Starting phenix.real_space_refine on Fri Aug 22 17:50:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bv5_16255/08_2025/8bv5_16255.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bv5_16255/08_2025/8bv5_16255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bv5_16255/08_2025/8bv5_16255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bv5_16255/08_2025/8bv5_16255.map" model { file = "/net/cci-nas-00/data/ceres_data/8bv5_16255/08_2025/8bv5_16255.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bv5_16255/08_2025/8bv5_16255.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 35 5.16 5 C 3971 2.51 5 N 1107 2.21 5 O 1179 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6296 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3518 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 9, 'TRANS': 427} Chain breaks: 4 Chain: "B" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2716 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 11, 'TRANS': 318} Chain breaks: 2 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'FOK': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.83, per 1000 atoms: 0.29 Number of scatterers: 6296 At special positions: 0 Unit cell: (112.2, 97.02, 82.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 35 16.00 P 3 15.00 Mg 1 11.99 O 1179 8.00 N 1107 7.00 C 3971 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 469 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 397.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1448 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 5 sheets defined 51.4% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 361 through 378 Processing helix chain 'A' and resid 381 through 393 removed outlier: 4.209A pdb=" N GLU A 387 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 429 Processing helix chain 'A' and resid 433 through 455 removed outlier: 3.549A pdb=" N HIS A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 500 Processing helix chain 'A' and resid 533 through 546 removed outlier: 3.734A pdb=" N ASP A 537 " --> pdb=" O SER A 533 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 562 removed outlier: 3.666A pdb=" N LEU A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N CYS A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 957 Processing helix chain 'A' and resid 958 through 967 removed outlier: 3.769A pdb=" N GLU A 967 " --> pdb=" O ARG A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 997 Processing helix chain 'A' and resid 1006 through 1025 Processing helix chain 'A' and resid 1059 through 1083 Processing helix chain 'A' and resid 1114 through 1126 removed outlier: 3.692A pdb=" N ASN A1118 " --> pdb=" O GLY A1114 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 64 Processing helix chain 'B' and resid 89 through 113 removed outlier: 3.907A pdb=" N SER B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 124 through 134 Processing helix chain 'B' and resid 143 through 155 Processing helix chain 'B' and resid 156 through 165 Processing helix chain 'B' and resid 166 through 169 Processing helix chain 'B' and resid 174 through 181 Processing helix chain 'B' and resid 181 through 186 Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 227 through 231 Processing helix chain 'B' and resid 233 through 238 Processing helix chain 'B' and resid 250 through 254 removed outlier: 3.679A pdb=" N ASN B 254 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 278 Processing helix chain 'B' and resid 293 through 304 Processing helix chain 'B' and resid 307 through 311 Processing helix chain 'B' and resid 312 through 318 removed outlier: 3.994A pdb=" N ALA B 316 " --> pdb=" O PHE B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 352 Processing helix chain 'B' and resid 369 through 388 removed outlier: 3.941A pdb=" N LEU B 388 " --> pdb=" O GLN B 384 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 410 through 417 removed outlier: 5.730A pdb=" N ARG A 411 " --> pdb=" O CYS A 519 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N CYS A 519 " --> pdb=" O ARG A 411 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N GLU A 413 " --> pdb=" O VAL A 517 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL A 517 " --> pdb=" O GLU A 413 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 463 removed outlier: 6.685A pdb=" N ARG A 459 " --> pdb=" O VAL A 470 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL A 470 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS A 461 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR A 468 " --> pdb=" O LYS A 461 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1032 through 1038 removed outlier: 5.633A pdb=" N LYS A1034 " --> pdb=" O VAL A1045 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL A1045 " --> pdb=" O LYS A1034 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS A1036 " --> pdb=" O MET A1043 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR A 976 " --> pdb=" O VAL A1102 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA A 982 " --> pdb=" O GLY A1096 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLY A1096 " --> pdb=" O ALA A 982 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY A 984 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N SER A1094 " --> pdb=" O GLY A 984 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET A 986 " --> pdb=" O GLY A1092 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY A1092 " --> pdb=" O MET A 986 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA A 988 " --> pdb=" O ARG A1090 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG A1090 " --> pdb=" O ALA A 988 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1032 through 1038 removed outlier: 5.633A pdb=" N LYS A1034 " --> pdb=" O VAL A1045 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL A1045 " --> pdb=" O LYS A1034 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS A1036 " --> pdb=" O MET A1043 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR A 976 " --> pdb=" O VAL A1102 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA A 982 " --> pdb=" O GLY A1096 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLY A1096 " --> pdb=" O ALA A 982 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY A 984 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N SER A1094 " --> pdb=" O GLY A 984 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET A 986 " --> pdb=" O GLY A1092 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY A1092 " --> pdb=" O MET A 986 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA A 988 " --> pdb=" O ARG A1090 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG A1090 " --> pdb=" O ALA A 988 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE A1091 " --> pdb=" O GLN A1133 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 208 through 214 removed outlier: 6.910A pdb=" N ARG B 42 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ILE B 245 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU B 44 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE B 244 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N PHE B 290 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE B 246 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LEU B 289 " --> pdb=" O HIS B 362 " (cutoff:3.500A) 317 hydrogen bonds defined for protein. 897 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.05 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1069 1.32 - 1.44: 1723 1.44 - 1.57: 3570 1.57 - 1.69: 5 1.69 - 1.82: 53 Bond restraints: 6420 Sorted by residual: bond pdb=" C8 FOK A1301 " pdb=" O1 FOK A1301 " ideal model delta sigma weight residual 1.419 1.450 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" CB VAL A 376 " pdb=" CG2 VAL A 376 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.30e+00 bond pdb=" CG LEU A 953 " pdb=" CD2 LEU A 953 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.66e+00 bond pdb=" C12 FOK A1301 " pdb=" C13 FOK A1301 " ideal model delta sigma weight residual 1.550 1.525 0.025 2.00e-02 2.50e+03 1.62e+00 bond pdb=" C7 FOK A1301 " pdb=" O4 FOK A1301 " ideal model delta sigma weight residual 1.430 1.455 -0.025 2.00e-02 2.50e+03 1.58e+00 ... (remaining 6415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 8462 1.81 - 3.61: 170 3.61 - 5.42: 32 5.42 - 7.23: 11 7.23 - 9.04: 3 Bond angle restraints: 8678 Sorted by residual: angle pdb=" CB MET B 221 " pdb=" CG MET B 221 " pdb=" SD MET B 221 " ideal model delta sigma weight residual 112.70 121.74 -9.04 3.00e+00 1.11e-01 9.07e+00 angle pdb=" C ASN B 239 " pdb=" N ASP B 240 " pdb=" CA ASP B 240 " ideal model delta sigma weight residual 121.54 127.25 -5.71 1.91e+00 2.74e-01 8.94e+00 angle pdb=" CA MET B 110 " pdb=" CB MET B 110 " pdb=" CG MET B 110 " ideal model delta sigma weight residual 114.10 119.49 -5.39 2.00e+00 2.50e-01 7.26e+00 angle pdb=" CB MET B 110 " pdb=" CG MET B 110 " pdb=" SD MET B 110 " ideal model delta sigma weight residual 112.70 120.72 -8.02 3.00e+00 1.11e-01 7.15e+00 angle pdb=" CA MET A 491 " pdb=" CB MET A 491 " pdb=" CG MET A 491 " ideal model delta sigma weight residual 114.10 118.88 -4.78 2.00e+00 2.50e-01 5.70e+00 ... (remaining 8673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 3212 17.98 - 35.96: 522 35.96 - 53.94: 139 53.94 - 71.92: 22 71.92 - 89.90: 20 Dihedral angle restraints: 3915 sinusoidal: 1681 harmonic: 2234 Sorted by residual: dihedral pdb=" CB CYS A 457 " pdb=" SG CYS A 457 " pdb=" SG CYS A 469 " pdb=" CB CYS A 469 " ideal model delta sinusoidal sigma weight residual -86.00 -132.37 46.37 1 1.00e+01 1.00e-02 2.98e+01 dihedral pdb=" CA ASN A1003 " pdb=" C ASN A1003 " pdb=" N ASN A1004 " pdb=" CA ASN A1004 " ideal model delta harmonic sigma weight residual 180.00 -157.84 -22.16 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA HIS A 552 " pdb=" C HIS A 552 " pdb=" N ILE A 553 " pdb=" CA ILE A 553 " ideal model delta harmonic sigma weight residual -180.00 -162.60 -17.40 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 3912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 749 0.051 - 0.102: 162 0.102 - 0.152: 27 0.152 - 0.203: 6 0.203 - 0.254: 2 Chirality restraints: 946 Sorted by residual: chirality pdb=" C8 FOK A1301 " pdb=" C7 FOK A1301 " pdb=" C9 FOK A1301 " pdb=" O1 FOK A1301 " both_signs ideal model delta sigma weight residual False 2.90 2.65 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB THR A 494 " pdb=" CA THR A 494 " pdb=" OG1 THR A 494 " pdb=" CG2 THR A 494 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" C13 FOK A1301 " pdb=" C12 FOK A1301 " pdb=" C16 FOK A1301 " pdb=" O1 FOK A1301 " both_signs ideal model delta sigma weight residual False -2.37 -2.56 0.19 2.00e-01 2.50e+01 8.72e-01 ... (remaining 943 not shown) Planarity restraints: 1118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 114 