 (mtmm) REVERT: A 909 ASN cc_start: 0.7483 (t0) cc_final: 0.7151 (t0) REVERT: A 980 LYS cc_start: 0.8244 (ttpp) cc_final: 0.7754 (ttpp) REVERT: C 32 HIS cc_start: 0.8207 (t-170) cc_final: 0.7923 (t70) REVERT: C 38 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.8095 (mtm) REVERT: C 143 ARG cc_start: 0.8113 (ttp80) cc_final: 0.7721 (tmm-80) outliers start: 19 outliers final: 6 residues processed: 111 average time/residue: 1.6596 time to fit residues: 193.8377 Evaluate side-chains 106 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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: 7.9990 chunk 54 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 20 optimal weight: 0.1980 chunk 85 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.130503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.095062 restraints weight = 11894.751| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.00 r_work: 0.2965 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1551 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= 0.237 Angle : 0.522 11.998 12390 Z= 0.271 Chirality : 0.043 0.169 1374 Planarity : 0.004 0.045 1604 Dihedral : 6.321 79.909 1250 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % 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: 0.88 (0.25), residues: 1126 helix: 1.45 (0.25), residues: 486 sheet: 0.32 (0.37), residues: 181 loop : -0.15 (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 0.010 0.001 PHE A 237 TYR 0.013 0.001 TYR C 145 ARG 0.006 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 115 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 1.185 Fit side-chains REVERT: A 32 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8668 (mmm) REVERT: A 85 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8061 (mt-10) REVERT: A 182 THR cc_start: 0.8800 (t) cc_final: 0.8562 (m) REVERT: A 185 ILE cc_start: 0.8796 (mt) cc_final: 0.8550 (mm) REVERT: A 228 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8382 (mmmt) REVERT: A 353 ASP cc_start: 0.8410 (t0) cc_final: 0.8147 (t0) REVERT: A 526 PHE cc_start: 0.9482 (OUTLIER) cc_final: 0.9109 (m-80) REVERT: A 562 LEU cc_start: 0.8680 (tp) cc_final: 0.8436 (tt) REVERT: A 668 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8181 (mmm) REVERT: A 699 GLN cc_start: 0.8613 (mp10) cc_final: 0.8348 (mp10) REVERT: A 755 ASN cc_start: 0.8796 (m-40) cc_final: 0.8224 (p0) REVERT: A 879 LYS cc_start: 0.8734 (mmmm) cc_final: 0.8456 (mtmm) REVERT: A 909 ASN cc_start: 0.7487 (t0) cc_final: 0.7161 (t0) REVERT: A 980 LYS cc_start: 0.8328 (ttpp) cc_final: 0.7789 (ttpp) REVERT: C 32 HIS cc_start: 0.8186 (t-170) cc_final: 0.7872 (t70) REVERT: C 38 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8138 (mtm) outliers start: 23 outliers final: 7 residues processed: 105 average time/residue: 1.5728 time to fit residues: 174.5871 Evaluate side-chains 100 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 668 MET 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: 0.8980 chunk 2 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 72 optimal weight: 0.0030 chunk 65 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.6990 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.130010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.095869 restraints weight = 11825.042| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.04 r_work: 0.2968 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1646 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= 0.250 Angle : 0.510 11.448 12390 Z= 0.264 Chirality : 0.043 0.170 1374 Planarity : 0.004 0.047 1604 Dihedral : 6.379 86.015 1250 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.62 % Allowed : 10.69 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.25), residues: 1126 helix: 1.46 (0.25), residues: 486 sheet: 0.28 (0.37), residues: 181 loop : -0.16 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 702 HIS 0.002 0.000 HIS A 818 PHE 0.009 0.001 PHE A 677 TYR 0.012 0.001 TYR C 145 ARG 0.007 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 117 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 1.041 Fit side-chains REVERT: A 32 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8654 (mmm) REVERT: A 85 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8060 (mt-10) REVERT: A 218 MET cc_start: 0.6991 (mtt) cc_final: 0.6322 (mmt) REVERT: A 228 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8369 (mmmt) REVERT: A 353 ASP cc_start: 0.8437 (t0) cc_final: 0.8195 (t0) REVERT: A 526 PHE cc_start: 0.9478 (OUTLIER) cc_final: 0.9107 (m-80) REVERT: A 562 LEU cc_start: 0.8698 (tp) cc_final: 0.8452 (tt) REVERT: A 699 GLN cc_start: 0.8643 (mp10) cc_final: 0.8383 (mp10) REVERT: A 755 ASN cc_start: 0.8790 (m-40) cc_final: 0.8227 (p0) REVERT: A 879 LYS cc_start: 0.8738 (mmmm) cc_final: 0.8489 (mtmm) REVERT: A 909 ASN cc_start: 0.7493 (t0) cc_final: 0.7171 (t0) REVERT: A 980 LYS cc_start: 0.8349 (ttpp) cc_final: 0.7794 (ttpp) REVERT: C 32 HIS cc_start: 0.8184 (t-170) cc_final: 0.7879 (t70) REVERT: C 38 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.8081 (mtm) REVERT: C 72 ARG cc_start: 0.8438 (tpp80) cc_final: 0.8212 (ttm-80) REVERT: C 143 ARG cc_start: 0.8120 (ttp80) cc_final: 0.7832 (tmm-80) outliers start: 26 outliers final: 10 residues processed: 106 average time/residue: 1.6181 time to fit residues: 181.0587 Evaluate side-chains 102 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 1003 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 85 CYS 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: 0.1980 chunk 26 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.128691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.090244 restraints weight = 11591.709| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.28 r_work: 0.2896 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9140 Z= 0.265 Angle : 0.510 11.318 12390 Z= 0.264 Chirality : 0.042 0.170 1374 Planarity : 0.004 0.047 1604 Dihedral : 6.320 79.998 1250 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.22 % Allowed : 10.79 % Favored : 87.00 % 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: 0.76 (0.26), residues: 1126 helix: 1.43 (0.24), residues: 486 sheet: -0.05 (0.37), residues: 189 loop : -0.14 (0.29), residues: 451 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 0.010 0.001 PHE A 677 TYR 0.010 0.001 TYR A 81 ARG 0.008 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 110 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 1.062 Fit side-chains REVERT: A 32 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8112 (mmm) REVERT: A 85 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8116 (mt-10) REVERT: A 184 MET cc_start: 0.7294 (ptp) cc_final: 0.6899 (ptm) REVERT: A 218 MET cc_start: 0.6486 (mtt) cc_final: 0.5877 (mmt) REVERT: A 353 ASP cc_start: 0.8470 (t0) cc_final: 0.8050 (t0) REVERT: A 526 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.8814 (m-80) REVERT: A 562 LEU cc_start: 0.8223 (tp) cc_final: 0.8004 (tt) REVERT: A 699 GLN cc_start: 0.8460 (mp10) cc_final: 0.8113 (mp10) REVERT: A 755 ASN cc_start: 0.8848 (m-40) cc_final: 0.8049 (p0) REVERT: A 804 ARG cc_start: 0.8214 (mmt90) cc_final: 0.7955 (mmm-85) REVERT: A 879 LYS cc_start: 0.8460 (mmmm) cc_final: 0.7911 (mtmm) REVERT: A 909 ASN cc_start: 0.7402 (t0) cc_final: 0.7085 (t0) REVERT: A 980 LYS cc_start: 0.8240 (ttpp) cc_final: 0.7543 (ttpp) REVERT: C 32 HIS cc_start: 0.7967 (t-170) cc_final: 0.7388 (t70) REVERT: C 72 ARG cc_start: 0.8451 (tpp80) cc_final: 0.8102 (ttm-80) outliers start: 22 outliers final: 10 residues processed: 101 average time/residue: 1.6751 time to fit residues: 178.5587 Evaluate side-chains 98 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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 1003 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 98 THR 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: 0.8980 chunk 26 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.129073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.090691 restraints weight = 11649.203| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.27 r_work: 0.2888 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9140 Z= 0.287 Angle : 0.514 10.432 12390 Z= 0.266 Chirality : 0.043 0.158 1374 Planarity : 0.004 0.048 1604 Dihedral : 6.382 81.583 1250 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.92 % Allowed : 12.00 