Starting phenix.real_space_refine on Fri Aug 22 19:26:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vyb_43655/08_2025/8vyb_43655.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vyb_43655/08_2025/8vyb_43655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vyb_43655/08_2025/8vyb_43655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vyb_43655/08_2025/8vyb_43655.map" model { file = "/net/cci-nas-00/data/ceres_data/8vyb_43655/08_2025/8vyb_43655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vyb_43655/08_2025/8vyb_43655.cif" } resolution = 3.37 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= 0.019 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: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 4637 2.51 5 N 1238 2.21 5 O 1339 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7249 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3700 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 434} Chain breaks: 3 Chain: "B" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3549 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 426} Chain breaks: 3 Time building chain proxies: 1.31, per 1000 atoms: 0.18 Number of scatterers: 7249 At special positions: 0 Unit cell: (84.37, 97.35, 149.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 1339 8.00 N 1238 7.00 C 4637 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 378.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1724 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 10 sheets defined 26.6% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 21 through 37 removed outlier: 3.962A pdb=" N TRP A 37 " --> pdb=" O VAL A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 98 through 104 Processing helix chain 'A' and resid 116 through 123 Processing helix chain 'A' and resid 141 through 160 Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.852A pdb=" N THR A 203 " --> pdb=" O ASN A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 217 removed outlier: 3.508A pdb=" N LEU A 208 " --> pdb=" O HIS A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 323 through 328 removed outlier: 3.710A pdb=" N PHE A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 323 through 328' Processing helix chain 'A' and resid 329 through 332 Processing helix chain 'A' and resid 782 through 782 No H-bonds generated for 'chain 'A' and resid 782 through 782' Processing helix chain 'A' and resid 783 through 800 removed outlier: 3.810A pdb=" N ALA A 787 " --> pdb=" O CYS A 783 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA A 788 " --> pdb=" O VAL A 784 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL A 789 " --> pdb=" O ILE A 785 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 790 " --> pdb=" O HIS A 786 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 793 " --> pdb=" O VAL A 789 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU A 798 " --> pdb=" O GLU A 794 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU A 799 " --> pdb=" O GLU A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 817 removed outlier: 4.350A pdb=" N LYS A 817 " --> pdb=" O SER A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 854 removed outlier: 4.418A pdb=" N LEU A 829 " --> pdb=" O GLU A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 871 removed outlier: 3.549A pdb=" N ASP A 866 " --> pdb=" O GLU A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 901 removed outlier: 4.212A pdb=" N ILE A 894 " --> pdb=" O ALA A 890 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 22 Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 221 through 241 removed outlier: 3.932A pdb=" N ARG B 229 " --> pdb=" O PHE B 225 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA B 230 " --> pdb=" O GLN B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 288 Processing helix chain 'B' and resid 508 through 515 removed outlier: 3.533A pdb=" N GLN B 513 " --> pdb=" O ASN B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 544 Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 61 Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 61 removed outlier: 4.280A pdb=" N MET A 176 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR A 177 " --> pdb=" O MET A 192 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N MET A 192 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N SER A 975 " --> pdb=" O PRO A 956 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY A 936 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 278 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS A 309 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 10 removed outlier: 6.677A pdb=" N VAL B 532 " --> pdb=" O PHE B 8 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 79 through 82 removed outlier: 3.595A pdb=" N GLY B 122 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL B 101 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N VAL B 118 " --> pdb=" O VAL B 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 106 Processing sheet with id=AA6, first strand: chain 'B' and resid 132 through 139 removed outlier: 6.536A pdb=" N GLY B 159 