Starting phenix.real_space_refine on Sat Aug 23 01:43:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5r_44222/08_2025/9b5r_44222.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5r_44222/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9b5r_44222/08_2025/9b5r_44222.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5r_44222/08_2025/9b5r_44222.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b5r_44222/08_2025/9b5r_44222.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5r_44222/08_2025/9b5r_44222.map" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.26, per 1000 atoms: 0.25 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: 0.79 Conformation dependent library (CDL) restraints added in 285.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.37 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: 1.42 Time building geometry restraints manager: 1.06 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: 3.630 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.910 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:6.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.950 ------------------------------------------------------------------------------- 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 : 0.010 0.867 9143 Z= 0.483 Angle : 0.626 45.241 12392 Z= 0.306 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 919 TYR 0.008 0.001 TYR A 732 PHE 0.010 0.001 PHE A 842 TRP 0.003 0.001 TRP A 608 HIS 0.002 0.000 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9140) covalent geometry : angle 0.45258 (12390) SS BOND : bond 0.86700 ( 1) SS BOND : angle 34.01991 ( 2) hydrogen bonds : bond 0.14587 ( 423) hydrogen bonds : angle 5.79624 ( 1209) Misc. bond : bond 0.07775 ( 2) *********************** 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 : 0.216 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: 0.6491 time to fit residues: 108.4326 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 : 0.338 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.3980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.0570 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.132685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.098297 restraints weight = 11666.188| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.93 r_work: 0.3011 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9143 Z= 0.131 Angle : 0.504 7.006 12392 Z= 0.263 Chirality : 0.042 0.144 1374 Planarity : 0.004 0.047 1604 Dihedral : 6.790 76.254 1256 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.71 % Allowed : 9.17 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.26), residues: 1126 helix: 1.54 (0.25), residues: 486 sheet: 0.29 (0.39), residues: 181 loop : 0.05 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 5 TYR 0.009 0.001 TYR C 145 PHE 0.010 0.001 PHE A 842 TRP 0.003 0.001 TRP C 141 HIS 0.002 0.000 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9140) covalent geometry : angle 0.49970 (12390) SS BOND : bond 0.00703 ( 1) SS BOND : angle 5.16927 ( 2) hydrogen bonds : bond 0.04119 ( 423) hydrogen bonds : angle 4.61206 ( 1209) Misc. bond : bond 0.00074 ( 2) *********************** 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: 17 poor density : 102 time to evaluate : 0.360 Fit side-chains REVERT: A 85 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8144 (mt-10) REVERT: A 182 THR cc_start: 0.8794 (t) cc_final: 0.8542 (m) REVERT: A 185 ILE cc_start: 0.8788 (mt) cc_final: 0.8509 (mm) REVERT: A 228 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8317 (tttp) REVERT: A 230 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6673 (mm-30) REVERT: A 353 ASP cc_start: 0.8317 (t0) cc_final: 0.8109 (t0) REVERT: A 562 LEU cc_start: 0.8667 (tp) cc_final: 0.8443 (tt) REVERT: A 668 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8139 (mmm) REVERT: A 699 