Starting phenix.real_space_refine on Thu Jul 2 11:57:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xcm_38247/07_2026/8xcm_38247.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xcm_38247/07_2026/8xcm_38247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xcm_38247/07_2026/8xcm_38247.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xcm_38247/07_2026/8xcm_38247.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xcm_38247/07_2026/8xcm_38247.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xcm_38247/07_2026/8xcm_38247.map" } resolution = 3.08 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= 0.001 sd= 0.014 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 Fe 6 7.16 5 P 2 5.49 5 S 46 5.16 5 C 5422 2.51 5 N 1490 2.21 5 O 1639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8605 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4168 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 503} Chain: "B" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1080 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "C" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3130 Classifications: {'peptide': 413} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 387} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'F3S': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 167 Unusual residues: {'HEC': 3, 'U10': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1} Unresolved non-hydrogen planarities: 25 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1767 SG CYS A 226 53.333 64.114 34.976 1.00127.49 S ATOM 1738 SG CYS A 222 53.792 68.828 30.722 1.00131.05 S ATOM 1698 SG CYS A 216 52.555 63.628 28.263 1.00131.75 S Time building chain proxies: 1.90, per 1000 atoms: 0.22 Number of scatterers: 8605 At special positions: 0 Unit cell: (104.06, 108.36, 75.68, 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) Fe 6 26.01 S 46 16.00 P 2 15.00 O 1639 8.00 N 1490 7.00 C 5422 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 205.5 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S A 602 " pdb="FE4 F3S A 602 " - pdb=" SG CYS A 216 " pdb="FE1 F3S A 602 " - pdb=" SG CYS A 226 " pdb="FE3 F3S A 602 " - pdb=" SG CYS A 222 " Number of angles added : 9 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 8 sheets defined 40.3% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 16 through 29 Processing helix chain 'A' and resid 43 through 53 Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.584A pdb=" N GLN A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.556A pdb=" N TYR A 96 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS A 97 " --> pdb=" O THR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 124 through 130 Processing helix chain 'A' and resid 138 through 154 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 233 through 245 removed outlier: 4.171A pdb=" N ALA A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 355 through 360 removed outlier: 3.883A pdb=" N ARG A 358 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 359 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 387 through 401 Processing helix chain 'A' and resid 441 through 463 removed outlier: 3.739A pdb=" N ILE A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 541 Processing helix chain 'B' and resid 49 through 63 Processing helix chain 'B' and resid 68 through 83 Processing helix chain 'B' and resid 85 through 100 Processing helix chain 'B' and resid 104 through 111 removed outlier: 3.791A pdb=" N LEU B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 150 through 154 Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.848A pdb=" N VAL B 171 " --> pdb=" O ASN B 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 51 Processing helix chain 'C' and resid 52 through 57 removed outlier: 3.547A pdb=" N HIS C 56 " --> pdb=" O CYS C 52 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 52 through 57' Processing helix chain 'C' and resid 95 through 105 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 127 through 141 Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 185 through 197 Processing helix chain 'C' and resid 201 through 206 Processing helix chain 'C' and resid 245 through 255 Processing helix chain 'C' and resid 265 through 274 Processing helix chain 'C' and resid 279 through 291 Processing helix chain 'C' and resid 318 through 322 removed outlier: 3.746A pdb=" N SER C 322 " --> pdb=" O ASN C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 373 through 382 Processing helix chain 'C' and resid 408 through 423 Processing helix chain 'C' and resid 431 through 441 Processing helix chain 'C' and resid 447 through 451 Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.464A pdb=" N VAL A 10 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU A 36 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE A 12 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.618A pdb=" N ILE A 87 " --> pdb=" O VAL A 436 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 200 removed outlier: 5.297A pdb=" N SER A 347 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR A 368 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ASP A 404 " --> pdb=" O ASN A 369 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N SER A 330 " --> pdb=" O ILE A 467 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ILE A 467 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 253 through 259 removed outlier: 6.280A pdb=" N VAL A 254 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE A 270 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ALA A 256 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ILE A 268 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLU A 258 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 270 " --> pdb=" O HIS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 321 through 322 Processing sheet with id=AA6, first strand: chain 'C' and resid 70 through 73 Processing sheet with id=AA7, first strand: chain 'C' and resid 223 through 224 Processing sheet with id=AA8, first strand: chain 'C' and resid 387 through 388 304 hydrogen bonds defined for protein. 849 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: 0.81 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.76: 8746 1.76 - 2.30: 90 2.30 - 2.84: 0 2.84 - 3.38: 0 3.38 - 3.92: 3 Bond restraints: 8839 Sorted by residual: bond pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 2.300 3.922 -1.622 2.00e-02 2.50e+03 6.58e+03 bond pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 2.258 3.801 -1.543 2.00e-02 2.50e+03 5.95e+03 bond pdb=" S4 F3S A 602 " pdb="FE1 F3S A 602 " ideal model delta sigma weight residual 2.233 3.708 -1.475 2.00e-02 2.50e+03 5.44e+03 bond pdb=" C2D HEC C 502 " pdb=" C3D HEC C 502 " ideal model delta sigma weight residual 1.544 1.325 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C2D HEC C 503 " pdb=" C3D HEC C 503 " ideal model delta sigma weight residual 1.544 1.333 0.211 2.00e-02 2.50e+03 1.12e+02 ... (remaining 8834 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.38: 12065 9.38 - 18.75: 8 18.75 - 28.13: 0 28.13 - 37.51: 8 37.51 - 46.89: 2 Bond angle restraints: 12083 Sorted by residual: angle pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " pdb=" S3 F3S A 602 " ideal model delta sigma weight residual 114.75 67.86 46.89 3.00e+00 1.11e-01 2.44e+02 angle pdb=" S3 F3S A 602 " pdb="FE1 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 112.59 71.35 41.24 3.00e+00 1.11e-01 1.89e+02 angle pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 103.26 67.65 35.61 3.00e+00 1.11e-01 1.41e+02 angle pdb="FE3 F3S A 602 " pdb=" S2 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 71.75 38.28 33.47 3.00e+00 1.11e-01 1.24e+02 angle pdb="FE1 F3S A 602 " pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 72.09 38.78 33.31 3.00e+00 1.11e-01 1.23e+02 ... (remaining 12078 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4436 17.92 - 35.84: 590 35.84 - 53.76: 166 53.76 - 71.68: 24 71.68 - 89.60: 13 Dihedral angle restraints: 5229 sinusoidal: 2077 harmonic: 3152 Sorted by residual: dihedral pdb=" CA ALA C 117 " pdb=" C ALA C 117 " pdb=" N MET C 118 " pdb=" CA MET C 118 " ideal model delta harmonic sigma weight residual 180.00 150.36 29.64 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA MET C 395 " pdb=" C MET C 395 " pdb=" N PRO C 396 " pdb=" CA PRO C 396 " ideal model delta harmonic sigma weight residual 180.00 151.54 28.46 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" C2C HEC C 503 " pdb=" C3C HEC C 503 " pdb=" CAC HEC C 503 " pdb=" CBC HEC C 503 " ideal model delta sinusoidal sigma weight residual 60.00 11.00 49.00 2 1.00e+01 1.00e-02 2.73e+01 ... (remaining 5226 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.271: 1276 3.271 - 6.543: 0 6.543 - 9.814: 0 9.814 - 13.085: 0 13.085 - 16.356: 1 Chirality restraints: 1277 Sorted by residual: chirality pdb=" S2 F3S A 602 " pdb="FE1 F3S A 602 " pdb="FE3 F3S A 602 " pdb="FE4 F3S A 602 " both_signs ideal model delta sigma weight residual False 10.77 -5.59 16.36 2.00e-01 2.50e+01 6.69e+03 chirality pdb=" CB ILE C 393 " pdb=" CA ILE C 393 " pdb=" CG1 ILE C 393 " pdb=" CG2 ILE C 393 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA PRO B 160 " pdb=" N PRO B 160 " pdb=" C PRO B 160 " pdb=" CB PRO B 160 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.44e-01 ... (remaining 1274 not shown) Planarity restraints: 1569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U10 C 504 " 0.114 2.00e-02 2.50e+03 1.89e-01 1.07e+03 