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA B 135 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL B 157 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N CYS B 137 " --> pdb=" O CYS B 155 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N CYS B 155 " --> pdb=" O CYS B 137 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR B 164 " --> pdb=" O PHE B 160 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 191 removed outlier: 3.602A pdb=" N GLN B 187 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 215 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS B 254 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS B 255 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU B 374 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N GLY B 257 " --> pdb=" O LEU B 374 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 263 through 271 removed outlier: 6.922A pdb=" N VAL B 307 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N HIS B 267 " --> pdb=" O ILE B 305 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE B 305 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N SER B 269 " --> pdb=" O GLN B 303 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLN B 303 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY B 271 " --> pdb=" O MET B 301 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N MET B 301 " --> pdb=" O GLY B 271 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR B 313 " --> pdb=" O LEU B 380 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE B 378 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 387 through 392 removed outlier: 6.556A pdb=" N THR B 402 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE B 390 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA B 400 " --> pdb=" O ILE B 390 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU B 392 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU B 398 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ARG B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL B 408 " --> pdb=" O MET B 421 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N MET B 421 " --> pdb=" O VAL B 408 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU B 410 " --> pdb=" O ILE B 419 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 429 through 435 309 hydrogen bonds defined for protein. 852 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.92 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1760 1.33 - 1.45: 1435 1.45 - 1.57: 4182 1.57 - 1.69: 0 1.69 - 1.81: 47 Bond restraints: 7424 Sorted by residual: bond pdb=" N SER A 62 " pdb=" CA SER A 62 " ideal model delta sigma weight residual 1.452 1.500 -0.048 1.22e-02 6.72e+03 1.54e+01 bond pdb=" N VAL A 945 " pdb=" CA VAL A 945 " ideal model delta sigma weight residual 1.462 1.495 -0.033 8.70e-03 1.32e+04 1.43e+01 bond pdb=" N ASN A 319 " pdb=" CA ASN A 319 " ideal model delta sigma weight residual 1.458 1.484 -0.026 7.40e-03 1.83e+04 1.28e+01 bond pdb=" N ILE B 5 " pdb=" CA ILE B 5 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.17e-02 7.31e+03 1.27e+01 bond pdb=" C HIS A 170 " pdb=" N HIS A 171 " ideal model delta sigma weight residual 1.332 1.285 0.047 1.41e-02 5.03e+03 1.10e+01 ... (remaining 7419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 8835 1.62 - 3.25: 1102 3.25 - 4.87: 122 4.87 - 6.49: 14 6.49 - 8.12: 5 Bond angle restraints: 10078 Sorted by residual: angle pdb=" C ARG A 947 " pdb=" CA ARG A 947 " pdb=" CB ARG A 947 " ideal model delta sigma weight residual 108.86 116.98 -8.12 1.44e+00 4.82e-01 3.18e+01 angle pdb=" N ARG A 947 " pdb=" CA ARG A 947 " pdb=" CB ARG A 947 " ideal model delta sigma weight residual 110.03 103.37 6.66 1.21e+00 6.83e-01 3.03e+01 angle pdb=" CA ARG A 947 " pdb=" C ARG A 947 " pdb=" O ARG A 947 " ideal model delta sigma weight residual 120.60 116.85 3.75 9.00e-01 1.23e+00 1.73e+01 angle pdb=" CA LEU B 258 " pdb=" C LEU B 258 " pdb=" O LEU B 258 " ideal model delta sigma weight residual 121.87 117.53 4.34 1.10e+00 8.26e-01 1.55e+01 angle pdb=" C HIS A 170 " pdb=" CA HIS A 170 " pdb=" CB HIS A 170 " ideal model delta sigma weight residual 116.63 112.10 4.53 1.16e+00 7.43e-01 1.52e+01 ... (remaining 10073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 3920 17.11 - 34.22: 395 34.22 - 51.34: 115 51.34 - 68.45: 20 68.45 - 85.56: 8 Dihedral angle restraints: 4458 sinusoidal: 1800 harmonic: 2658 Sorted by residual: dihedral pdb=" N ARG B 229 " pdb=" C ARG B 229 " pdb=" CA ARG B 229 " pdb=" CB ARG B 229 " ideal model delta harmonic sigma weight residual 122.80 113.81 8.99 0 2.50e+00 1.60e-01 1.29e+01 dihedral pdb=" CA ASP B 13 " pdb=" CB ASP B 13 " pdb=" CG ASP B 13 " pdb=" OD1 ASP B 13 " ideal model delta sinusoidal sigma weight residual -30.00 -85.70 55.70 1 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CB GLU A 142 " pdb=" CG GLU A 142 " pdb=" CD GLU A 142 " pdb=" OE1 GLU A 142 " ideal model delta sinusoidal sigma weight residual 0.00 -85.56 85.56 1 3.00e+01 1.11e-03 9.84e+00 ... (remaining 4455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 678 0.052 - 0.103: 251 0.103 - 0.155: 144 0.155 - 0.206: 41 0.206 - 0.258: 9 Chirality restraints: 