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.77e+00 pdb=" N PRO B 115 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 115 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 115 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 995 " -0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" CG ASP A 995 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASP A 995 " -0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP A 995 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 239 " 0.005 2.00e-02 2.50e+03 1.09e-02 1.19e+00 pdb=" C ASN B 239 " -0.019 2.00e-02 2.50e+03 pdb=" O ASN B 239 " 0.007 2.00e-02 2.50e+03 pdb=" N ASP B 240 " 0.006 2.00e-02 2.50e+03 ... (remaining 1115 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 54 2.53 - 3.12: 4954 3.12 - 3.71: 10409 3.71 - 4.31: 13343 4.31 - 4.90: 21784 Nonbonded interactions: 50544 Sorted by model distance: nonbonded pdb=" O2B GSP B 501 " pdb="MG MG B 502 " model vdw 1.934 2.170 nonbonded pdb=" O2G GSP B 501 " pdb="MG MG B 502 " model vdw 1.960 2.170 nonbonded pdb=" OG1 THR B 204 " pdb="MG MG B 502 " model vdw 2.119 2.170 nonbonded pdb=" OG1 THR A1000 " pdb=" OD1 ASN A1003 " model vdw 2.179 3.040 nonbonded pdb=" OG1 THR B 204 " pdb=" O2G GSP B 501 " model vdw 2.184 3.040 ... (remaining 50539 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 group one per residue 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: 5.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.060 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6387 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6421 Z= 0.158 Angle : 0.665 9.037 8680 Z= 0.333 Chirality : 0.046 0.254 946 Planarity : 0.003 0.033 1118 Dihedral : 19.374 89.899 2464 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.59 % Allowed : 35.19 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.31), residues: 751 helix: 0.94 (0.28), residues: 346 sheet: 0.19 (0.59), residues: 87 loop : -1.55 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 439 TYR 0.018 0.001 TYR A 468 PHE 0.016 0.001 PHE B 178 TRP 0.007 0.001 TRP B 154 HIS 0.008 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 6420) covalent geometry : angle 0.66471 ( 8678) SS BOND : bond 0.00225 ( 1) SS BOND : angle 0.87547 ( 2) hydrogen bonds : bond 0.14260 ( 303) hydrogen bonds : angle 5.93643 ( 897) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: A 454 GLU cc_start: 0.7148 (tp30) cc_final: 0.6748 (tm-30) REVERT: A 555 LYS cc_start: 0.7927 (ttpt) cc_final: 0.7537 (tttt) REVERT: A 971 ASP cc_start: 0.6310 (m-30) cc_final: 0.5609 (t70) REVERT: B 64 HIS cc_start: 0.7098 (p-80) cc_final: 0.6652 (p90) REVERT: B 375 VAL cc_start: 0.4423 (t) cc_final: 0.4208 (m) outliers start: 4 outliers final: 1 residues processed: 114 average time/residue: 0.0927 time to fit residues: 13.7322 Evaluate side-chains 89 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 582 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1109 GLN ** B 41 HIS ** 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 = 0.4590 r_free = 0.4590 target = 0.195596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.166707 restraints weight = 10173.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.171188 restraints weight = 5462.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.174116 restraints weight = 3572.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.176131 restraints weight = 2681.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.177099 restraints weight = 2195.789| |-----------------------------------------------------------------------------| r_work (final): 0.4372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6421 Z= 0.153 Angle : 0.621 5.993 8680 Z= 0.324 Chirality : 0.044 0.205 946 Planarity : 0.004 0.054 1118 Dihedral : 6.170 48.684 933 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.13 % Favored : 93.74 % Rotamer: Outliers : 4.84 % Allowed : 32.99 % Favored : 62.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.30), residues: 751 helix: 0.98 (0.28), residues: 346 sheet: 0.16 (0.59), residues: 90 loop : -1.71 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 283 TYR 0.020 0.001 TYR A 468 PHE 0.021 0.002 PHE B 340 TRP 0.009 0.001 TRP B 281 HIS 0.011 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6420) covalent geometry : angle 0.62085 ( 8678) SS BOND : bond 0.00333 ( 1) SS BOND : angle 1.56768 ( 2) hydrogen bonds : bond 0.05224 ( 303) hydrogen bonds : angle 5.01474 ( 897) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 93 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 419 PHE cc_start: 0.7126 (OUTLIER) cc_final: 0.6206 (t80) REVERT: A 448 PHE cc_start: 0.5069 (OUTLIER) cc_final: 0.4551 (t80) REVERT: A 454 GLU cc_start: 0.7525 (tp30) cc_final: 0.6963 (tm-30) REVERT: A 467 TYR cc_start: 0.7090 (t80) cc_final: 0.6840 (t80) REVERT: A 478 GLN cc_start: 0.3173 (OUTLIER) cc_final: 0.2940 (pm20) REVERT: A 555 LYS cc_start: 0.7828 (ttpt) cc_final: 0.7262 (tttt) REVERT: A 971 ASP cc_start: 0.6335 (m-30) cc_final: 0.5691 (t70) REVERT: A 1143 LYS cc_start: 0.5278 (OUTLIER) cc_final: 0.4902 (mmtt) REVERT: B 64 HIS cc_start: 0.7052 (p-80) cc_final: 0.6593 (p90) REVERT: B 181 LYS cc_start: 0.7650 (tppt) cc_final: 0.7363 (tppt) outliers start: 33 outliers final: 14 residues processed: 115 average time/residue: 0.0713 time to fit residues: 11.1452 Evaluate side-chains 98 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1143 LYS Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 372 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 1 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN A 480 HIS A 528 GLN ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 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 = 0.4573 r_free = 0.4573 target = 0.194304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.165524 restraints weight = 10234.