Starting phenix.real_space_refine on Fri Aug 22 16:21:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tgl_41240/08_2025/8tgl_41240_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tgl_41240/08_2025/8tgl_41240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tgl_41240/08_2025/8tgl_41240_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tgl_41240/08_2025/8tgl_41240_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tgl_41240/08_2025/8tgl_41240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tgl_41240/08_2025/8tgl_41240.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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 57 5.16 5 C 3817 2.51 5 N 892 2.21 5 O 968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 5734 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2838 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 23, 'TRANS': 357} Chain breaks: 1 Chain: "B" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2840 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 21, 'TRANS': 357} Chain breaks: 2 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'LNR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'YHR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.58, per 1000 atoms: 0.28 Number of scatterers: 5734 At special positions: 0 Unit cell: (72.5973, 51.3493, 114.208, 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 57 16.00 O 968 8.00 N 892 7.00 C 3817 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: 0.55 Conformation dependent library (CDL) restraints added in 331.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1360 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 0 sheets defined 89.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.690A pdb=" N LEU A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 50 removed outlier: 3.527A pdb=" N TYR A 50 " --> pdb=" O PRO A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 removed outlier: 3.796A pdb=" N LEU A 142 " --> pdb=" O ARG A 138 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 158 Proline residue: A 155 - end of helix Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 166 through 187 Processing helix chain 'A' and resid 189 through 219 Processing helix chain 'A' and resid 221 through 253 removed outlier: 3.632A pdb=" N ARG A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Proline residue: A 245 - end of helix Processing helix chain 'A' and resid 256 through 278 removed outlier: 4.358A pdb=" N PHE A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 299 through 331 Proline residue: A 321 - end of helix Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.949A pdb=" N PHE A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 364 removed outlier: 5.254A pdb=" N ASN A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LYS A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 383 Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 392 through 421 Proline residue: A 412 - end of helix removed outlier: 3.902A pdb=" N GLY A 415 " --> pdb=" O MET A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 455 removed outlier: 3.576A pdb=" N TYR A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Proline residue: A 445 - end of helix removed outlier: 4.802A pdb=" N GLY A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ALA A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 472 Processing helix chain 'A' and resid 473 through 480 removed outlier: 4.286A pdb=" N SER A 480 " --> pdb=" O TYR A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 41 Processing helix chain 'B' and resid 44 through 54 removed outlier: 3.676A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 165 removed outlier: 4.247A pdb=" N LYS B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA B 147 " --> pdb=" O PHE B 143 " (cutoff:3.500A) Proline residue: B 155 - end of helix removed outlier: 4.056A pdb=" N GLY B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 166 through 187 Processing helix chain 'B' and resid 189 through 219 Processing helix chain 'B' and resid 223 through 250 removed outlier: 4.000A pdb=" N ALA B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Proline residue: B 245 - end of helix removed outlier: 3.550A pdb=" N SER B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 276 Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 299 through 331 removed outlier: 4.016A pdb=" N GLY B 315 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL B 316 " --> pdb=" O ALA B 312 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 319 " --> pdb=" O GLY B 315 " (cutoff:3.500A) Proline residue: B 321 - end of