GLN cc_start: 0.8564 (mp10) cc_final: 0.7706 (mp10) REVERT: A 755 ASN cc_start: 0.8744 (m-40) cc_final: 0.8220 (p0) REVERT: A 879 LYS cc_start: 0.8686 (mmmm) cc_final: 0.8478 (mtmm) REVERT: A 909 ASN cc_start: 0.7545 (t0) cc_final: 0.7201 (t0) REVERT: A 980 LYS cc_start: 0.8197 (ttpp) cc_final: 0.7727 (ttpp) REVERT: C 8 ARG cc_start: 0.7710 (mtt-85) cc_final: 0.7502 (mtt90) REVERT: C 32 HIS cc_start: 0.8163 (t-170) cc_final: 0.7874 (t70) REVERT: C 143 ARG cc_start: 0.8112 (ttp80) cc_final: 0.7807 (tmm-80) outliers start: 17 outliers final: 6 residues processed: 112 average time/residue: 0.6886 time to fit residues: 81.0702 Evaluate side-chains 98 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 51 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 21 optimal weight: 0.0980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.130542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.095286 restraints weight = 11706.415| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.96 r_work: 0.2970 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9143 Z= 0.158 Angle : 0.520 11.344 12392 Z= 0.269 Chirality : 0.043 0.186 1374 Planarity : 0.004 0.046 1604 Dihedral : 6.334 84.422 1250 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.22 % Allowed : 11.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.26), residues: 1126 helix: 1.43 (0.24), residues: 492 sheet: 0.51 (0.39), residues: 173 loop : -0.03 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 139 TYR 0.013 0.001 TYR A 627 PHE 0.009 0.001 PHE A 237 TRP 0.005 0.001 TRP C 141 HIS 0.002 0.000 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 9140) covalent geometry : angle 0.51979 (12390) SS BOND : bond 0.02566 ( 1) SS BOND : angle 1.72018 ( 2) hydrogen bonds : bond 0.04149 ( 423) hydrogen bonds : angle 4.52653 ( 1209) Misc. bond : bond 0.00121 ( 2) *********************** 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 114 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.352 Fit side-chains REVERT: A 85 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8076 (mt-10) REVERT: A 182 THR cc_start: 0.8784 (t) cc_final: 0.8545 (m) REVERT: A 184 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7551 (ptp) REVERT: A 185 ILE cc_start: 0.8798 (mt) cc_final: 0.8544 (mm) REVERT: A 353 ASP cc_start: 0.8397 (t0) cc_final: 0.8140 (t0) REVERT: A 526 PHE cc_start: 0.9485 (OUTLIER) cc_final: 0.9110 (m-80) REVERT: A 562 LEU cc_start: 0.8676 (tp) cc_final: 0.8438 (tt) REVERT: A 668 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8190 (mmm) REVERT: A 699 GLN cc_start: 0.8625 (mp10) cc_final: 0.8357 (mp10) REVERT: A 755 ASN cc_start: 0.8780 (m-40) cc_final: 0.8227 (p0) REVERT: A 879 LYS cc_start: 0.8722 (mmmm) cc_final: 0.8456 (mtmm) REVERT: A 909 ASN cc_start: 0.7587 (t0) cc_final: 0.7225 (t0) REVERT: A 980 LYS cc_start: 0.8324 (ttpp) cc_final: 0.7783 (ttpp) REVERT: C 32 HIS cc_start: 0.8183 (t-170) cc_final: 0.7871 (t70) outliers start: 22 outliers final: 7 residues processed: 104 average time/residue: 0.7121 time to fit residues: 77.9279 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 : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 184 MET 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 0.3980 chunk 80 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 104 optimal weight: 0.0970 chunk 53 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.131029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.096784 restraints weight = 11904.484| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.00 r_work: 0.2965 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9143 Z= 0.133 Angle : 0.496 10.721 12392 Z= 0.256 Chirality : 0.042 0.155 1374 Planarity : 0.004 0.058 1604 Dihedral : 6.312 87.406 1250 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.22 % Allowed : 10.99 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.26), residues: 