pdb=" C1M U10 C 504 " 0.160 2.00e-02 2.50e+03 pdb=" C2 U10 C 504 " -0.016 2.00e-02 2.50e+03 pdb=" C3 U10 C 504 " -0.053 2.00e-02 2.50e+03 pdb=" C4 U10 C 504 " 0.009 2.00e-02 2.50e+03 pdb=" C5 U10 C 504 " 0.146 2.00e-02 2.50e+03 pdb=" C6 U10 C 504 " 0.191 2.00e-02 2.50e+03 pdb=" C7 U10 C 504 " -0.189 2.00e-02 2.50e+03 pdb=" O2 U10 C 504 " -0.411 2.00e-02 2.50e+03 pdb=" O3 U10 C 504 " 0.300 2.00e-02 2.50e+03 pdb=" O4 U10 C 504 " -0.148 2.00e-02 2.50e+03 pdb=" O5 U10 C 504 " -0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 U10 C 504 " 0.021 2.00e-02 2.50e+03 2.16e-01 5.83e+02 pdb=" C11 U10 C 504 " -0.179 2.00e-02 2.50e+03 pdb=" C7 U10 C 504 " -0.262 2.00e-02 2.50e+03 pdb=" C8 U10 C 504 " 0.358 2.00e-02 2.50e+03 pdb=" C9 U10 C 504 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C27 U10 C 504 " -0.122 2.00e-02 2.50e+03 9.93e-02 1.23e+02 pdb=" C28 U10 C 504 " 0.157 2.00e-02 2.50e+03 pdb=" C29 U10 C 504 " 0.028 2.00e-02 2.50e+03 pdb=" C30 U10 C 504 " 0.027 2.00e-02 2.50e+03 pdb=" C31 U10 C 504 " -0.090 2.00e-02 2.50e+03 ... (remaining 1566 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 252 2.67 - 3.23: 8905 3.23 - 3.79: 14843 3.79 - 4.34: 19937 4.34 - 4.90: 31824 Nonbonded interactions: 75761 Sorted by model distance: nonbonded pdb=" OH TYR A 79 " pdb=" O GLN A 98 " model vdw 2.118 3.040 nonbonded pdb=" OH TYR A 118 " pdb=" OG SER A 522 " model vdw 2.132 3.040 nonbonded pdb=" OH TYR A 145 " pdb=" OD2 ASP A 535 " model vdw 2.132 3.040 nonbonded pdb=" OH TYR A 118 " pdb=" O SER A 517 " model vdw 2.165 3.040 nonbonded pdb=" OD1 ASN A 369 " pdb=" OG1 THR A 371 " model vdw 2.187 3.040 ... (remaining 75756 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: 1.560 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.210 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 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 : 0.030 1.622 8854 Z= 1.483 Angle : 1.395 46.886 12092 Z= 0.540 Chirality : 0.460 16.356 1277 Planarity : 0.011 0.216 1569 Dihedral : 17.818 89.597 3217 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.68 % Allowed : 29.23 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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 are not related in a simple way. whole: -0.04 (0.26), residues: 1083 helix: 1.25 (0.28), residues: 375 sheet: -1.91 (0.65), residues: 58 loop : -0.59 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 172 TYR 0.023 0.002 TYR A 271 PHE 0.012 0.001 PHE A 270 TRP 0.016 0.001 TRP A 51 HIS 0.006 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.02991 / 1.48 ( 8839) covalent geometry : angle 1.35305 / 0.54 (12083) hydrogen bonds : bond 0.16807 / 11.04 ( 304) hydrogen bonds : angle 6.94723 / 5.18 ( 849) metal coordination : bond 0.00238 / 0.12 ( 3) metal coordination : angle 12.47362 / 10.61 ( 9) Misc. bond : bond 0.06990 / 3.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8366 (t0) cc_final: 0.7955 (m-30) REVERT: A 146 TYR cc_start: 0.7958 (OUTLIER) cc_final: 0.7608 (t80) REVERT: A 262 LYS cc_start: 0.9159 (tptp) cc_final: 0.8807 (tppt) REVERT: A 490 ARG cc_start: 0.8281 (ptt-90) cc_final: 0.7776 (pmt-80) REVERT: B 141 VAL cc_start: 0.8530 (t) cc_final: 0.8256 (p) REVERT: B 169 TYR cc_start: 0.9015 (p90) cc_final: 0.8720 (p90) REVERT: C 120 TYR cc_start: 0.8737 (p90) cc_final: 0.8387 (p90) REVERT: C 172 ARG cc_start: 0.8618 (ttp-110) cc_final: 0.7719 (mmt-90) outliers start: 6 outliers final: 2 residues processed: 144 average time/residue: 0.0825 time to fit residues: 16.4471 Evaluate side-chains 127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 124 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 30.0000 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN A 221 ASN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 GLN ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.090424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.073137 restraints weight = 17884.946| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.18 r_work: 0.2884 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.186 8854 Z= 0.194 Angle : 1.417 72.401 12092 Z= 0.429 Chirality : 0.082 2.438 1277 Planarity : 0.006 0.068 1569 Dihedral : 9.637 79.357 1290 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.16 % Allowed : 24.15 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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 are not related in a simple way. whole: 0.06 (0.26), residues: 1083 helix: 1.33 (0.28), residues: 381 sheet: -1.85 (0.61), residues: 62 loop : -0.54 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 60 TYR 0.017 0.002 TYR A 271 PHE 0.014 0.002 PHE B 86 TRP 0.016 0.001 TRP A 51 HIS 0.004 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 ( 8839) covalent geometry : angle 1.06024 / 0.42 (12083) hydrogen bonds : bond 0.03405 / 2.39 ( 304) hydrogen bonds : angle 5.34437 / 3.94 ( 849) metal coordination : bond 0.01211 / 0.60 ( 3) metal coordination : angle 34.45787 / 21.14 ( 9) Misc. bond : bond 0.06877 / 3.73 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.8765 (tp40) cc_final: 0.8315 (tp-100) REVERT: A 57 ASP cc_start: 0.8383 (t0) cc_final: 0.7928 (m-30) REVERT: A 98 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8441 (mm110) REVERT: A 221 ASN cc_start: 0.8409 (t0) cc_final: 0.7856 (t0) REVERT: A 262 LYS cc_start: 0.9106 (tptp) cc_final: 0.8882 (tppp) REVERT: A 266 THR cc_start: 0.8631 (m) cc_final: 0.8401 (p) REVERT: A 285 PHE cc_start: 0.7627 (m-80) cc_final: 0.7418 (m-80) REVERT: A 305 ARG cc_start: 0.8353 (tpt90) cc_final: 0.7310 (ttm110) REVERT: A 456 MET cc_start: 0.8686 (mmm) cc_final: 0.8454 (tpp) REVERT: A 490 ARG cc_start: 0.8431 (ptt-90) cc_final: 0.7933 (pmt-80) REVERT: A 535 ASP cc_start: 0.8587 (t0) cc_final: 0.8002 (m-30) REVERT: B 100 ASN cc_start: 0.8293 (t0) cc_final: 0.8025 (t0) REVERT: B 141 VAL cc_start: 0.8642 (t) cc_final: 0.8397 (p) REVERT: C 118 MET cc_start: 0.8655 (tpt) cc_final: 0.7534 (tpt) REVERT: C 120 TYR cc_start: 0.8810 (p90) cc_final: 0.8336 (p90) REVERT: C 395 MET cc_start: 0.8073 (tpt) cc_final: 0.7639 (tpt) outliers start: 28 outliers final: 18 residues processed: 167 average time/residue: 0.0848 time to fit residues: 19.8847 Evaluate side-chains 146 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 15 optimal weight: 0.8980 chunk 94 optimal weight: 8.9990 chunk 50 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN A 98 GLN ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.091762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.073817 restraints weight = 17885.733| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.21 r_work: 0.2892 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 8854 Z= 0.168 Angle : 1.433 83.133 12092 Z= 0.420 Chirality : 0.061 1.504 1277 Planarity : 0.005 0.059 1569 Dihedral : 9.297 81.387 1289 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.51 % Allowed : 22.46 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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 are not related in a simple way. whole: 0.21 (0.26), residues: 1083 helix: 1.48 (0.28), residues: 381 sheet: -1.24 (0.61), residues: 72 loop : -0.52 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 161 TYR 0.019 0.001 TYR A 79 PHE 0.013 0.001 PHE B 86 TRP 0.013 0.001 TRP A 51 HIS 0.004 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 8839) covalent geometry : angle 1.06383 / 0.41 (12083) hydrogen bonds : bond 0.03127 / 2.20 ( 304) hydrogen bonds : angle 5.05050 / 3.75 ( 849) metal coordination : bond 0.00506 / 0.25 ( 3) metal coordination : angle 35.20926 / 20.67 ( 9) Misc. bond : bond 0.04912 / 2.61 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 133 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.8717 (tp40) cc_final: 0.8316 (tp-100) REVERT: A 57 ASP cc_start: 0.8412 (t0) cc_final: 0.7881 (m-30) REVERT: A 156 MET cc_start: 0.8725 (mtp) cc_final: 0.8274 (mtp) REVERT: A 175 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7014 (mmt) REVERT: A 305 ARG cc_start: 0.8480 (tpt90) cc_final: 0.7345 (ttm110) REVERT: A 490 ARG cc_start: 0.8556 (ptt-90) cc_final: 0.8032 (pmt-80) REVERT: A 535 ASP cc_start: 0.8571 (t0) cc_final: 0.8044 (m-30) REVERT: B 49 ASP cc_start: 0.8412 (m-30) cc_final: 0.8022 (t0) REVERT: B 100 ASN cc_start: 0.8393 (t0) cc_final: 0.8190 (t0) REVERT: B 141 VAL cc_start: 0.8637 (t) cc_final: 0.8407 (p) REVERT: B 173 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8497 (mm-30) REVERT: C 118 MET cc_start: 0.8658 (tpt) cc_final: 0.7725 (tpt) REVERT: C 161 ARG cc_start: 0.8368 (ptp-110) cc_final: 0.7706 (ttm170) REVERT: C 395 MET cc_start: 0.8123 (tpt) cc_final: 0.7785 (tpt) outliers start: 40 outliers final: 23 residues processed: 161 average time/residue: 0.0861 time to fit residues: 19.6402 Evaluate side-chains 141 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 80 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 HIS A 505 ASN B 123 GLN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.091392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.073368 restraints weight = 18039.188| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.22 r_work: 0.2881 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 8854 Z= 0.169 Angle : 1.430 83.577 12092 Z= 0.420 Chirality : 0.061 1.487 1277 Planarity : 0.005 0.057 1569 Dihedral : 9.157 82.537 1289 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 5.19 % Allowed : 21.33 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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 are not related in a simple