1123 Sorted by residual: chirality pdb=" CA ARG B 229 " pdb=" N ARG B 229 " pdb=" C ARG B 229 " pdb=" CB ARG B 229 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA VAL B 535 " pdb=" N VAL B 535 " pdb=" C VAL B 535 " pdb=" CB VAL B 535 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA LEU A 941 " pdb=" N LEU A 941 " pdb=" C LEU A 941 " pdb=" CB LEU A 941 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 1120 not shown) Planarity restraints: 1300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 61 " 0.020 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C LYS A 61 " -0.068 2.00e-02 2.50e+03 pdb=" O LYS A 61 " 0.025 2.00e-02 2.50e+03 pdb=" N SER A 62 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 171 " 0.017 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C HIS A 171 " -0.061 2.00e-02 2.50e+03 pdb=" O HIS A 171 " 0.022 2.00e-02 2.50e+03 pdb=" N LYS A 172 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 191 " -0.264 9.50e-02 1.11e+02 1.18e-01 8.56e+00 pdb=" NE ARG B 191 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 191 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B 191 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 191 " -0.009 2.00e-02 2.50e+03 ... (remaining 1297 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 2405 2.85 - 3.37: 6346 3.37 - 3.88: 11516 3.88 - 4.39: 12644 4.39 - 4.90: 22156 Nonbonded interactions: 55067 Sorted by model distance: nonbonded pdb=" OG SER A 66 " pdb=" O PHE A 70 " model vdw 2.344 3.040 nonbonded pdb=" O HIS A 135 " pdb=" OG SER A 136 " model vdw 2.358 3.040 nonbonded pdb=" OE1 GLU A 191 " pdb=" NZ LYS B 282 " model vdw 2.365 3.120 nonbonded pdb=" N LEU A 205 " pdb=" OD2 ASP A 295 " model vdw 2.379 3.120 nonbonded pdb=" N GLU B 369 " pdb=" OE1 GLU B 369 " model vdw 2.439 3.120 ... (remaining 55062 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 23.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.400 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6253 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 : 0.008 0.048 7424 Z= 0.633 Angle : 1.054 8.118 10078 Z= 0.756 Chirality : 0.073 0.258 1123 Planarity : 0.009 0.118 1300 Dihedral : 15.537 85.562 2734 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 19.85 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -1.28 (0.27), residues: 904 helix: -0.06 (0.36), residues: 204 sheet: 0.06 (0.31), residues: 276 loop : -1.89 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 471 TYR 0.026 0.002 TYR B 425 PHE 0.012 0.001 PHE B 22 TRP 0.013 0.001 TRP B 422 HIS 0.006 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00845 ( 7424) covalent geometry : angle 1.05372 (10078) hydrogen bonds : bond 0.16732 ( 305) hydrogen bonds : angle 7.09636 ( 852) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.0960 time to fit residues: 18.9355 Evaluate side-chains 73 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.2980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.0060 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS A 109 ASN A 860 GLN B 243 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.139616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.108580 restraints weight = 16478.640| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 4.28 r_work: 0.3714 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7424 Z= 0.141 Angle : 0.643 11.030 10078 Z= 0.324 Chirality : 0.044 0.206 1123 Planarity : 0.005 0.048 1300 Dihedral : 3.955 16.201 978 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.37 % Allowed : 22.35 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -0.49 (0.28), residues: 904 helix: 0.84 (0.35), residues: 207 sheet: 0.52 (0.32), residues: 274 loop : -1.53 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 93 TYR 0.016 0.002 TYR B 168 PHE 0.015 0.002 PHE A 67 TRP 0.022 0.001 TRP B 256 HIS 0.004 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 7424) covalent geometry : angle 0.64337 (10078) hydrogen bonds : bond 0.03928 ( 305) hydrogen bonds : angle 5.57769 ( 852) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8415 (t80) cc_final: 0.7932 (t80) REVERT: A 77 HIS cc_start: 0.7951 (OUTLIER) cc_final: 0.7721 (m90) REVERT: A 165 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7625 (tt) REVERT: A 180 GLU cc_start: 0.7764 (tt0) cc_final: 0.7447 (tt0) REVERT: A 959 MET cc_start: 0.8459 (tpp) cc_final: 0.8132 (ttt) REVERT: B 10 TYR cc_start: 0.7310 (OUTLIER) cc_final: 0.6770 (t80) outliers start: 19 outliers final: 9 residues processed: 94 average time/residue: 0.0532 time to fit residues: 7.1922 Evaluate side-chains 76 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 170 HIS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 495 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 89 optimal weight: 0.0980 chunk 23 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 chunk 49 optimal weight: 0.0870 chunk 27 optimal weight: 0.0010 overall best weight: 0.