1126 helix: 1.59 (0.25), residues: 486 sheet: 0.43 (0.38), residues: 181 loop : -0.06 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 8 TYR 0.011 0.001 TYR C 145 PHE 0.009 0.001 PHE A 237 TRP 0.003 0.001 TRP A 702 HIS 0.002 0.000 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9140) covalent geometry : angle 0.49538 (12390) SS BOND : bond 0.01709 ( 1) SS BOND : angle 1.65096 ( 2) hydrogen bonds : bond 0.03802 ( 423) hydrogen bonds : angle 4.43434 ( 1209) Misc. bond : bond 0.00008 ( 2) *********************** 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 122 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.361 Fit side-chains REVERT: A 85 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8089 (mt-10) REVERT: A 185 ILE cc_start: 0.8746 (mt) cc_final: 0.8464 (mm) REVERT: A 353 ASP cc_start: 0.8431 (t0) cc_final: 0.8176 (t0) REVERT: A 526 PHE cc_start: 0.9485 (OUTLIER) cc_final: 0.9110 (m-80) REVERT: A 562 LEU cc_start: 0.8703 (tp) cc_final: 0.8463 (tt) REVERT: A 699 GLN cc_start: 0.8586 (mp10) cc_final: 0.8318 (mp10) REVERT: A 755 ASN cc_start: 0.8772 (m-40) cc_final: 0.8198 (p0) REVERT: A 879 LYS cc_start: 0.8731 (mmmm) cc_final: 0.8462 (mtmm) REVERT: A 909 ASN cc_start: 0.7475 (t0) cc_final: 0.7140 (t0) REVERT: A 980 LYS cc_start: 0.8357 (ttpp) cc_final: 0.7796 (ttpp) REVERT: C 32 HIS cc_start: 0.8173 (t-170) cc_final: 0.7818 (t70) REVERT: C 72 ARG cc_start: 0.8474 (tpp80) cc_final: 0.8260 (ttm-80) REVERT: C 143 ARG cc_start: 0.8144 (ttp80) cc_final: 0.7817 (tmm-80) outliers start: 22 outliers final: 11 residues processed: 114 average time/residue: 0.6451 time to fit residues: 77.6378 Evaluate side-chains 108 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 955 ASN 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 38 optimal weight: 0.0170 chunk 110 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 80 optimal weight: 0.2980 chunk 93 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.129849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.092345 restraints weight = 11636.394| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.48 r_work: 0.2915 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9143 Z= 0.125 Angle : 0.488 9.743 12392 Z= 0.253 Chirality : 0.042 0.157 1374 Planarity : 0.004 0.046 1604 Dihedral : 6.272 88.894 1250 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.32 % Allowed : 11.69 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.26), residues: 1126 helix: 1.58 (0.24), residues: 486 sheet: 0.43 (0.38), residues: 182 loop : -0.05 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 139 TYR 0.011 0.001 TYR C 145 PHE 0.008 0.001 PHE A 237 TRP 0.003 0.001 TRP A 702 HIS 0.002 0.000 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9140) covalent geometry : angle 0.48816 (12390) SS BOND : bond 0.01941 ( 1) SS BOND : angle 0.67076 ( 2) hydrogen bonds : bond 0.03640 ( 423) hydrogen bonds : angle 4.35952 ( 1209) Misc. bond : bond 0.00008 ( 2) *********************** 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 119 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.304 Fit side-chains REVERT: A 85 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8147 (mt-10) REVERT: A 112 VAL cc_start: 0.8649 (OUTLIER) cc_final: 0.8438 (m) REVERT: A 218 MET cc_start: 0.6427 (mtt) cc_final: 0.5774 (mmt) REVERT: A 353 ASP cc_start: 0.8458 (t0) cc_final: 0.8070 (t0) REVERT: A 562 LEU cc_start: 0.8244 (tp) cc_final: 0.8028 (tt) REVERT: A 699 GLN cc_start: 0.8468 (mp10) cc_final: 0.8109 (mp10) REVERT: A 755 ASN cc_start: 0.8850 (m-40) cc_final: 0.8050 (p0) REVERT: A 804 ARG cc_start: 0.8087 (mmt90) cc_final: 0.7755 (mmm-85) REVERT: A 879 LYS cc_start: 0.8469 (mmmm) cc_final: 0.7912 (mtmm) REVERT: A 909 ASN cc_start: 0.7399 (t0) cc_final: 0.7054 (t0) REVERT: A 980 LYS cc_start: 0.8219 (ttpp) cc_final: 0.7414 (ttpp) REVERT: C 32 HIS cc_start: 0.7910 (t-170) cc_final: 0.7303 (t70) REVERT: C 72 ARG cc_start: 0.8401 (tpp80) cc_final: 0.8077 (ttm-80) outliers start: 23 outliers final: 13 residues processed: 109 average time/residue: 0.7376 time to fit residues: 84.5028 Evaluate side-chains 110 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 112 VAL 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 497 ILE Chi-restraints excluded: chain A residue 955 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 56 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3567 r_free = 0.3567 target = 0.129638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.091096 restraints weight = 11664.852| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.30 r_work: 0.2912 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9143 Z= 0.130 Angle : 0.487 9.383 12392 Z= 0.251 Chirality : 0.042 0.158 1374 Planarity : 0.004 0.048 1604 Dihedral : 6.125 77.976 1250 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.22 % Allowed : 12.10 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.26), residues: 1126 helix: 1.57 (0.24), residues: 486 sheet: 0.13 (0.38), residues: 190 loop : 0.00 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 139 TYR 0.009 0.001 TYR C 74 PHE 0.008 0.001 PHE A 237 TRP 0.004 0.001 TRP A 669 HIS 0.002 0.000 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9140) covalent geometry : angle 0.48733 (12390) SS BOND : bond 0.01539 ( 1) SS BOND : angle 0.67899 ( 2) hydrogen bonds : bond 0.03619 ( 423) hydrogen bonds : angle 4.33130 ( 1209) Misc. bond : bond 0.00031 ( 2) *********************** 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 117 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.289 Fit side-chains REVERT: A 85 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8132 (mt-10) REVERT: A 112 VAL cc_start: 0.8617 (OUTLIER) cc_final: 0.8391 (m) REVERT: A 114 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8198 (tm-30) REVERT: A 184 MET cc_start: 0.7193 (ptp) cc_final: 0.6867 (ptm) REVERT: A 218 MET cc_start: 0.6466 (mtt) cc_final: 0.5803 (mmt) REVERT: A 353 ASP cc_start: 0.8462 (t0) cc_final: 0.8065 (t0) REVERT: A 526 PHE cc_start: 0.9252 (OUTLIER) cc_final: 0.8814 (m-80) REVERT: A 562 LEU cc_start: 0.8223 (tp) cc_final: 0.8021 (tt) REVERT: A 699 GLN cc_start: 0.8532 (mp10) cc_final: 0.8180 (mp10) REVERT: A 755 ASN cc_start: 0.8848 (m-40) cc_final: 0.8029 (p0) REVERT: A 879 LYS cc_start: 0.8453 (mmmm) cc_final: 0.7888 (mtmm) REVERT: A 909 ASN cc_start: 0.7397 (t0) cc_final: 0.7054 (t0) REVERT: A 980 LYS cc_start: 0.8172 (ttpp) cc_final: 0.7379 (ttpp) REVERT: C 32 HIS cc_start: 0.7889 (t-170) cc_final: 0.7281 (t70) REVERT: C 72 ARG cc_start: 0.8406 (tpp80) cc_final: 0.8073 (ttm-80) outliers start: 22 outliers final: 13 residues processed: 110 average time/residue: 0.7575 time to fit residues: 87.8618 Evaluate side-chains 112 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 112 VAL 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 497 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 3.9990 chunk 72 optimal weight: 0.0070 chunk 52 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 chunk 17 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 45 optimal weight: 0.3980 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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 = 0.130100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.093429 restraints weight = 11669.436| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.22 r_work: 0.2916 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9143 Z= 0.123 Angle : 0.490 9.638 12392 Z= 0.252 Chirality : 0.041 0.152 1374 Planarity : 0.004 0.046 1604 Dihedral : 5.995 70.375 1250 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.92 % Allowed : 13.10 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.26), residues: 