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.169950 restraints weight = 5504.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.172915 restraints weight = 3608.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.174888 restraints weight = 2702.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.176287 restraints weight = 2221.515| |-----------------------------------------------------------------------------| r_work (final): 0.4364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6421 Z= 0.156 Angle : 0.617 8.341 8680 Z= 0.319 Chirality : 0.045 0.200 946 Planarity : 0.004 0.043 1118 Dihedral : 5.409 31.152 931 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.66 % Favored : 93.21 % Rotamer: Outliers : 6.01 % Allowed : 30.35 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.30), residues: 751 helix: 0.93 (0.27), residues: 352 sheet: 0.23 (0.62), residues: 85 loop : -1.80 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 371 TYR 0.019 0.001 TYR A 468 PHE 0.039 0.002 PHE B 142 TRP 0.011 0.002 TRP B 281 HIS 0.006 0.001 HIS A 948 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 6420) covalent geometry : angle 0.61654 ( 8678) SS BOND : bond 0.00274 ( 1) SS BOND : angle 1.54861 ( 2) hydrogen bonds : bond 0.04955 ( 303) hydrogen bonds : angle 4.90972 ( 897) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 85 time to evaluate : 0.227 Fit side-chains REVERT: A 392 MET cc_start: 0.7770 (mtp) cc_final: 0.7482 (mtm) REVERT: A 405 HIS cc_start: 0.8048 (OUTLIER) cc_final: 0.7504 (t70) REVERT: A 419 PHE cc_start: 0.7211 (OUTLIER) cc_final: 0.6265 (t80) REVERT: A 448 PHE cc_start: 0.5091 (OUTLIER) cc_final: 0.4616 (t80) REVERT: A 454 GLU cc_start: 0.7635 (tp30) cc_final: 0.7092 (tm-30) REVERT: A 467 TYR cc_start: 0.7181 (t80) cc_final: 0.6927 (t80) REVERT: A 478 GLN cc_start: 0.3190 (OUTLIER) cc_final: 0.2846 (pm20) REVERT: A 486 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6570 (mm-30) REVERT: A 541 LYS cc_start: 0.6849 (OUTLIER) cc_final: 0.6497 (mmmt) REVERT: A 555 LYS cc_start: 0.7946 (ttpt) cc_final: 0.7362 (tttt) REVERT: A 971 ASP cc_start: 0.6439 (m-30) cc_final: 0.5801 (t0) REVERT: B 56 ILE cc_start: 0.6434 (OUTLIER) cc_final: 0.6172 (tt) REVERT: B 64 HIS cc_start: 0.7051 (p-80) cc_final: 0.6595 (p90) outliers start: 41 outliers final: 21 residues processed: 111 average time/residue: 0.0679 time to fit residues: 10.4537 Evaluate side-chains 104 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 372 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 62 optimal weight: 0.0980 chunk 31 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.193338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.164345 restraints weight = 10399.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.168943 restraints weight = 5369.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.172021 restraints weight = 3454.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.173810 restraints weight = 2562.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.175308 restraints weight = 2121.478| |-----------------------------------------------------------------------------| r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6421 Z= 0.139 Angle : 0.595 8.530 8680 Z= 0.305 Chirality : 0.044 0.287 946 Planarity : 0.004 0.044 1118 Dihedral : 5.122 29.207 931 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.39 % Favored : 93.48 % Rotamer: Outliers : 5.13 % Allowed : 30.21 % Favored : 64.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.30), residues: 751 helix: 1.12 (0.27), residues: 348 sheet: 0.29 (0.63), residues: 85 loop : -1.83 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 374 TYR 0.015 0.001 TYR A 468 PHE 0.014 0.002 PHE B 340 TRP 0.010 0.001 TRP B 281 HIS 0.005 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 6420) covalent geometry : angle 0.59486 ( 8678) SS BOND : bond 0.00179 ( 1) SS BOND : angle 1.39118 ( 2) hydrogen bonds : bond 0.04596 ( 303) hydrogen bonds : angle 4.74410 ( 897) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 88 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 405 HIS cc_start: 0.8043 (OUTLIER) cc_final: 0.7499 (t70) REVERT: A 419 PHE cc_start: 0.7135 (OUTLIER) cc_final: 0.6201 (t80) REVERT: A 448 PHE cc_start: 0.5026 (OUTLIER) cc_final: 0.4458 (t80) REVERT: A 454 GLU cc_start: 0.7696 (tp30) cc_final: 0.6884 (tm-30) REVERT: A 455 HIS cc_start: 0.5685 (OUTLIER) cc_final: 0.4442 (m90) REVERT: A 467 TYR cc_start: 0.7199 (t80) cc_final: 0.6951 (t80) REVERT: A 478 GLN cc_start: 0.3217 (OUTLIER) cc_final: 0.2883 (pm20) REVERT: A 486 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6159 (mm-30) REVERT: A 555 LYS cc_start: 0.7991 (ttpt) cc_final: 0.7399 (tttt) REVERT: A 971 ASP cc_start: 0.6553 (m-30) cc_final: 0.5903 (t0) REVERT: A 1029 PHE cc_start: 0.5422 (OUTLIER) cc_final: 0.4938 (m-80) REVERT: A 1143 LYS cc_start: 0.5440 (OUTLIER) cc_final: 0.4829 (mmtt) REVERT: B 56 ILE cc_start: 0.6344 (OUTLIER) cc_final: 0.6078 (tt) REVERT: B 64 HIS cc_start: 0.7080 (p-80) cc_final: 0.6596 (p90) REVERT: B 119 LEU cc_start: 0.4927 (OUTLIER) cc_final: 0.4263 (mp) outliers start: 35 outliers final: 20 residues processed: 112 average time/residue: 0.0757 time to fit residues: 11.3887 Evaluate side-chains 110 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1143 LYS Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 372 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 34 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 GLN ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 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 = 0.4541 r_free = 0.4541 target = 0.192489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.163639 restraints weight = 10492.