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.139588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.108519 restraints weight = 16369.948| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 4.32 r_work: 0.3715 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7424 Z= 0.108 Angle : 0.567 9.446 10078 Z= 0.287 Chirality : 0.043 0.153 1123 Planarity : 0.004 0.044 1300 Dihedral : 3.812 15.898 978 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.12 % Allowed : 22.10 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -0.27 (0.28), residues: 904 helix: 1.11 (0.35), residues: 210 sheet: 0.75 (0.32), residues: 274 loop : -1.54 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 93 TYR 0.012 0.001 TYR B 168 PHE 0.011 0.001 PHE A 127 TRP 0.016 0.001 TRP B 256 HIS 0.004 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 7424) covalent geometry : angle 0.56715 (10078) hydrogen bonds : bond 0.03429 ( 305) hydrogen bonds : angle 5.26959 ( 852) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8365 (t80) cc_final: 0.7976 (t80) REVERT: A 180 GLU cc_start: 0.7749 (tt0) cc_final: 0.7226 (tt0) REVERT: A 959 MET cc_start: 0.8448 (tpp) cc_final: 0.8167 (ttt) REVERT: B 10 TYR cc_start: 0.7380 (OUTLIER) cc_final: 0.6904 (t80) REVERT: B 207 GLU cc_start: 0.7420 (mt-10) cc_final: 0.7208 (mt-10) outliers start: 25 outliers final: 11 residues processed: 90 average time/residue: 0.0523 time to fit residues: 6.9879 Evaluate side-chains 75 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 525 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 0.0670 chunk 2 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.138641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.106870 restraints weight = 16744.298| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 4.41 r_work: 0.3678 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7424 Z= 0.118 Angle : 0.551 9.978 10078 Z= 0.279 Chirality : 0.043 0.132 1123 Planarity : 0.004 0.047 1300 Dihedral : 3.852 16.349 978 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.62 % Allowed : 20.97 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -0.12 (0.28), residues: 904 helix: 1.30 (0.35), residues: 209 sheet: 0.84 (0.32), residues: 277 loop : -1.50 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 869 TYR 0.014 0.001 TYR B 168 PHE 0.014 0.001 PHE B 22 TRP 0.015 0.001 TRP B 256 HIS 0.003 0.001 HIS A 814 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 7424) covalent geometry : angle 0.55104 (10078) hydrogen bonds : bond 0.03260 ( 305) hydrogen bonds : angle 5.06244 ( 852) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 67 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8383 (t80) cc_final: 0.8041 (t80) REVERT: A 77 HIS cc_start: 0.7866 (OUTLIER) cc_final: 0.7592 (m90) REVERT: A 180 GLU cc_start: 0.7878 (tt0) cc_final: 0.7445 (tt0) REVERT: A 959 MET cc_start: 0.8494 (tpp) cc_final: 0.8216 (ttt) REVERT: B 10 TYR cc_start: 0.7574 (OUTLIER) cc_final: 0.7030 (t80) REVERT: B 207 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7260 (mt-10) outliers start: 29 outliers final: 19 residues processed: 87 average time/residue: 0.0586 time to fit residues: 7.3015 Evaluate side-chains 84 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 834 HIS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 525 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 34 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 76 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.134980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.104457 restraints weight = 16662.375| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 4.13 r_work: 0.3666 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7424 Z= 0.130 Angle : 0.565 10.688 10078 Z= 0.284 Chirality : 0.043 0.207 1123 Planarity : 0.004 0.048 1300 Dihedral : 3.854 15.819 978 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.62 % Allowed : 21.47 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -0.08 (0.28), residues: 904 helix: 1.29 (0.35), residues: 215 sheet: 0.82 (0.32), residues: 278 loop : -1.45 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 93 TYR 0.014 0.001 TYR B 168 PHE 0.014 0.001 PHE A 67 TRP 0.012 0.001 TRP B 478 HIS 0.015 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 7424) covalent geometry : angle 0.56489 (10078) hydrogen bonds : bond 0.03382 ( 305) hydrogen bonds : angle 5.04405 ( 852) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 67 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8424 (t80) cc_final: 0.8131 (t80) REVERT: A 180 GLU cc_start: 0.7827 (tt0) cc_final: 0.7362 (tt0) REVERT: A 195 LEU cc_start: 0.9144 (tp) cc_final: 0.8925 (tt) REVERT: A 959 MET cc_start: 0.8461 (tpp) cc_final: 0.8208 (ttt) REVERT: B 10 TYR cc_start: 0.7634 (OUTLIER) cc_final: 0.7086 (t80) REVERT: B 207 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7282 (mt-10) REVERT: B 244 GLU cc_start: -0.3966 (OUTLIER) cc_final: -0.4430 (tp30) outliers start: 29 outliers final: 22 residues processed: 89 average time/residue: 0.0522 time to fit residues: 6.9426 Evaluate side-chains 84 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 834 HIS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 525 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 90 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS ** A 194 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 = 0.4235 r_free = 0.4235 target = 0.132763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.102399 restraints weight = 16708.338| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 4.11 r_work: 0.3638 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7424 Z= 0.149 Angle : 0.571 10.271 10078 Z= 0.289 Chirality : 0.044 0.216 1123 Planarity : 0.004 0.048 1300 Dihedral : 4.008 16.545 978 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.87 % Allowed : 20.10 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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 (0.28), residues: 904 helix: 1.29 (0.34), residues: 214 sheet: 0.84 (0.32), residues: 278 loop : -1.42 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 93 TYR 0.014 0.001 TYR B 168 PHE 0.018 0.001 PHE A 67 TRP 0.016 0.001 TRP A 58 HIS 0.010 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 7424) covalent geometry : angle 0.57118 (10078) hydrogen bonds : bond 0.03447 ( 305) hydrogen bonds : angle 5.05028 ( 852) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 62 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8483 (t80) cc_final: 0.8259 (t80) REVERT: A 180 GLU cc_start: 0.7839 (tt0) cc_final: 0.7385 (tt0) REVERT: A 195 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8896 (tt) REVERT: A 959 MET cc_start: 0.8451 (tpp) cc_final: 0.8210 (ttt) REVERT: B 244 GLU cc_start: -0.3863 (OUTLIER) cc_final: -0.4335 (tp30) REVERT: B 463 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7623 (mt0) outliers start: 39 outliers final: 24 residues processed: 91 average time/residue: 0.0680 time to fit residues: 8.8342 Evaluate side-chains 85 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 58 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 525 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 61 optimal weight: 0.8980 chunk 51 optimal weight: 0.0050 chunk 78 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.133515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.103123 restraints weight = 16814.282| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 4.16 r_work: 0.3651 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7424 Z= 0.118 Angle : 0.554 10.616 10078 Z= 0.277 Chirality : 0.043 0.192 1123 Planarity : 0.004 0.046 1300 Dihedral : 3.899 16.199 978 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.37 % Allowed : 21.85 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.07 (0.28), residues: 904 helix: 1.47 (0.35), residues: 214 sheet: 0.88 (0.32), residues: 278 loop : -1.37 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 93 TYR 0.012 0.001 TYR B 168 PHE 0.013 0.001 PHE A 67 TRP 0.011 0.001 TRP B 478 HIS 0.003 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 7424) covalent geometry : angle 0.55435 (10078) hydrogen bonds : bond 0.03185 ( 305) hydrogen bonds : angle 4.92827 ( 852) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8452 (t80) cc_final: 0.8237 (t80) REVERT: A 180 GLU cc_start: 0.7726 (tt0) cc_final: 0.7288 (tt0) REVERT: A 195 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8882 (tt) REVERT: A 959 MET cc_start: 0.8440 (tpp) cc_final: 0.8180 (ttt) REVERT: B 244 GLU cc_start: -0.3867 (OUTLIER) cc_final: -0.4473 (tp30) REVERT: B 463 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7618 (mt0) outliers start: 27 outliers final: 19 residues processed: 89 average time/residue: 0.0616 time to fit residues: 7.9335 Evaluate side-chains 82 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 834 HIS Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 525 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 33 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.132757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.101373 restraints weight = 17134.474| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 4.38 r_work: 0.3606 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7424 Z= 0.147 Angle : 0.589 10.038 10078 Z= 0.295 Chirality : 0.045 0.269 1123 Planarity : 0.004 0.048 1300 Dihedral : 4.055 17.212 978 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.75 % Allowed : 21.47 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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 (0.28), residues: 904 helix: 1.25 (0.34), residues: 215 sheet: 0.77 (0.32), residues: 280 loop : -1.35 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 93 TYR 0.015 0.002 TYR B 168 PHE 0.017 0.001 PHE A 67 TRP 0.010 0.001 TRP A 285 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 7424) covalent geometry : angle 0.58863 (10078) hydrogen bonds : bond 0.03499 ( 305) hydrogen bonds : angle 4.96378 ( 852) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 64 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8508 (t80) cc_final: 0.8293 (t80) REVERT: A 77 HIS cc_start: 0.8101 (OUTLIER) cc_final: 0.7865 (m90) REVERT: A 180 GLU cc_start: 0.7866 (tt0) cc_final: 0.7385 (tt0) REVERT: A 195 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8894 (tt) REVERT: B 463 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7692 (mt0) outliers start: 30 outliers final: 