1126 helix: 1.58 (0.24), residues: 486 sheet: 0.16 (0.38), residues: 190 loop : 0.01 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 139 TYR 0.009 0.001 TYR C 74 PHE 0.008 0.001 PHE A 237 TRP 0.004 0.001 TRP A 669 HIS 0.001 0.000 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9140) covalent geometry : angle 0.49024 (12390) SS BOND : bond 0.01119 ( 1) SS BOND : angle 0.93438 ( 2) hydrogen bonds : bond 0.03527 ( 423) hydrogen bonds : angle 4.29379 ( 1209) Misc. bond : bond 0.00033 ( 2) *********************** 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 116 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.393 Fit side-chains REVERT: A 85 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: A 112 VAL cc_start: 0.8632 (OUTLIER) cc_final: 0.8411 (m) REVERT: A 114 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8229 (tm-30) REVERT: A 184 MET cc_start: 0.7260 (ptp) cc_final: 0.6981 (ptm) REVERT: A 353 ASP cc_start: 0.8471 (t0) cc_final: 0.8081 (t0) REVERT: A 562 LEU cc_start: 0.8224 (tp) cc_final: 0.8007 (tt) REVERT: A 699 GLN cc_start: 0.8545 (mp10) cc_final: 0.8191 (mp10) REVERT: A 755 ASN cc_start: 0.8860 (m-40) cc_final: 0.8045 (p0) REVERT: A 879 LYS cc_start: 0.8472 (mmmm) cc_final: 0.7913 (mtmm) REVERT: A 909 ASN cc_start: 0.7416 (t0) cc_final: 0.7073 (t0) REVERT: A 980 LYS cc_start: 0.8195 (ttpp) cc_final: 0.7410 (ttpp) REVERT: C 32 HIS cc_start: 0.7884 (t-170) cc_final: 0.7297 (t70) REVERT: C 38 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8175 (mtm) REVERT: C 72 ARG cc_start: 0.8424 (tpp80) cc_final: 0.8102 (ttm-80) outliers start: 19 outliers final: 12 residues processed: 111 average time/residue: 0.7595 time to fit residues: 88.8788 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 : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 112 VAL 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 51 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 13 optimal weight: 0.0670 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 75 optimal weight: 6.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.129784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.091266 restraints weight = 11680.097| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.31 r_work: 0.2912 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9143 Z= 0.135 Angle : 0.501 11.116 12392 Z= 0.256 Chirality : 0.042 0.158 1374 Planarity : 0.004 0.046 1604 Dihedral : 5.972 66.446 1250 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.22 % Allowed : 12.80 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.26), residues: 1126 helix: 1.54 (0.24), residues: 487 sheet: 0.14 (0.38), residues: 190 loop : -0.02 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 139 TYR 0.009 0.001 TYR C 74 PHE 0.008 0.001 PHE A 677 TRP 0.004 0.001 TRP A 669 HIS 0.001 0.000 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9140) covalent geometry : angle 0.50118 (12390) SS BOND : bond 0.01220 ( 1) SS BOND : angle 0.92449 ( 2) hydrogen bonds : bond 0.03607 ( 423) hydrogen bonds : angle 4.31735 ( 1209) Misc. bond : bond 0.00026 ( 2) *********************** 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 117 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.371 Fit side-chains REVERT: A 85 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8115 (mt-10) REVERT: A 112 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8380 (m) REVERT: A 114 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8210 (tm-30) REVERT: A 184 MET cc_start: 0.7276 (ptp) cc_final: 0.6972 (ptm) REVERT: A 228 LYS cc_start: 0.8357 (mmmt) cc_final: 0.8049 (tppt) REVERT: A 353 ASP cc_start: 0.8445 (t0) cc_final: 0.8063 (t0) REVERT: A 562 LEU cc_start: 0.8182 (tp) cc_final: 0.7967 (tt) REVERT: A 699 GLN cc_start: 0.8564 (mp10) cc_final: 0.8300 (mp10) REVERT: A 755 ASN cc_start: 0.8865 (m-40) cc_final: 0.8045 (p0) REVERT: A 879 LYS cc_start: 0.8436 (mmmm) cc_final: 0.7886 (mtmm) REVERT: A 909 ASN cc_start: 0.7410 (t0) cc_final: 0.7073 (t0) REVERT: A 980 LYS cc_start: 0.8185 (ttpp) cc_final: 0.7393 (ttpp) REVERT: C 8 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7111 (mmm160) REVERT: C 32 HIS cc_start: 0.7861 (t-170) cc_final: 0.7462 (t-90) REVERT: C 38 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8179 (mtm) REVERT: C 72 ARG cc_start: 0.8426 (tpp80) cc_final: 0.8048 (ttm-80) outliers start: 22 outliers final: 14 residues processed: 110 average time/residue: 0.7577 time to fit residues: 88.0084 Evaluate side-chains 113 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 112 VAL 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 497 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 8 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 87 optimal weight: 0.0670 chunk 42 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 95 optimal weight: 0.4980 chunk 107 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.129932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.092191 restraints weight = 11645.141| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.42 r_work: 0.2907 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9143 Z= 0.133 Angle : 0.510 12.208 12392 Z= 0.261 Chirality : 0.042 0.150 1374 Planarity : 0.004 0.048 1604 Dihedral : 5.868 58.990 1250 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.81 % Allowed : 14.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.26), residues: 1126 helix: 1.56 (0.24), residues: 486 sheet: 0.13 (0.38), residues: 190 loop : -0.02 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 139 TYR 0.028 0.001 TYR C 145 PHE 0.008 0.001 PHE A 677 TRP 0.004 0.001 TRP A 669 HIS 0.001 0.000 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9140) covalent geometry : angle 0.50947 (12390) SS BOND : bond 0.01066 ( 1) SS BOND : angle 0.93034 ( 2) hydrogen bonds : bond 0.03616 ( 423) hydrogen bonds : angle 4.30632 ( 1209) Misc. bond : bond 0.00031 ( 2) *********************** 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 114 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.377 Fit side-chains REVERT: A 32 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8040 (mmm) REVERT: A 85 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8122 (mt-10) REVERT: A 112 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8404 (m) REVERT: A 114 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8230 (tm-30) REVERT: A 184 MET cc_start: 0.7221 (ptp) cc_final: 0.6953 (ptm) REVERT: A 353 ASP cc_start: 0.8457 (t0) cc_final: 0.8082 (t0) REVERT: A 562 LEU cc_start: 0.8218 (tp) cc_final: 0.8001 (tt) REVERT: A 699 GLN cc_start: 0.8564 (mp10) cc_final: 0.8301 (mp10) REVERT: A 755 ASN cc_start: 0.8867 (m-40) cc_final: 0.8057 (p0) REVERT: A 879 LYS cc_start: 0.8459 (mmmm) cc_final: 0.7913 (mtmm) REVERT: A 909 ASN cc_start: 0.7401 (t0) cc_final: 0.7080 (t0) REVERT: A 980 LYS cc_start: 0.8199 (ttpp) cc_final: 0.7412 (ttpp) REVERT: C 32 HIS cc_start: 0.7881 (t-170) cc_final: 0.7489 (t-90) REVERT: C 38 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8181 (mtm) REVERT: C 72 ARG cc_start: 0.8533 (tpp80) cc_final: 0.8132 (ttm-80) outliers start: 18 outliers final: 12 residues processed: 109 average time/residue: 0.7524 time to fit residues: 86.4838 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 : 0.334 ------------------------------------------------------------------------------- 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 112 VAL 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 8 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 109 optimal weight: 0.0050 chunk 86 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.129771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.092809 restraints weight = 