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.168170 restraints weight = 5500.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.171254 restraints weight = 3550.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.173274 restraints weight = 2637.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.174389 restraints weight = 2155.773| |-----------------------------------------------------------------------------| r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6421 Z= 0.141 Angle : 0.596 9.703 8680 Z= 0.303 Chirality : 0.044 0.281 946 Planarity : 0.004 0.043 1118 Dihedral : 5.181 28.853 931 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.39 % Favored : 93.48 % Rotamer: Outliers : 7.04 % Allowed : 29.77 % Favored : 63.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.31), residues: 751 helix: 1.11 (0.27), residues: 350 sheet: 0.25 (0.63), residues: 85 loop : -1.81 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 356 TYR 0.015 0.001 TYR A 468 PHE 0.048 0.002 PHE B 142 TRP 0.012 0.001 TRP B 281 HIS 0.004 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6420) covalent geometry : angle 0.59513 ( 8678) SS BOND : bond 0.00114 ( 1) SS BOND : angle 1.51136 ( 2) hydrogen bonds : bond 0.04564 ( 303) hydrogen bonds : angle 4.73900 ( 897) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 87 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 405 HIS cc_start: 0.8100 (OUTLIER) cc_final: 0.7586 (t70) REVERT: A 419 PHE cc_start: 0.7259 (OUTLIER) cc_final: 0.6349 (t80) REVERT: A 448 PHE cc_start: 0.5039 (OUTLIER) cc_final: 0.4548 (t80) REVERT: A 454 GLU cc_start: 0.7817 (tp30) cc_final: 0.7028 (tm-30) REVERT: A 455 HIS cc_start: 0.5650 (OUTLIER) cc_final: 0.4490 (m90) REVERT: A 478 GLN cc_start: 0.3309 (OUTLIER) cc_final: 0.2959 (pm20) REVERT: A 486 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6162 (mm-30) REVERT: A 541 LYS cc_start: 0.6871 (OUTLIER) cc_final: 0.6553 (mmmt) REVERT: A 555 LYS cc_start: 0.8013 (ttpt) cc_final: 0.7454 (tttt) REVERT: A 971 ASP cc_start: 0.6463 (m-30) cc_final: 0.5831 (t0) REVERT: A 1029 PHE cc_start: 0.5474 (OUTLIER) cc_final: 0.5134 (m-80) REVERT: A 1151 TYR cc_start: 0.6717 (OUTLIER) cc_final: 0.4518 (p90) REVERT: B 56 ILE cc_start: 0.6455 (OUTLIER) cc_final: 0.6173 (tt) REVERT: B 64 HIS cc_start: 0.7088 (p-80) cc_final: 0.6527 (p90) REVERT: B 119 LEU cc_start: 0.4997 (OUTLIER) cc_final: 0.4368 (mp) outliers start: 48 outliers final: 24 residues processed: 120 average time/residue: 0.0772 time to fit residues: 12.2327 Evaluate side-chains 115 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 80 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 357 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 34 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 41 optimal weight: 0.4980 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1080 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 = 0.4532 r_free = 0.4532 target = 0.191661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.162909 restraints weight = 10275.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.167409 restraints weight = 5369.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.170388 restraints weight = 3475.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.172360 restraints weight = 2586.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.173568 restraints weight = 2116.211| |-----------------------------------------------------------------------------| r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6412 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6421 Z= 0.149 Angle : 0.618 10.820 8680 Z= 0.312 Chirality : 0.045 0.327 946 Planarity : 0.004 0.051 1118 Dihedral : 5.260 29.739 931 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.66 % Favored : 93.21 % Rotamer: Outliers : 7.18 % Allowed : 30.21 % Favored : 62.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.31), residues: 751 helix: 1.15 (0.27), residues: 350 sheet: 0.31 (0.63), residues: 85 loop : -1.78 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 459 TYR 0.016 0.001 TYR A 468 PHE 0.016 0.002 PHE A 448 TRP 0.009 0.001 TRP B 277 HIS 0.005 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 6420) covalent geometry : angle 0.61721 ( 8678) SS BOND : bond 0.00091 ( 1) SS BOND : angle 1.39131 ( 2) hydrogen bonds : bond 0.04617 ( 303) hydrogen bonds : angle 4.74137 ( 897) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 86 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 405 HIS cc_start: 0.8114 (OUTLIER) cc_final: 0.7555 (t70) REVERT: A 419 PHE cc_start: 0.7277 (OUTLIER) cc_final: 0.6381 (t80) REVERT: A 448 PHE cc_start: 0.5123 (OUTLIER) cc_final: 0.4727 (t80) REVERT: A 454 GLU cc_start: 0.7863 (tp30) cc_final: 0.7069 (tm-30) REVERT: A 455 HIS cc_start: 0.5675 (OUTLIER) cc_final: 0.4628 (m90) REVERT: A 478 GLN cc_start: 0.3224 (OUTLIER) cc_final: 0.2868 (pm20) REVERT: A 486 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6188 (mm-30) REVERT: A 541 LYS cc_start: 0.6839 (OUTLIER) cc_final: 0.6529 (mmmt) REVERT: A 555 LYS cc_start: 0.7971 (ttpt) cc_final: 0.7354 (tttt) REVERT: A 971 ASP cc_start: 0.6479 (m-30) cc_final: 0.5839 (t0) REVERT: A 1029 PHE cc_start: 0.5464 (OUTLIER) cc_final: 0.5163 (m-80) REVERT: A 1143 LYS cc_start: 0.5594 (OUTLIER) cc_final: 0.4835 (mmtt) REVERT: A 1151 TYR cc_start: 0.6737 (OUTLIER) cc_final: 0.4490 (p90) REVERT: B 56 ILE cc_start: 0.6369 (OUTLIER) cc_final: 0.6090 (tt) REVERT: B 64 HIS cc_start: 0.7161 (p-80) cc_final: 0.6556 (p90) REVERT: B 119 LEU cc_start: 0.4898 (OUTLIER) cc_final: 0.4267 (mp) outliers start: 49 outliers final: 30 residues processed: 121 average time/residue: 0.0703 time to fit residues: 11.5872 Evaluate side-chains 121 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 79 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 995 ASP Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1143 LYS Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 372 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** 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 = 0.4560 r_free = 0.4560 target = 0.193088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.164336 restraints weight = 10354.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.168615 restraints weight = 5391.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.171570 restraints weight = 3526.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.173564 restraints weight = 2638.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.174622 restraints weight = 2166.786| |-----------------------------------------------------------------------------| r_work (final): 0.4344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6421 Z= 0.149 Angle : 0.626 11.466 8680 Z= 0.318 Chirality : 0.045 0.333 946 Planarity : 0.004 0.045 1118 Dihedral : 5.290 31.233 931 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.26 % Favored : 93.61 % Rotamer: Outliers : 7.62 % Allowed : 29.77 % Favored : 62.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.31), residues: 751 helix: 1.16 (0.27), residues: 350 sheet: 0.27 (0.62), residues: 86 loop : -1.83 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 374 TYR 0.015 0.001 TYR A 468 PHE 0.054 0.002 PHE B 142 TRP 0.010 0.001 TRP B 277 HIS 0.006 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 6420) covalent geometry : angle 0.62601 ( 8678) SS BOND : bond 0.00072 ( 1) SS BOND : angle 1.40619 ( 2) hydrogen bonds : bond 0.04622 ( 303) hydrogen bonds : angle 4.73147 ( 897) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 81 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 405 HIS cc_start: 0.8116 (OUTLIER) cc_final: 0.7561 (t70) REVERT: A 419 PHE cc_start: 0.7325 (OUTLIER) cc_final: 0.6448 (t80) REVERT: A 448 PHE cc_start: 0.5125 (OUTLIER) cc_final: 0.4850 (t80) REVERT: A 454 GLU cc_start: 0.7849 (tp30) cc_final: 0.7101 (tm-30) REVERT: A 455 HIS cc_start: 0.5615 (OUTLIER) cc_final: 0.4644 (m90) REVERT: A 471 SER cc_start: 0.6984 (OUTLIER) cc_final: 0.6695 (m) REVERT: A 478 GLN cc_start: 0.3234 (OUTLIER) cc_final: 0.2850 (pm20) REVERT: A 486 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6199 (mm-30) REVERT: A 541 LYS cc_start: 0.6908 (OUTLIER) cc_final: 0.6569 (mmmt) REVERT: A 555 LYS cc_start: 0.8070 (ttpt) cc_final: 0.7383 (tttt) REVERT: A 971 ASP cc_start: 0.6566 (m-30) cc_final: 0.5901 (t0) REVERT: A 1029 PHE cc_start: 0.5554 (OUTLIER) cc_final: 0.5224 (m-80) REVERT: A 1143 LYS cc_start: 0.5596 (OUTLIER) cc_final: 0.4813 (mmtt) REVERT: A 1151 TYR cc_start: 0.6866 (OUTLIER) cc_final: 0.4658 (p90) REVERT: B 56 ILE cc_start: 0.6447 (OUTLIER) cc_final: 0.6154 (tt) REVERT: B 64 HIS cc_start: 0.7153 (p-80) cc_final: 0.6495 (p90) REVERT: B 119 LEU cc_start: 0.4910 (OUTLIER) cc_final: 0.4334 (mp) REVERT: B 302 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6207 (tt) outliers start: 52 outliers final: 31 residues processed: 120 average time/residue: 0.0842 time to fit residues: 13.3555 Evaluate side-chains 121 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 76 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 995 ASP Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1085 ASN Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1143 LYS Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 372 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 70 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 61 optimal weight: 0.5980 chunk 54 optimal weight: 0.0020 chunk 71 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 59 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 50 optimal weight: 0.8980 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** 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 = 0.4579 r_free = 0.4579 target = 0.195013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.166505 restraints weight = 10356.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.170882 restraints weight = 5388.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.173814 restraints weight = 3484.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.175775 restraints weight = 2608.