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1126 helix: 1.40 (0.24), residues: 486 sheet: -0.06 (0.37), residues: 189 loop : -0.18 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS A 818 PHE 0.010 0.001 PHE A 677 TYR 0.010 0.001 TYR A 81 ARG 0.010 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 105 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 1.136 Fit side-chains REVERT: A 32 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8108 (mmm) REVERT: A 85 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8106 (mt-10) REVERT: A 184 MET cc_start: 0.7291 (ptp) cc_final: 0.6938 (ptm) REVERT: A 218 MET cc_start: 0.6529 (mtt) cc_final: 0.5900 (mmt) REVERT: A 353 ASP cc_start: 0.8484 (t0) cc_final: 0.8047 (t0) REVERT: A 526 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.8828 (m-80) REVERT: A 562 LEU cc_start: 0.8251 (tp) cc_final: 0.8025 (tt) REVERT: A 699 GLN cc_start: 0.8502 (mp10) cc_final: 0.8156 (mp10) REVERT: A 755 ASN cc_start: 0.8859 (m-40) cc_final: 0.8047 (p0) REVERT: A 804 ARG cc_start: 0.8215 (mmt90) cc_final: 0.7944 (mmm-85) REVERT: A 879 LYS cc_start: 0.8457 (mmmm) cc_final: 0.7925 (mtmm) REVERT: A 909 ASN cc_start: 0.7420 (t0) cc_final: 0.7106 (t0) REVERT: A 980 LYS cc_start: 0.8197 (ttpp) cc_final: 0.7384 (ttpp) REVERT: C 32 HIS cc_start: 0.7911 (t-170) cc_final: 0.7327 (t70) REVERT: C 72 ARG cc_start: 0.8507 (tpp80) cc_final: 0.8096 (ttm-80) outliers start: 19 outliers final: 11 residues processed: 98 average time/residue: 1.7032 time to fit residues: 176.0447 Evaluate side-chains 98 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 1003 VAL 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: 0.6980 chunk 53 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3550 r_free = 0.3550 target = 0.128429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.089822 restraints weight = 11698.680| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.30 r_work: 0.2890 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9140 Z= 0.266 Angle : 0.515 10.178 12390 Z= 0.266 Chirality : 0.043 0.160 1374 Planarity : 0.004 0.048 1604 Dihedral : 6.265 73.694 1250 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.12 % Allowed : 12.30 % Favored : 85.58 % 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: 0.73 (0.25), residues: 1126 helix: 1.42 (0.25), residues: 480 sheet: -0.09 (0.37), residues: 190 loop : -0.15 (0.29), residues: 456 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 0.010 0.001 PHE A 123 TYR 0.010 0.001 TYR A 81 ARG 0.007 0.001 ARG C 8 *********************** 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 105 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 1.088 Fit side-chains REVERT: A 32 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8198 (mmm) REVERT: A 85 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8105 (mt-10) REVERT: A 184 MET cc_start: 0.7339 (ptp) cc_final: 0.7002 (ptm) REVERT: A 218 MET cc_start: 0.6564 (mtt) cc_final: 0.5847 (mmt) REVERT: A 353 ASP cc_start: 0.8483 (t0) cc_final: 0.8042 (t0) REVERT: A 526 PHE cc_start: 0.9261 (OUTLIER) cc_final: 0.8820 (m-80) REVERT: A 562 LEU cc_start: 0.8233 (tp) cc_final: 0.8003 (tt) REVERT: A 699 GLN cc_start: 0.8491 (mp10) cc_final: 0.8142 (mp10) REVERT: A 755 ASN cc_start: 0.8852 (m-40) cc_final: 0.8031 (p0) REVERT: A 804 ARG cc_start: 0.8181 (mmt90) cc_final: 0.7878 (mmm-85) REVERT: A 879 LYS cc_start: 0.8455 (mmmm) cc_final: 0.7922 (mtmm) REVERT: A 909 ASN cc_start: 0.7424 (t0) cc_final: 0.7110 (t0) REVERT: A 980 LYS cc_start: 0.8212 (ttpp) cc_final: 0.7432 (ttpp) REVERT: C 32 HIS cc_start: 0.7906 (t-170) cc_final: 0.7326 (t70) REVERT: C 72 ARG cc_start: 0.8528 (tpp80) cc_final: 0.8111 (ttm-80) outliers start: 21 outliers final: 12 residues processed: 98 average time/residue: 1.6188 time to fit residues: 167.7803 Evaluate side-chains 99 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 56 VAL 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 1003 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 85 CYS 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: 0.5980 chunk 28 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 99 optimal weight: 0.0070 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 