way. whole: 0.27 (0.26), residues: 1083 helix: 1.60 (0.28), residues: 381 sheet: -1.33 (0.61), residues: 72 loop : -0.51 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 264 TYR 0.015 0.001 TYR A 271 PHE 0.013 0.001 PHE A 80 TRP 0.012 0.001 TRP A 51 HIS 0.004 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 ( 8839) covalent geometry : angle 1.06351 / 0.41 (12083) hydrogen bonds : bond 0.02977 / 2.12 ( 304) hydrogen bonds : angle 4.89952 / 3.64 ( 849) metal coordination : bond 0.00304 / 0.15 ( 3) metal coordination : angle 35.06645 / 20.73 ( 9) Misc. bond : bond 0.04375 / 2.32 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 120 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8443 (t0) cc_final: 0.8033 (m-30) REVERT: A 156 MET cc_start: 0.8741 (mtp) cc_final: 0.8326 (mtp) REVERT: A 175 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7017 (mmt) REVERT: A 247 LYS cc_start: 0.7964 (mmmm) cc_final: 0.7635 (tttm) REVERT: A 305 ARG cc_start: 0.8513 (tpt90) cc_final: 0.7412 (ttm110) REVERT: A 477 GLN cc_start: 0.8654 (mp10) cc_final: 0.8183 (mp10) REVERT: A 535 ASP cc_start: 0.8588 (t0) cc_final: 0.8063 (m-30) REVERT: B 49 ASP cc_start: 0.8407 (m-30) cc_final: 0.8087 (t0) REVERT: B 100 ASN cc_start: 0.8377 (t0) cc_final: 0.8126 (t0) REVERT: B 141 VAL cc_start: 0.8646 (t) cc_final: 0.8414 (p) REVERT: B 173 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8572 (mm-30) REVERT: C 118 MET cc_start: 0.8701 (tpt) cc_final: 0.7883 (tpt) REVERT: C 395 MET cc_start: 0.8185 (tpt) cc_final: 0.7766 (tpt) outliers start: 46 outliers final: 32 residues processed: 156 average time/residue: 0.0861 time to fit residues: 19.4480 Evaluate side-chains 145 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 56 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 99 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.088139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.070758 restraints weight = 17788.305| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.17 r_work: 0.2836 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.133 8854 Z= 0.171 Angle : 1.426 83.649 12092 Z= 0.417 Chirality : 0.061 1.482 1277 Planarity : 0.005 0.055 1569 Dihedral : 9.087 83.617 1289 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.74 % Allowed : 21.22 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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 are not related in a simple way. whole: 0.42 (0.26), residues: 1083 helix: 1.79 (0.28), residues: 374 sheet: -1.19 (0.64), residues: 72 loop : -0.44 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 490 TYR 0.014 0.001 TYR A 271 PHE 0.015 0.001 PHE B 60 TRP 0.012 0.001 TRP A 51 HIS 0.004 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 ( 8839) covalent geometry : angle 1.05934 / 0.41 (12083) hydrogen bonds : bond 0.02899 / 2.06 ( 304) hydrogen bonds : angle 4.82099 / 3.58 ( 849) metal coordination : bond 0.00308 / 0.15 ( 3) metal coordination : angle 35.02600 / 20.76 ( 9) Misc. bond : bond 0.04133 / 2.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 121 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.9051 (t0) cc_final: 0.8754 (t0) REVERT: A 156 MET cc_start: 0.8723 (mtp) cc_final: 0.8381 (mtp) REVERT: A 175 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.7070 (mmt) REVERT: A 247 LYS cc_start: 0.8088 (mmmm) cc_final: 0.7776 (tttm) REVERT: A 305 ARG cc_start: 0.8565 (tpt90) cc_final: 0.7472 (ttm110) REVERT: A 477 GLN cc_start: 0.8729 (mp10) cc_final: 0.8428 (mp10) REVERT: A 535 ASP cc_start: 0.8580 (t0) cc_final: 0.8110 (m-30) REVERT: B 49 ASP cc_start: 0.8406 (m-30) cc_final: 0.8094 (t0) REVERT: B 100 ASN cc_start: 0.8420 (t0) cc_final: 0.8202 (t0) REVERT: B 141 VAL cc_start: 0.8687 (t) cc_final: 0.8445 (p) REVERT: B 173 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8634 (mm-30) REVERT: B 177 VAL cc_start: 0.8841 (m) cc_final: 0.8546 (t) REVERT: C 118 MET cc_start: 0.8769 (tpt) cc_final: 0.7936 (tpt) REVERT: C 395 MET cc_start: 0.8194 (tpt) cc_final: 0.7500 (tpt) outliers start: 42 outliers final: 33 residues processed: 151 average time/residue: 0.0888 time to fit residues: 19.1394 Evaluate side-chains 146 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 2 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 93 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 19 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 0.0980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.088337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.070328 restraints weight = 18015.150| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.07 r_work: 0.2828 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.151 8854 Z= 0.193 Angle : 1.445 83.790 12092 Z= 0.424 Chirality : 0.061 1.479 1277 Planarity : 