11580.936| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.37 r_work: 0.2905 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9143 Z= 0.141 Angle : 0.520 13.001 12392 Z= 0.265 Chirality : 0.042 0.161 1374 Planarity : 0.004 0.050 1604 Dihedral : 5.815 59.227 1250 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.81 % Allowed : 14.31 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.26), residues: 1126 helix: 1.52 (0.24), residues: 486 sheet: 0.03 (0.37), residues: 200 loop : -0.00 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 139 TYR 0.021 0.001 TYR C 145 PHE 0.009 0.001 PHE A 677 TRP 0.004 0.001 TRP A 669 HIS 0.002 0.000 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9140) covalent geometry : angle 0.52037 (12390) SS BOND : bond 0.01159 ( 1) SS BOND : angle 0.94833 ( 2) hydrogen bonds : bond 0.03738 ( 423) hydrogen bonds : angle 4.32623 ( 1209) Misc. bond : bond 0.00036 ( 2) ********************** 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 114 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.379 Fit side-chains REVERT: A 32 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8199 (mmm) REVERT: A 85 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8115 (mt-10) REVERT: A 112 VAL cc_start: 0.8633 (OUTLIER) cc_final: 0.8407 (m) REVERT: A 114 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8232 (tm-30) REVERT: A 184 MET cc_start: 0.7177 (ptp) cc_final: 0.6941 (ptm) REVERT: A 353 ASP cc_start: 0.8468 (t0) cc_final: 0.8090 (t0) REVERT: A 562 LEU cc_start: 0.8251 (tp) cc_final: 0.8035 (tt) REVERT: A 699 GLN cc_start: 0.8581 (mp10) cc_final: 0.8322 (mp10) REVERT: A 755 ASN cc_start: 0.8871 (m-40) cc_final: 0.8056 (p0) REVERT: A 804 ARG cc_start: 0.7780 (mmt90) cc_final: 0.7543 (mmm-85) REVERT: A 879 LYS cc_start: 0.8456 (mmmm) cc_final: 0.7907 (mtmm) REVERT: A 909 ASN cc_start: 0.7411 (t0) cc_final: 0.7098 (t0) REVERT: A 980 LYS cc_start: 0.8207 (ttpp) cc_final: 0.7420 (ttpp) REVERT: C 32 HIS cc_start: 0.7902 (t-170) cc_final: 0.7516 (t-90) REVERT: C 38 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8180 (mtm) REVERT: C 72 ARG cc_start: 0.8515 (tpp80) cc_final: 0.8116 (ttm-80) outliers start: 18 outliers final: 12 residues processed: 109 average time/residue: 0.7756 time to fit residues: 89.4108 Evaluate side-chains 111 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 112 VAL 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 7 optimal weight: 0.7980 chunk 87 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 0.0000 chunk 101 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 108 optimal weight: 0.6980 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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 = 0.3571 r_free = 0.3571 target = 0.129987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.093138 restraints weight = 11511.592| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.35 r_work: 0.2913 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9143 Z= 0.128 Angle : 0.512 11.265 12392 Z= 0.262 Chirality : 0.042 0.150 1374 Planarity : 0.004 0.051 1604 Dihedral : 5.759 58.892 1250 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.61 % Allowed : 14.72 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.26), residues: 1126 helix: 1.57 (0.24), residues: 486 sheet: 0.05 (0.37), residues: 200 loop : 0.01 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 139 TYR 0.039 0.001 TYR C 145 PHE 0.008 0.001 PHE A 677 TRP 0.004 0.001 TRP A 669 HIS 0.002 0.000 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9140) covalent geometry : angle 0.51176 (12390) SS BOND : bond 0.01261 ( 1) SS BOND : angle 1.00339 ( 2) hydrogen bonds : bond 0.03601 ( 423) hydrogen bonds : angle 4.29678 ( 1209) Misc. bond : bond 0.00031 ( 2) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 3090.01 seconds wall clock time: 53 minutes 12.70 seconds (3192.70 seconds total)