50 optimal weight: 0.0270 overall best weight: 0.3856 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.130245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.093620 restraints weight = 11819.333| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.22 r_work: 0.2909 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9140 Z= 0.168 Angle : 0.486 10.708 12390 Z= 0.249 Chirality : 0.041 0.151 1374 Planarity : 0.004 0.047 1604 Dihedral : 5.978 63.807 1250 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.21 % Allowed : 13.41 % Favored : 85.38 % 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: 0.91 (0.26), residues: 1126 helix: 1.55 (0.25), residues: 480 sheet: 0.06 (0.38), residues: 190 loop : -0.06 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 669 HIS 0.001 0.000 HIS C 125 PHE 0.008 0.001 PHE A1007 TYR 0.009 0.001 TYR A 736 ARG 0.015 0.001 ARG C 5 *********************** 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 98 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.951 Fit side-chains REVERT: A 32 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8190 (mmm) REVERT: A 85 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8137 (mt-10) REVERT: A 184 MET cc_start: 0.7241 (ptp) cc_final: 0.6873 (ptm) REVERT: A 353 ASP cc_start: 0.8471 (t0) cc_final: 0.8088 (t0) REVERT: A 562 LEU cc_start: 0.8235 (tp) cc_final: 0.8007 (tt) REVERT: A 661 LEU cc_start: 0.8080 (mt) cc_final: 0.7676 (tp) REVERT: A 699 GLN cc_start: 0.8518 (mp10) cc_final: 0.8257 (mp10) REVERT: A 755 ASN cc_start: 0.8869 (m-40) cc_final: 0.8086 (p0) REVERT: A 804 ARG cc_start: 0.8200 (mmt90) cc_final: 0.7922 (mmm-85) REVERT: A 879 LYS cc_start: 0.8473 (mmmm) cc_final: 0.7967 (mtmm) REVERT: A 909 ASN cc_start: 0.7430 (t0) cc_final: 0.7097 (t0) REVERT: A 980 LYS cc_start: 0.8199 (ttpp) cc_final: 0.7418 (ttpp) REVERT: C 32 HIS cc_start: 0.7971 (t-170) cc_final: 0.7403 (t70) REVERT: C 72 ARG cc_start: 0.8487 (tpp80) cc_final: 0.8065 (ttm-80) outliers start: 12 outliers final: 7 residues processed: 95 average time/residue: 1.6549 time to fit residues: 165.8775 Evaluate side-chains 100 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 461 VAL 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 104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 44 optimal weight: 0.7980 chunk 68 optimal weight: 0.0970 chunk 33 optimal weight: 0.9990 chunk 16 optimal weight: 0.0030 chunk 28 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 50 optimal weight: 0.3980 chunk 6 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.2788 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.130735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.092395 restraints weight = 11625.501| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.30 r_work: 0.2930 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9140 Z= 0.153 Angle : 0.495 12.367 12390 Z= 0.252 Chirality : 0.041 0.152 1374 Planarity : 0.004 0.047 1604 Dihedral : 5.825 58.195 1250 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.61 % Allowed : 13.71 % Favored : 84.68 % 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: 0.99 (0.26), residues: 1126 helix: 1.57 (0.25), residues: 481 sheet: 0.17 (0.38), residues: 190 loop : -0.01 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 669 HIS 0.001 0.000 HIS C 75 PHE 0.008 0.001 PHE A 633 TYR 0.009 0.001 TYR A 736 ARG 0.008 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 110 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.986 Fit side-chains REVERT: A 32 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8132 (mmm) REVERT: A 85 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8128 (mt-10) REVERT: A 184 MET cc_start: 0.7196 (ptp) cc_final: 0.6857 (ptm) REVERT: A 353 ASP cc_start: 0.8435 (t0) cc_final: 0.8051 (t0) REVERT: A 562 LEU cc_start: 0.8190 (tp) cc_final: 0.7985 (tt) REVERT: A 661 LEU cc_start: 0.8046 (mt) cc_final: 0.7656 (tp) REVERT: A 699 GLN cc_start: 0.8506 (mp10) cc_final: 0.8237 (mp10) REVERT: A 755 ASN cc_start: 0.8869 (m-40) cc_final: 0.8060 (p0) REVERT: A 804 ARG cc_start: 0.8155 (mmt90) cc_final: 0.7853 (mmm-85) REVERT: A 879 LYS cc_start: 0.8442 (mmmm) cc_final: 0.7926 (mtmm) REVERT: A 909 ASN cc_start: 0.7403 (t0) cc_final: 0.7077 (t0) REVERT: A 980 LYS cc_start: 0.8173 (ttpp) cc_final: 0.7386 (ttpp) REVERT: C 8 ARG cc_start: 0.7859 (mtt180) cc_final: 0.7654 (mmm160) REVERT: C 32 HIS cc_start: 0.7865 (t-170) cc_final: 0.7478 (t-90) REVERT: C 72 ARG cc_start: 0.8469 (tpp80) cc_final: 0.8028 (ttm-80) outliers start: 16 outliers final: 9 residues processed: 104 average time/residue: 1.6149 time to fit residues: 177.7274 Evaluate side-chains 105 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 262 LYS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR 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 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 57 optimal weight: 0.0170 overall best weight: 0.7018 ------------------------------------------------------------------------------- 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 = 0.129422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.092565 restraints weight = 11672.663| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.37 r_work: 0.2904 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 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 0.043 9140 Z= 0.262 Angle : 0.534 12.140 12390 Z= 0.273 Chirality : 0.043 0.188 1374 Planarity : 0.005 0.049 1604 Dihedral : 5.860 59.297 1250 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.31 % Allowed : 14.42 % Favored : 84.27 % 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: 1.46 (0.24), residues: 487 sheet: 0.11 (0.38), residues: 190 loop : -0.04 (0.30), residues: 449 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 0.010 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 105 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8210 (mmm) REVERT: A 85 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8031 (mt-10) REVERT: A 184 MET cc_start: 0.7234 (ptp) cc_final: 0.6895 (ptm) REVERT: A 228 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8249 (mmmt) REVERT: A 353 ASP cc_start: 0.8478 (t0) cc_final: 0.8087 (t0) REVERT: A 562 LEU cc_start: 0.8261 (tp) cc_final: 0.8056 (tt) REVERT: A 699 GLN cc_start: 0.8520 (mp10) cc_final: 0.8252 (mp10) REVERT: A 755 ASN cc_start: 0.8869 (m-40) cc_final: 0.8064 (p0) REVERT: A 804 ARG cc_start: 0.8170 (mmt90) cc_final: 0.7868 (mmm-85) REVERT: A 879 LYS cc_start: 0.8466 (mmmm) cc_final: 0.7948 (mtmm) REVERT: A 909 ASN cc_start: 0.7428 (t0) cc_final: 0.7098 (t0) REVERT: A 980 LYS cc_start: 0.8205 (ttpp) cc_final: 0.7417 (ttpp) REVERT: C 29 ASP cc_start: 0.8367 (t0) cc_final: 0.8137 (t0) REVERT: C 32 HIS cc_start: 0.7900 (t-170) cc_final: 0.7464 (t-90) REVERT: C 72 ARG cc_start: 0.8493 (tpp80) cc_final: 0.8053 (ttm-80) REVERT: C 117 ASP cc_start: 0.8350 (t0) cc_final: 0.7965 (t0) outliers start: 13 outliers final: 10 residues processed: 102 average time/residue: 1.6715 time to fit residues: 179.9593 Evaluate side-chains 103 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 228 LYS Chi-restraints excluded: chain A residue 236 THR 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 944 MET 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 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: 3.9990 chunk 31 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 73 optimal weight: 0.0870 chunk 76 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3564 r_free = 0.3564 target = 0.129608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.092460 restraints weight = 11719.962| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.38 r_work: 0.2902 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9140 Z= 0.241 Angle : 0.526 12.635 12390 Z= 0.270 Chirality : 0.043 0.168 1374 Planarity : 0.005 0.049 1604 Dihedral : 5.847 59.834 1250 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.51 % Allowed : 14.11 % 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: 0.90 (0.26), residues: 1126 helix: 1.46 (0.24), residues: 487 sheet: 0.13 (0.38), residues: 190 loop : -0.04 (0.30), residues: 449 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 123 TYR 0.013 0.001 TYR C 74 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: 6611.63 seconds wall clock time: 117 minutes 16.30 seconds (7036.30 seconds total)