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.177081 restraints weight = 2146.034| |-----------------------------------------------------------------------------| r_work (final): 0.4378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6421 Z= 0.126 Angle : 0.627 11.962 8680 Z= 0.314 Chirality : 0.044 0.337 946 Planarity : 0.004 0.055 1118 Dihedral : 5.123 32.637 931 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.99 % Favored : 93.87 % Rotamer: Outliers : 5.72 % Allowed : 31.52 % Favored : 62.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.31), residues: 751 helix: 1.25 (0.27), residues: 346 sheet: 0.32 (0.62), residues: 86 loop : -1.79 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 439 TYR 0.013 0.001 TYR A 468 PHE 0.019 0.001 PHE B 290 TRP 0.012 0.001 TRP B 277 HIS 0.005 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 6420) covalent geometry : angle 0.62685 ( 8678) SS BOND : bond 0.00076 ( 1) SS BOND : angle 1.03110 ( 2) hydrogen bonds : bond 0.04354 ( 303) hydrogen bonds : angle 4.57060 ( 897) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 88 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 405 HIS cc_start: 0.8069 (OUTLIER) cc_final: 0.7516 (t70) REVERT: A 419 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.6371 (t80) REVERT: A 448 PHE cc_start: 0.5194 (OUTLIER) cc_final: 0.4824 (t80) REVERT: A 454 GLU cc_start: 0.7817 (tp30) cc_final: 0.7054 (tm-30) REVERT: A 455 HIS cc_start: 0.5606 (OUTLIER) cc_final: 0.4546 (m90) REVERT: A 486 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6156 (mm-30) REVERT: A 491 MET cc_start: 0.8070 (tmm) cc_final: 0.7864 (tmm) REVERT: A 541 LYS cc_start: 0.6880 (OUTLIER) cc_final: 0.6584 (mmmt) REVERT: A 555 LYS cc_start: 0.8001 (ttpt) cc_final: 0.7299 (tttt) REVERT: A 971 ASP cc_start: 0.6571 (m-30) cc_final: 0.5973 (t0) REVERT: A 1029 PHE cc_start: 0.5475 (OUTLIER) cc_final: 0.5156 (m-80) REVERT: A 1143 LYS cc_start: 0.5473 (OUTLIER) cc_final: 0.4714 (mmtt) REVERT: A 1151 TYR cc_start: 0.6854 (OUTLIER) cc_final: 0.4726 (p90) REVERT: B 56 ILE cc_start: 0.6438 (OUTLIER) cc_final: 0.6181 (tt) REVERT: B 64 HIS cc_start: 0.7046 (p-80) cc_final: 0.6445 (p90) REVERT: B 119 LEU cc_start: 0.4919 (OUTLIER) cc_final: 0.4361 (mp) REVERT: B 302 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6147 (tt) outliers start: 39 outliers final: 23 residues processed: 118 average time/residue: 0.0731 time to fit residues: 11.4996 Evaluate side-chains 114 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 79 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1143 LYS Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 372 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 75 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 20 optimal weight: 0.2980 chunk 47 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** 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 = 0.4563 r_free = 0.4563 target = 0.193387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.164841 restraints weight = 10515.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.169125 restraints weight = 5454.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.172148 restraints weight = 3549.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.174133 restraints weight = 2627.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.175390 restraints weight = 2147.470| |-----------------------------------------------------------------------------| r_work (final): 0.4363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6421 Z= 0.149 Angle : 0.648 12.083 8680 Z= 0.325 Chirality : 0.046 0.373 946 Planarity : 0.004 0.048 1118 Dihedral : 5.308 32.903 931 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.52 % Favored : 93.34 % Rotamer: Outliers : 6.01 % Allowed : 32.55 % Favored : 61.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.31), residues: 751 helix: 1.22 (0.27), residues: 346 sheet: 0.36 (0.65), residues: 76 loop : -1.77 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 371 TYR 0.013 0.001 TYR A 468 PHE 0.054 0.002 PHE B 142 TRP 0.011 0.001 TRP B 277 HIS 0.006 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6420) covalent geometry : angle 0.64728 ( 8678) SS BOND : bond 0.00145 ( 1) SS BOND : angle 1.29868 ( 2) hydrogen bonds : bond 0.04593 ( 303) hydrogen bonds : angle 4.68318 ( 897) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 80 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 405 HIS cc_start: 0.8081 (OUTLIER) cc_final: 0.7522 (t70) REVERT: A 419 PHE cc_start: 0.7332 (OUTLIER) cc_final: 0.6441 (t80) REVERT: A 448 PHE cc_start: 0.5306 (OUTLIER) cc_final: 0.4909 (t80) REVERT: A 454 GLU cc_start: 0.7830 (tp30) cc_final: 0.7095 (tm-30) REVERT: A 455 HIS cc_start: 0.5643 (OUTLIER) cc_final: 0.4643 (m90) REVERT: A 471 SER cc_start: 0.7015 (OUTLIER) cc_final: 0.6674 (m) REVERT: A 478 GLN cc_start: 0.3218 (OUTLIER) cc_final: 0.2963 (pm20) REVERT: A 486 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6186 (mm-30) REVERT: A 541 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.6614 (mmmt) REVERT: A 555 LYS cc_start: 0.8048 (ttpt) cc_final: 0.7408 (tttt) REVERT: A 971 ASP cc_start: 0.6613 (m-30) cc_final: 0.5992 (t0) REVERT: A 1029 PHE cc_start: 0.5493 (OUTLIER) cc_final: 0.5162 (m-80) REVERT: A 1151 TYR cc_start: 0.6910 (OUTLIER) cc_final: 0.4709 (p90) REVERT: B 56 ILE cc_start: 0.6443 (OUTLIER) cc_final: 0.6157 (tt) REVERT: B 64 HIS cc_start: 