0.005 0.053 1569 Dihedral : 9.095 85.303 1289 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 5.08 % Allowed : 21.67 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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 are not related in a simple way. whole: 0.42 (0.27), residues: 1083 helix: 1.78 (0.28), residues: 374 sheet: -1.25 (0.65), residues: 72 loop : -0.43 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 60 TYR 0.014 0.001 TYR A 271 PHE 0.018 0.001 PHE A 80 TRP 0.011 0.001 TRP A 51 HIS 0.004 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.19 ( 8839) covalent geometry : angle 1.07143 / 0.42 (12083) hydrogen bonds : bond 0.02979 / 2.10 ( 304) hydrogen bonds : angle 4.82836 / 3.58 ( 849) metal coordination : bond 0.00374 / 0.19 ( 3) metal coordination : angle 35.56604 / 20.83 ( 9) Misc. bond : bond 0.04930 / 2.70 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 122 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8124 (m-30) REVERT: A 84 ASN cc_start: 0.8986 (t0) cc_final: 0.8740 (t0) REVERT: A 156 MET cc_start: 0.8726 (mtp) cc_final: 0.8347 (mtp) REVERT: A 175 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.6915 (mmt) REVERT: A 247 LYS cc_start: 0.8065 (mmmm) cc_final: 0.7755 (tttm) REVERT: A 305 ARG cc_start: 0.8690 (tpt90) cc_final: 0.7460 (ttm110) REVERT: A 477 GLN cc_start: 0.8731 (mp10) cc_final: 0.8390 (mp10) REVERT: A 535 ASP cc_start: 0.8587 (t0) cc_final: 0.8144 (m-30) REVERT: B 49 ASP cc_start: 0.8381 (m-30) cc_final: 0.8041 (t0) REVERT: B 104 ASP cc_start: 0.8421 (m-30) cc_final: 0.7485 (p0) REVERT: B 141 VAL cc_start: 0.8697 (t) cc_final: 0.8458 (p) REVERT: B 173 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8650 (mm-30) REVERT: C 118 MET cc_start: 0.8788 (tpt) cc_final: 0.7905 (tpt) REVERT: C 328 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8391 (p) REVERT: C 395 MET cc_start: 0.8237 (tpt) cc_final: 0.7705 (tpt) outliers start: 45 outliers final: 31 residues processed: 156 average time/residue: 0.0852 time to fit residues: 19.2275 Evaluate side-chains 147 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 95 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 92 optimal weight: 0.4980 chunk 103 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN B 123 GLN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.089665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.071933 restraints weight = 18112.240| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.07 r_work: 0.2863 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 8854 Z= 0.162 Angle : 1.427 83.582 12092 Z= 0.415 Chirality : 0.060 1.475 1277 Planarity : 0.005 0.055 1569 Dihedral : 8.998 86.260 1289 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.72 % Allowed : 23.14 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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 are not related in a simple way. whole: 0.45 (0.27), residues: 1083 helix: 1.81 (0.28), residues: 374 sheet: -1.28 (0.63), residues: 72 loop : -0.41 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 490 TYR 0.014 0.001 TYR A 271 PHE 0.017 0.001 PHE B 60 TRP 0.011 0.001 TRP A 51 HIS 0.004 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 ( 8839) covalent geometry : angle 1.05554 / 0.41 (12083) hydrogen bonds : bond 0.02830 / 2.00 ( 304) hydrogen bonds : angle 4.73576 / 3.52 ( 849) metal coordination : bond 0.00298 / 0.15 ( 3) metal coordination : angle 35.20653 / 20.91 ( 9) Misc. bond : bond 0.04033 / 2.14 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8994 (t0) cc_final: 0.8679 (t0) REVERT: A 156 MET cc_start: 0.8675 (mtp) cc_final: 0.8306 (mtp) REVERT: A 175 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.6997 (mmt) REVERT: A 247 LYS cc_start: 0.7988 (mmmm) cc_final: 0.7683 (tttm) REVERT: A 305 ARG cc_start: 0.8676 (tpt90) cc_final: 0.7551 (ttm110) REVERT: A 526 MET cc_start: 0.8272 (mtm) cc_final: 0.7868 (mtt) REVERT: A 535 ASP cc_start: 0.8565 (t0) cc_final: 0.8148 (m-30) REVERT: B 49 ASP cc_start: 0.8351 (m-30) cc_final: 0.8015 (t0) REVERT: B 104 ASP cc_start: 0.8431 (m-30) cc_final: 0.7505 (p0) REVERT: B 141 VAL cc_start: 0.8658 (t) cc_final: 0.8426 (p) REVERT: B 173 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8655 (mm-30) REVERT: B 177 VAL cc_start: 0.8853 (m) cc_final: 0.8600 (t) REVERT: C 118 MET cc_start: 0.8786 (tpt) cc_final: 0.7921 (tpt) REVERT: C 182 HIS cc_start: 0.9196 (m90) cc_final: 0.8962 (m-70) REVERT: C 328 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8401 (p) REVERT: C 395 MET cc_start: 0.8155 (tpt) cc_final: 0.7607 (tpt) outliers start: 33 outliers final: 28 residues processed: 149 average time/residue: 0.0910 time to fit residues: 19.3170 Evaluate side-chains 142 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 