helix Proline residue: B 324 - end of helix Processing helix chain 'B' and resid 342 through 364 removed outlier: 5.847A pdb=" N ASN B 361 " --> pdb=" O GLY B 357 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LYS B 362 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N MET B 363 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 383 Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 389 through 391 No H-bonds generated for 'chain 'B' and resid 389 through 391' Processing helix chain 'B' and resid 392 through 421 Proline residue: B 412 - end of helix Processing helix chain 'B' and resid 427 through 455 Proline residue: B 445 - end of helix removed outlier: 3.567A pdb=" N GLY B 449 " --> pdb=" O PRO B 445 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 472 Processing helix chain 'B' and resid 473 through 479 467 hydrogen bonds defined for protein. 1371 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: 0.94 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 849 1.31 - 1.43: 1561 1.43 - 1.56: 3367 1.56 - 1.69: 1 1.69 - 1.81: 100 Bond restraints: 5878 Sorted by residual: bond pdb=" CAI LNR A 601 " pdb=" OAB LNR A 601 " ideal model delta sigma weight residual 1.351 1.452 -0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" C PRO B 481 " pdb=" O PRO B 481 " ideal model delta sigma weight residual 1.246 1.205 0.041 8.50e-03 1.38e+04 2.29e+01 bond pdb=" CAJ LNR A 601 " pdb=" OAC LNR A 601 " ideal model delta sigma weight residual 1.353 1.433 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C31 YHR B 601 " pdb=" O30 YHR B 601 " ideal model delta sigma weight residual 1.326 1.400 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C SER B 480 " pdb=" N PRO B 481 " ideal model delta sigma weight residual 1.331 1.363 -0.032 8.70e-03 1.32e+04 1.37e+01 ... (remaining 5873 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.18: 7963 4.18 - 8.36: 40 8.36 - 12.54: 4 12.54 - 16.71: 0 16.71 - 20.89: 1 Bond angle restraints: 8008 Sorted by residual: angle pdb=" N ARG B 225 " pdb=" CA ARG B 225 " pdb=" C ARG B 225 " ideal model delta sigma weight residual 111.28 103.22 8.06 1.09e+00 8.42e-01 5.46e+01 angle pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " pdb=" C9 YHR B 601 " ideal model delta sigma weight residual 111.89 132.78 -20.89 3.00e+00 1.11e-01 4.85e+01 angle pdb=" N HIS B 223 " pdb=" CA HIS B 223 " pdb=" C HIS B 223 " ideal model delta sigma weight residual 114.12 104.55 9.57 1.39e+00 5.18e-01 4.74e+01 angle pdb=" N PRO A 280 " pdb=" CA PRO A 280 " pdb=" CB PRO A 280 " ideal model delta sigma weight residual 102.35 106.19 -3.84 7.10e-01 1.98e+00 2.93e+01 angle pdb=" N GLY B 226 " pdb=" CA GLY B 226 " pdb=" C GLY B 226 " ideal model delta sigma weight residual 112.73 106.41 6.32 1.20e+00 6.94e-01 2.77e+01 ... (remaining 8003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.65: 3086 23.65 - 47.30: 317 47.30 - 70.95: 46 70.95 - 94.60: 1 94.60 - 118.25: 3 Dihedral angle restraints: 3453 sinusoidal: 1314 harmonic: 2139 Sorted by residual: dihedral pdb=" CA PHE A 294 " pdb=" C PHE A 294 " pdb=" N MET A 295 " pdb=" CA MET A 295 " ideal model delta harmonic sigma weight residual 180.00 154.61 25.39 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA VAL B 358 " pdb=" C VAL B 358 " pdb=" N LEU B 359 " pdb=" CA LEU B 359 " ideal model delta harmonic sigma weight residual 180.00 -155.40 -24.60 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA VAL A 358 " pdb=" C VAL A 358 " pdb=" N LEU A 359 " pdb=" CA LEU A 359 " ideal model delta harmonic sigma weight residual -180.00 -157.83 -22.17 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 3450 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 830 0.058 - 0.116: 121 0.116 - 0.174: 7 0.174 - 0.232: 3 0.232 - 0.290: 2 Chirality restraints: 963 Sorted by residual: chirality pdb=" C13 YHR B 601 " pdb=" C12 YHR B 601 " pdb=" C14 YHR B 601 " pdb=" N8 YHR B 601 " both_signs ideal model delta sigma weight residual False -2.29 -2.58 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CAL LNR A 601 " pdb=" CAH LNR A 601 " pdb=" CAK LNR A 601 " pdb=" OAD LNR A 601 " both_signs ideal model delta sigma weight residual False -2.28 -2.53 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C16 YHR B 601 " pdb=" C15 YHR B 601 " pdb=" C17 YHR B 601 " pdb=" C3 YHR B 601 " both_signs ideal model delta sigma weight residual False 2.40 2.62 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 960 not shown) Planarity restraints: 973 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 252 " 0.020 2.00e-02 2.50e+03 4.03e-02 1.63e+01 pdb=" C GLU A 252 " -0.070 2.00e-02 