0.7149 (p-80) cc_final: 0.6482 (p90) REVERT: B 119 LEU cc_start: 0.4804 (OUTLIER) cc_final: 0.4268 (mp) REVERT: B 302 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6153 (tt) outliers start: 41 outliers final: 24 residues processed: 111 average time/residue: 0.0732 time to fit residues: 11.1242 Evaluate side-chains 112 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 75 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 372 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 1 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 67 optimal weight: 0.0030 chunk 9 optimal weight: 0.2980 chunk 13 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** 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 = 0.4579 r_free = 0.4579 target = 0.194850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.166455 restraints weight = 10249.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.170767 restraints weight = 5398.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.173714 restraints weight = 3512.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.175372 restraints weight = 2618.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.176835 restraints weight = 2181.943| |-----------------------------------------------------------------------------| r_work (final): 0.4380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6421 Z= 0.134 Angle : 0.644 12.477 8680 Z= 0.321 Chirality : 0.045 0.350 946 Planarity : 0.004 0.054 1118 Dihedral : 5.191 33.666 931 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.86 % Favored : 94.01 % Rotamer: Outliers : 5.57 % Allowed : 32.84 % Favored : 61.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.31), residues: 751 helix: 1.27 (0.27), residues: 346 sheet: 0.31 (0.65), residues: 76 loop : -1.73 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 439 TYR 0.013 0.001 TYR A 468 PHE 0.025 0.002 PHE A1147 TRP 0.013 0.001 TRP B 277 HIS 0.010 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 6420) covalent geometry : angle 0.64352 ( 8678) SS BOND : bond 0.00169 ( 1) SS BOND : angle 1.22952 ( 2) hydrogen bonds : bond 0.04364 ( 303) hydrogen bonds : angle 4.59609 ( 897) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 80 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 419 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.6451 (t80) REVERT: A 448 PHE cc_start: 0.5247 (OUTLIER) cc_final: 0.4812 (t80) REVERT: A 454 GLU cc_start: 0.7814 (tp30) cc_final: 0.7089 (tm-30) REVERT: A 455 HIS cc_start: 0.5627 (OUTLIER) cc_final: 0.4622 (m90) REVERT: A 471 SER cc_start: 0.6956 (OUTLIER) cc_final: 0.6626 (m) REVERT: A 486 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6254 (mm-30) REVERT: A 541 LYS cc_start: 0.6878 (OUTLIER) cc_final: 0.6589 (mmmt) REVERT: A 555 LYS cc_start: 0.8065 (ttpt) cc_final: 0.7364 (tttt) REVERT: A 971 ASP cc_start: 0.6582 (m-30) cc_final: 0.5994 (t0) REVERT: A 1029 PHE cc_start: 0.5421 (OUTLIER) cc_final: 0.5065 (m-80) REVERT: A 1151 TYR cc_start: 0.6929 (OUTLIER) cc_final: 0.4836 (p90) REVERT: B 56 ILE cc_start: 0.6478 (OUTLIER) cc_final: 0.6211 (tt) REVERT: B 64 HIS cc_start: 0.7075 (p-80) cc_final: 0.6479 (p90) REVERT: B 119 LEU cc_start: 0.4760 (OUTLIER) cc_final: 0.4352 (mp) REVERT: B 302 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.6136 (tt) outliers start: 38 outliers final: 24 residues processed: 109 average time/residue: 0.0580 time to fit residues: 9.0039 Evaluate side-chains 114 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 79 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 372 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 0.0010 chunk 6 optimal weight: 0.0060 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 62 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 0.0040 chunk 52 optimal weight: 5.9990 overall best weight: 0.2614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.198551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.170684 restraints weight = 10343.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.175137 restraints weight = 5336.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.178074 restraints weight = 3408.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.180023 restraints weight = 2524.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.181160 restraints weight = 2068.829| |-----------------------------------------------------------------------------| r_work (final): 0.4414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6421 Z= 0.120 Angle : 0.622 12.726 8680 Z= 0.310 Chirality : 0.045 0.359 946 Planarity : 0.004 0.050 1118 Dihedral : 5.067 36.787 931 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.73 % Favored : 94.14 % Rotamer: Outliers : 4.84 % Allowed : 33.43 % Favored : 61.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.31), residues: 751 helix: 1.41 (0.27), residues: 346 sheet: 0.22 (0.61), residues: 86 loop : -1.81 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 283 TYR 0.010 0.001 TYR A 468 PHE 0.052 0.002 PHE B 142 TRP 0.014 0.001 TRP B 277 HIS 0.013 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 6420) covalent geometry : angle 0.62171 ( 8678) SS BOND : bond 0.00151 ( 1) SS BOND : angle 0.84852 ( 2) hydrogen bonds : bond 0.04148 ( 303) hydrogen bonds : angle 4.47598 ( 897) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1268.22 seconds wall clock time: 22 minutes 35.86 seconds (1355.86 seconds total)