21 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 67 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.090538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.072984 restraints weight = 17978.187| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.08 r_work: 0.2884 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 8854 Z= 0.153 Angle : 1.412 83.545 12092 Z= 0.412 Chirality : 0.060 1.479 1277 Planarity : 0.005 0.063 1569 Dihedral : 8.958 87.322 1289 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.95 % Allowed : 22.91 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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 are not related in a simple way. whole: 0.42 (0.26), residues: 1083 helix: 1.79 (0.28), residues: 376 sheet: -1.38 (0.63), residues: 74 loop : -0.43 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 490 TYR 0.014 0.001 TYR A 271 PHE 0.018 0.001 PHE B 60 TRP 0.011 0.001 TRP A 51 HIS 0.005 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 ( 8839) covalent geometry : angle 1.04908 / 0.40 (12083) hydrogen bonds : bond 0.02740 / 1.94 ( 304) hydrogen bonds : angle 4.64520 / 3.46 ( 849) metal coordination : bond 0.00282 / 0.14 ( 3) metal coordination : angle 34.67575 / 20.75 ( 9) Misc. bond : bond 0.03645 / 1.92 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8964 (t0) cc_final: 0.8553 (t0) REVERT: A 156 MET cc_start: 0.8685 (mtp) cc_final: 0.8355 (mtp) REVERT: A 175 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.7068 (mmt) REVERT: A 247 LYS cc_start: 0.8066 (mmmm) cc_final: 0.7768 (tttm) REVERT: A 305 ARG cc_start: 0.8707 (tpt90) cc_final: 0.7531 (ttm110) REVERT: A 526 MET cc_start: 0.8261 (mtm) cc_final: 0.7896 (mtt) REVERT: A 535 ASP cc_start: 0.8556 (t0) cc_final: 0.8149 (m-30) REVERT: B 49 ASP cc_start: 0.8313 (m-30) cc_final: 0.7955 (t0) REVERT: B 104 ASP cc_start: 0.8520 (m-30) cc_final: 0.7687 (p0) REVERT: B 123 GLN cc_start: 0.8516 (tt0) cc_final: 0.8260 (tt0) REVERT: B 141 VAL cc_start: 0.8686 (t) cc_final: 0.8452 (p) REVERT: B 173 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8648 (mm-30) REVERT: B 177 VAL cc_start: 0.8871 (m) cc_final: 0.8648 (t) REVERT: C 118 MET cc_start: 0.8771 (tpt) cc_final: 0.7962 (tpt) REVERT: C 182 HIS cc_start: 0.9186 (m90) cc_final: 0.8958 (m-70) REVERT: C 328 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8385 (p) REVERT: C 395 MET cc_start: 0.8124 (tpt) cc_final: 0.7522 (tpt) outliers start: 35 outliers final: 31 residues processed: 154 average time/residue: 0.0864 time to fit residues: 19.0532 Evaluate side-chains 151 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 37 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 104 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 0.0470 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.091761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.074353 restraints weight = 17916.734| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.09 r_work: 0.2906 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 8854 Z= 0.147 Angle : 1.404 83.589 12092 Z= 0.414 Chirality : 0.060 1.469 1277 Planarity : 0.005 0.057 1569 Dihedral : 8.823 87.649 1287 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.84 % Allowed : 23.48 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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 are not related in a simple way. whole: 0.45 (0.27), residues: 1083 helix: 1.87 (0.28), residues: 370 sheet: -1.18 (0.63), residues: 73 loop : -0.44 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 264 TYR 0.025 0.001 TYR A 79 PHE 0.008 0.001 PHE B 183 TRP 0.011 0.001 TRP A 51 HIS 0.006 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 8839) covalent geometry : angle 1.05204 / 0.41 (12083) hydrogen bonds : bond 0.02694 / 1.92 ( 304) hydrogen bonds : angle 4.59367 / 3.42 ( 849) metal coordination : bond 0.00272 / 0.13 ( 3) metal coordination : angle 34.07100 / 20.62 ( 9) Misc. bond : bond 0.03379 / 1.80 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8904 (t0) cc_final: 0.8469 (t0) REVERT: A 156 MET cc_start: 0.8658 (mtp) cc_final: 0.8321 (mtp) REVERT: A 175 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.7154 (mmt) REVERT: A 247 LYS cc_start: 0.8062 (mmmm) cc_final: 0.7770 (tttm) REVERT: A 305 ARG cc_start: 0.8679 (tpt90) cc_final: 0.7481 (ttm110) REVERT: A 526 MET cc_start: 0.8247 (mtm) cc_final: 0.7844 (mtt) REVERT: A 535 ASP cc_start: 0.8557 (t0) cc_final: 0.8158 (m-30) REVERT: B 49 ASP cc_start: 0.8316 (m-30) cc_final: 0.7961 (t70) REVERT: B 104 ASP cc_start: 0.8464 (m-30) cc_final: 0.7574 (p0) REVERT: B 123 GLN cc_start: 0.8514 (tt0) cc_final: 0.8265 (tt0) REVERT: B 141 VAL cc_start: 0.8679 (t) cc_final: 0.8441 (p) REVERT: B 173 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8672 (mm-30) REVERT: B 177 VAL cc_start: 0.8859 (m) cc_final: 0.8652 (t) REVERT: C 118 MET cc_start: 0.8711 (tpt) cc_final: 0.7922 (tpt) REVERT: C 182 HIS cc_start: 0.9192 (m90) cc_final: 0.8966 (m-70) REVERT: C 328 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8355 (p) REVERT: C 395 MET cc_start: 0.7996 (tpt) cc_final: 0.7374 (tpt) outliers start: 34 outliers final: 28 residues processed: 152 average time/residue: 0.0891 time to fit residues: 19.4412 Evaluate side-chains 155 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 32 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 49 optimal weight: 0.1980 chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 53 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 ASN B 100 ASN B 123 GLN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.088028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.070855 restraints weight = 17941.586| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.02 r_work: 0.2842 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.135 8854 Z= 0.183 Angle : 1.421 83.711 12092 Z= 0.425 Chirality : 0.061 1.481 1277 Planarity : 0.005 0.055 1569 Dihedral : 8.965 88.428 1287 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.61 % Allowed : 24.15 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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 are not related in a simple way. whole: 0.44 (0.27), residues: 1083 helix: 1.83 (0.28), residues: 370 sheet: -1.19 (0.60), residues: 83 loop : -0.42 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 264 TYR 0.027 0.001 TYR A 79 PHE 0.021 0.001 PHE B 60 TRP 0.010 0.001 TRP A 51 HIS 0.004 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.18 ( 8839) covalent geometry : angle 1.07138 / 0.42 (12083) hydrogen bonds : bond 0.02855 / 2.03 ( 304) hydrogen bonds : angle 4.69076 / 3.48 ( 849) metal coordination : bond 0.00325 / 0.16 ( 3) metal coordination : angle 34.22883 / 20.40 ( 9) Misc. bond : bond 0.04067 / 2.13 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8885 (t0) cc_final: 0.8470 (t0) REVERT: A 156 MET cc_start: 0.8746 (mtp) cc_final: 0.8390 (mtp) REVERT: A 175 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.6972 (mmt) REVERT: A 247 LYS cc_start: 0.8084 (mmmm) cc_final: 0.7792 (tttm) REVERT: A 305 ARG cc_start: 0.8692 (tpt90) cc_final: 0.8244 (mmm160) REVERT: A 526 MET cc_start: 0.8260 (mtm) cc_final: 0.7639 (mtt) REVERT: A 535 ASP cc_start: 0.8573 (t0) cc_final: 0.8173 (m-30) REVERT: B 49 ASP cc_start: 0.8311 (m-30) cc_final: 0.7938 (t70) REVERT: B 104 ASP cc_start: 0.8499 (m-30) cc_final: 0.7596 (p0) REVERT: B 123 GLN cc_start: 0.8579 (tt0) cc_final: 0.8353 (tt0) REVERT: B 136 GLU cc_start: 0.9178 (pm20) cc_final: 0.8750 (pm20) REVERT: B 141 VAL cc_start: 0.8713 (t) cc_final: 0.8478 (p) REVERT: B 173 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8718 (mm-30) REVERT: B 177 VAL cc_start: 0.8884 (m) cc_final: 0.8654 (t) REVERT: C 118 MET cc_start: 0.8796 (tpt) cc_final: 0.8181 (tpt) REVERT: C 182 HIS cc_start: 0.9188 (m90) cc_final: 0.8968 (m-70) REVERT: C 328 THR cc_start: 0.8781 (OUTLIER) cc_final: 0.8408 (p) REVERT: C 395 MET cc_start: 0.8212 (tpt) cc_final: 0.7553 (tpt) outliers start: 32 outliers final: 28 residues processed: 148 average time/residue: 0.0861 time to fit residues: 18.3324 Evaluate side-chains 151 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 42 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.088040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.070954 restraints weight = 18015.429| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.02 r_work: 0.2848 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.140 8854 Z= 0.176 Angle : 1.400 83.852 12092 Z= 0.422 Chirality : 0.060 1.472 1277 Planarity : 0.005 0.053 1569 Dihedral : 8.926 89.785 1287 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.72 % Allowed : 24.04 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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 are not related in a simple way. whole: 0.39 (0.27), residues: 1083 helix: 1.79 (0.28), residues: 370 sheet: -1.49 (0.57), residues: 88 loop : -0.39 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 264 TYR 0.025 0.001 TYR A 79 PHE 0.012 0.001 PHE A 80 TRP 0.008 0.001 TRP A 51 HIS 0.004 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 ( 8839) covalent geometry : angle 1.06720 / 0.42 (12083) hydrogen bonds : bond 0.02805 / 1.98 ( 304) hydrogen bonds : angle 4.67367 / 3.47 ( 849) metal coordination : bond 0.00332 / 0.17 ( 3) metal coordination : angle 33.20769 / 20.31 ( 9) Misc. bond : bond 0.04157 / 2.19 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1887.05 seconds wall clock time: 33 minutes 27.56 seconds (2007.56 seconds total)