21 residues processed: 87 average time/residue: 0.0568 time to fit residues: 7.0835 Evaluate side-chains 85 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 525 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 61 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.132480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.101573 restraints weight = 16934.112| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 4.31 r_work: 0.3601 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7424 Z= 0.143 Angle : 0.595 10.615 10078 Z= 0.298 Chirality : 0.044 0.224 1123 Planarity : 0.004 0.050 1300 Dihedral : 4.081 17.903 978 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.37 % Allowed : 21.72 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -0.02 (0.28), residues: 904 helix: 1.29 (0.35), residues: 214 sheet: 0.76 (0.32), residues: 280 loop : -1.31 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 93 TYR 0.014 0.001 TYR B 168 PHE 0.016 0.001 PHE A 67 TRP 0.010 0.001 TRP A 285 HIS 0.003 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 7424) covalent geometry : angle 0.59509 (10078) hydrogen bonds : bond 0.03421 ( 305) hydrogen bonds : angle 4.95188 ( 852) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 63 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 77 HIS cc_start: 0.8105 (OUTLIER) cc_final: 0.7845 (m90) REVERT: A 180 GLU cc_start: 0.7846 (tt0) cc_final: 0.7375 (tt0) REVERT: A 195 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8872 (tt) REVERT: B 463 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7713 (mt0) outliers start: 27 outliers final: 23 residues processed: 83 average time/residue: 0.0578 time to fit residues: 6.9129 Evaluate side-chains 88 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 802 SER Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 525 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 73 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 84 optimal weight: 0.3980 chunk 38 optimal weight: 0.0770 chunk 80 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 0.0010 overall best weight: 0.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 786 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.133020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.104097 restraints weight = 16561.577| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 4.07 r_work: 0.3680 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 7424 Z= 0.105 Angle : 0.589 15.169 10078 Z= 0.288 Chirality : 0.044 0.217 1123 Planarity : 0.004 0.047 1300 Dihedral : 3.901 16.464 978 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.62 % Allowed : 22.60 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.10 (0.28), residues: 904 helix: 1.34 (0.35), residues: 214 sheet: 0.92 (0.32), residues: 280 loop : -1.27 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 471 TYR 0.012 0.001 TYR B 168 PHE 0.017 0.001 PHE A 26 TRP 0.010 0.001 TRP B 478 HIS 0.003 0.001 HIS A 889 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 7424) covalent geometry : angle 0.58938 (10078) hydrogen bonds : bond 0.03159 ( 305) hydrogen bonds : angle 4.81665 ( 852) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 180 GLU cc_start: 0.7705 (tt0) cc_final: 0.7065 (tt0) REVERT: B 463 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7692 (mt0) REVERT: B 471 ARG cc_start: 0.6973 (OUTLIER) cc_final: 0.6524 (mtm180) outliers start: 21 outliers final: 18 residues processed: 78 average time/residue: 0.0724 time to fit residues: 7.7591 Evaluate side-chains 83 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 525 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 8 optimal weight: 0.0870 chunk 89 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 0.0020 chunk 64 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 85 optimal weight: 0.1980 chunk 7 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 0.3980 chunk 63 optimal weight: 0.9990 overall best weight: 0.2966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.133560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.104512 restraints weight = 16532.855| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 4.08 r_work: 0.3686 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 7424 Z= 0.101 Angle : 0.605 15.787 10078 Z= 0.294 Chirality : 0.043 0.214 1123 Planarity : 0.004 0.052 1300 Dihedral : 3.846 15.524 978 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.37 % Allowed : 23.10 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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 (0.29), residues: 904 helix: 1.37 (0.35), residues: 208 sheet: 1.04 (0.32), residues: 280 loop : -1.09 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 93 TYR 0.011 0.001 TYR B 168 PHE 0.025 0.001 PHE B 22 TRP 0.012 0.001 TRP B 74 HIS 0.006 0.001 HIS A 786 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 7424) covalent geometry : angle 0.60468 (10078) hydrogen bonds : bond 0.03106 ( 305) hydrogen bonds : angle 4.77949 ( 852) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2026.23 seconds wall clock time: 35 minutes 25.06 seconds (2125.06 seconds total)