2.50e+03 pdb=" O GLU A 252 " 0.026 2.00e-02 2.50e+03 pdb=" N PHE A 253 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 225 " -0.013 2.00e-02 2.50e+03 2.75e-02 7.56e+00 pdb=" C ARG B 225 " 0.048 2.00e-02 2.50e+03 pdb=" O ARG B 225 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY B 226 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 168 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO A 169 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 169 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 169 " 0.028 5.00e-02 4.00e+02 ... (remaining 970 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 960 2.75 - 3.29: 6089 3.29 - 3.83: 9758 3.83 - 4.36: 10836 4.36 - 4.90: 19420 Nonbonded interactions: 47063 Sorted by model distance: nonbonded pdb=" O VAL B 304 " pdb=" OH TYR B 471 " model vdw 2.218 3.040 nonbonded pdb=" O THR B 291 " pdb=" OG1 THR B 291 " model vdw 2.225 3.040 nonbonded pdb=" O VAL A 375 " pdb=" OG SER A 379 " model vdw 2.236 3.040 nonbonded pdb=" O ARG B 138 " pdb=" OH TYR B 190 " model vdw 2.238 3.040 nonbonded pdb=" O ILE A 277 " pdb=" NE2 GLN A 279 " model vdw 2.246 3.120 ... (remaining 47058 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 278 or resid 289 through 483)) selection = (chain 'B' and (resid 19 through 50 or resid 136 through 483)) } 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: 2.090 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.320 Find NCS groups from input model: 0.120 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 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 : 0.005 0.101 5878 Z= 0.287 Angle : 0.797 20.892 8008 Z= 0.440 Chirality : 0.043 0.290 963 Planarity : 0.006 0.050 973 Dihedral : 17.874 118.249 2093 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 30.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.73 % Favored : 98.13 % Rotamer: Outliers : 0.82 % Allowed : 32.57 % Favored : 66.61 % 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: 1.90 (0.32), residues: 750 helix: 1.78 (0.22), residues: 589 sheet: None (None), residues: 0 loop : -0.59 (0.50), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 365 TYR 0.009 0.001 TYR A 426 PHE 0.024 0.001 PHE B 28 TRP 0.005 0.001 TRP B 459 HIS 0.018 0.002 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00505 ( 5878) covalent geometry : angle 0.79705 ( 8008) hydrogen bonds : bond 0.15178 ( 467) hydrogen bonds : angle 6.07989 ( 1371) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 122 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: A 426 TYR cc_start: 0.7150 (m-80) cc_final: 0.6919 (m-80) REVERT: A 447 THR cc_start: 0.7420 (p) cc_final: 0.7003 (m) REVERT: B 410 MET cc_start: 0.6502 (mmp) cc_final: 0.6212 (tpp) outliers start: 5 outliers final: 1 residues processed: 124 average time/residue: 0.0611 time to fit residues: 10.5881 Evaluate side-chains 120 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.0980 chunk 45 optimal weight: 0.4980 chunk 74 optimal weight: 0.0070 overall best weight: 0.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 396 ASN B 154 ASN B 329 GLN B 468 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.147579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.134719 restraints weight = 7906.508| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.87 r_work: 0.3602 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5878 Z= 0.161 Angle : 0.692 9.926 8008 Z= 0.335 Chirality : 0.043 0.162 963 Planarity : 0.006 0.046 973 Dihedral : 7.685 57.139 871 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.75 % Allowed : 26.68 % Favored : 68.58 % 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: 1.72 (0.32), residues: 750 helix: 1.65 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -0.89 (0.50), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 225 TYR 0.010 0.001 TYR B 349 PHE 0.036 0.002 PHE A 206 TRP 0.008 0.001 TRP B 326 HIS 0.006 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 5878) covalent geometry : angle 0.69171 ( 8008) hydrogen bonds : bond 0.04984 ( 467) hydrogen bonds : angle 4.90831 ( 1371) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.211 Fit side-chains REVERT: A 151 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6560 (tt) REVERT: A 163 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.6403 (mpt180) REVERT: A 363 MET cc_start: 0.7538 (ttt) cc_final: 0.7321 (ttt) REVERT: A 410 MET cc_start: 0.6728 (mmm) cc_final: 0.6389 (mmp) REVERT: B 236 LEU cc_start: 0.7751 (tt) cc_final: 0.7516 (tp) REVERT: B 325 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7746 (mp) REVERT: B 356 PHE cc_start: 0.7796 (m-80) cc_final: 0.7502 (m-80) outliers start: 29 outliers final: 8 residues processed: 145 average time/residue: 0.0583 time to fit residues: 12.0142 Evaluate side-chains 137 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 439 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 6 optimal weight: 0.0770 chunk 48 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 3 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 396 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.146570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.132609 restraints weight = 7997.308| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.09 r_work: 0.3563 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5878 Z= 0.170 Angle : 0.673 10.718 8008 Z= 0.323 Chirality : 0.042 0.137 963 Planarity : 0.005 0.043 973 Dihedral : 6.074 49.221 868 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.75 % Allowed : 25.37 % Favored : 69.89 % 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: 1.61 (0.32), residues: 750 helix: 1.54 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -0.89 (0.51), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 479 TYR 0.010 0.002 TYR B 349 PHE 0.026 0.001 PHE A 206 TRP 0.008 0.001 TRP B 326 HIS 0.004 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 5878) covalent geometry : angle 0.67299 ( 8008) hydrogen bonds : bond 0.04668 ( 467) hydrogen bonds : angle 4.81966 ( 1371) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 266 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7666 (mp) REVERT: A 279 GLN cc_start: 0.8509 (mp10) cc_final: 0.8102 (mp10) REVERT: A 295 MET cc_start: 0.6718 (OUTLIER) cc_final: 0.6245 (mmt) REVERT: A 359 LEU cc_start: 0.7801 (tt) cc_final: 0.7477 (tp) REVERT: A 410 MET cc_start: 0.6671 (mmm) cc_final: 0.6349 (mmp) REVERT: A 467 ILE cc_start: 0.7498 (mt) cc_final: 0.7259 (mp) REVERT: B 54 PHE cc_start: 0.6221 (OUTLIER) cc_final: 0.6004 (m-10) outliers start: 29 outliers final: 14 residues processed: 146 average time/residue: 0.0546 time to fit residues: 11.3685 Evaluate side-chains 147 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 23 optimal weight: 0.0370 chunk 19 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 56 optimal weight: 0.0970 chunk 65 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.147219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.133145 restraints weight = 8019.046| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.13 r_work: 0.3574 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5878 Z= 0.153 Angle : 0.662 9.386 8008 Z= 0.319 Chirality : 0.042 0.131 963 Planarity : 0.005 0.042 973 Dihedral : 5.645 45.541 868 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.76 % Allowed : 26.19 % Favored : 70.05 % 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: 1.65 (0.31), residues: 750 helix: 1.57 (0.22), residues: 609 sheet: None (None), residues: 0 loop : -0.88 (0.51), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 421 TYR 0.010 0.001 TYR B 476 PHE 0.024 0.001 PHE A 206 TRP 0.008 0.001 TRP B 326 HIS 0.001 0.000 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 5878) covalent geometry : angle 0.66249 ( 8008) hydrogen bonds : bond 0.04419 ( 467) hydrogen bonds : angle 4.71527 ( 1371) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 266 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7658 (mp) REVERT: A 279 GLN cc_start: 0.8560 (mp10) cc_final: 0.8186 (mp10) REVERT: A 405 MET cc_start: 0.7249 (mtp) cc_final: 0.6987 (ttm) REVERT: A 410 MET cc_start: 0.6628 (mmm) cc_final: 0.6290 (mmp) REVERT: B 54 PHE cc_start: 0.6235 (OUTLIER) cc_final: 0.6015 (m-10) REVERT: B 254 VAL cc_start: 0.7563 (m) cc_final: 0.7267 (p) REVERT: B 261 LEU cc_start: 0.7596 (mm) cc_final: 0.7282 (mm) outliers start: 23 outliers final: 15 residues processed: 141 average time/residue: 0.0566 time to fit residues: 11.3630 Evaluate side-chains 147 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 53 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 69 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 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 35 ASN ** A 361 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 = 0.3854 r_free = 0.3854 target = 0.145357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.131254 restraints weight = 8073.952| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.13 r_work: 0.3547 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5878 Z= 0.192 Angle : 0.691 11.020 8008 Z= 0.334 Chirality : 0.044 0.141 963 Planarity : 0.005 0.043 973 Dihedral : 5.596 44.128 868 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.42 % Allowed : 26.84 % Favored : 68.74 % 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: 1.42 (0.31), residues: 750 helix: 1.40 (0.21), residues: 609 sheet: None (None), residues: 0 loop : -0.91 (0.50), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 479 TYR 0.010 0.002 TYR B 349 PHE 0.017 0.001 PHE B 28 TRP 0.008 0.001 TRP B 326 HIS 0.002 0.001 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 5878) covalent geometry : angle 0.69148 ( 8008) hydrogen bonds : bond 0.04649 ( 467) hydrogen bonds : angle 4.79459 ( 1371) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: A 266 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7677 (mp) REVERT: A 279 GLN cc_start: 0.8587 (mp10) cc_final: 0.8165 (mp10) REVERT: A 359 LEU cc_start: 0.7759 (tt) cc_final: 0.7484 (tp) REVERT: A 376 VAL cc_start: 0.7415 (t) cc_final: 0.7205 (t) REVERT: A 410 MET cc_start: 0.6747 (mmm) cc_final: 0.6423 (mmp) REVERT: B 254 VAL cc_start: 0.7551 (m) cc_final: 0.7237 (p) outliers start: 27 outliers final: 20 residues processed: 143 average time/residue: 0.0555 time to fit residues: 11.3021 Evaluate side-chains 148 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 439 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 36 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.144581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.130351 restraints weight = 8063.625| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.14 r_work: 0.3528 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5878 Z= 0.212 Angle : 0.697 9.978 8008 Z= 0.340 Chirality : 0.045 0.155 963 Planarity : 0.005 0.044 973 Dihedral : 5.587 42.278 868 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.91 % Allowed : 27.17 % Favored : 67.92 % 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: 1.23 (0.31), residues: 750 helix: 1.28 (0.22), residues: 609 sheet: None (None), residues: 0 loop : -1.03 (0.49), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 225 TYR 0.010 0.002 TYR A 477 PHE 0.031 0.002 PHE A 206 TRP 0.007 0.001 TRP B 326 HIS 0.002 0.001 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 5878) covalent geometry : angle 0.69721 ( 8008) hydrogen bonds : bond 0.04768 ( 467) hydrogen bonds : angle 4.87691 ( 1371) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 151 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6537 (tt) REVERT: A 266 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7705 (mp) REVERT: A 359 LEU cc_start: 0.7789 (tt) cc_final: 0.7537 (tp) REVERT: A 376 VAL cc_start: 0.7486 (t) cc_final: 0.7282 (t) REVERT: A 410 MET cc_start: 0.6778 (mmm) cc_final: 0.6484 (mmp) REVERT: B 254 VAL cc_start: 0.7529 (m) cc_final: 0.7251 (p) REVERT: B 261 LEU cc_start: 0.7602 (mm) cc_final: 0.7312 (mm) outliers start: 30 outliers final: 23 residues processed: 148 average time/residue: 0.0558 time to fit residues: 11.7486 Evaluate side-chains 154 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 439 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 71 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 0.0050 chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN ** A 361 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 = 0.3832 r_free = 0.3832 target = 0.143883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.129782 restraints weight = 8101.025| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.15 r_work: 0.3525 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5878 Z= 0.222 Angle : 0.724 9.935 8008 Z= 0.349 Chirality : 0.045 0.155 963 Planarity : 0.005 0.044 973 Dihedral : 5.579 44.533 868 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.91 % Allowed : 27.17 % Favored : 67.92 % 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: 1.21 (0.31), residues: 750 helix: 1.25 (0.21), residues: 607 sheet: None (None), residues: 0 loop : -0.93 (0.49), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 421 TYR 0.011 0.002 TYR A 477 PHE 0.027 0.002 PHE A 206 TRP 0.008 0.001 TRP B 326 HIS 0.002 0.001 HIS B 422 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 5878) covalent geometry : angle 0.72433 ( 8008) hydrogen bonds : bond 0.04857 ( 467) hydrogen bonds : angle 4.93275 ( 1371) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: A 266 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7702 (mp) REVERT: A 359 LEU cc_start: 0.7789 (tt) cc_final: 0.7532 (tp) REVERT: A 376 VAL cc_start: 0.7448 (t) cc_final: 0.7235 (t) REVERT: B 254 VAL cc_start: 0.7469 (m) cc_final: 0.7184 (p) REVERT: B 376 VAL cc_start: 0.7937 (OUTLIER) cc_final: 0.7716 (t) REVERT: B 479 ARG cc_start: 0.7078 (tmm160) cc_final: 0.6600 (tmm160) outliers start: 30 outliers final: 24 residues processed: 148 average time/residue: 0.0550 time to fit residues: 11.6221 Evaluate side-chains 154 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 439 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 56 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 73 optimal weight: 0.3980 chunk 54 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 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 361 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 = 0.3818 r_free = 0.3818 target = 0.141516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.127394 restraints weight = 8047.615| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.14 r_work: 0.3511 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5878 Z= 0.206 Angle : 0.725 10.761 8008 Z= 0.348 Chirality : 0.045 0.145 963 Planarity : 0.005 0.044 973 Dihedral : 5.537 44.140 868 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.42 % Allowed : 27.82 % Favored : 67.76 % 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: 1.19 (0.31), residues: 750 helix: 1.26 (0.22), residues: 605 sheet: None (None), residues: 0 loop : -1.05 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 421 TYR 0.011 0.002 TYR A 477 PHE 0.032 0.002 PHE A 206 TRP 0.008 0.001 TRP B 326 HIS 0.001 0.001 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 5878) covalent geometry : angle 0.72501 ( 8008) hydrogen bonds : bond 0.04804 ( 467) hydrogen bonds : angle 4.91279 ( 1371) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.204 Fit side-chains REVERT: A 151 LEU cc_start: 0.6776 (OUTLIER) cc_final: 0.6532 (tt) REVERT: A 266 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7724 (mp) REVERT: A 359 LEU cc_start: 0.7810 (tt) cc_final: 0.7563 (tp) REVERT: A 376 VAL cc_start: 0.7503 (t) cc_final: 0.7276 (t) REVERT: B 254 VAL cc_start: 0.7452 (m) cc_final: 0.7157 (p) REVERT: B 376 VAL cc_start: 0.7960 (OUTLIER) cc_final: 0.7738 (t) REVERT: B 479 ARG cc_start: 0.7072 (tmm160) cc_final: 0.6595 (tmm160) outliers start: 27 outliers final: 21 residues processed: 142 average time/residue: 0.0576 time to fit residues: 11.7008 Evaluate side-chains 154 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 439 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 0.0060 chunk 55 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.0170 chunk 48 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 overall best weight: 0.4634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN ** A 361 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 = 0.3826 r_free = 0.3826 target = 0.141957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.127925 restraints weight = 8059.890| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.15 r_work: 0.3525 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5878 Z= 0.177 Angle : 0.719 10.657 8008 Z= 0.343 Chirality : 0.044 0.140 963 Planarity : 0.005 0.047 973 Dihedral : 5.463 43.857 868 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.09 % Allowed : 28.31 % Favored : 67.59 % 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: 1.33 (0.31), residues: 750 helix: 1.36 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -0.98 (0.49), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 421 TYR 0.008 0.001 TYR B 349 PHE 0.033 0.001 PHE A 206 TRP 0.009 0.001 TRP B 326 HIS 0.002 0.000 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 5878) covalent geometry : angle 0.71856 ( 8008) hydrogen bonds : bond 0.04631 ( 467) hydrogen bonds : angle 4.86448 ( 1371) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.204 Fit side-chains REVERT: A 151 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6506 (tt) REVERT: A 266 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7751 (mp) REVERT: A 279 GLN cc_start: 0.8597 (mp10) cc_final: 0.8215 (mp10) REVERT: A 359 LEU cc_start: 0.7793 (tt) cc_final: 0.7542 (tp) REVERT: A 376 VAL cc_start: 0.7493 (t) cc_final: 0.7241 (t) REVERT: A 405 MET cc_start: 0.7400 (mtp) cc_final: 0.7159 (ttm) REVERT: B 170 MET cc_start: 0.7633 (tpp) cc_final: 0.7424 (ttt) REVERT: B 254 VAL cc_start: 0.7398 (m) cc_final: 0.7115 (p) REVERT: B 376 VAL cc_start: 0.7914 (OUTLIER) cc_final: 0.7688 (t) REVERT: B 479 ARG cc_start: 0.7071 (tmm160) cc_final: 0.6587 (tmm160) outliers start: 25 outliers final: 21 residues processed: 140 average time/residue: 0.0561 time to fit residues: 11.2638 Evaluate side-chains 149 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 439 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.6980 chunk 3 optimal weight: 0.3980 chunk 20 optimal weight: 0.0980 chunk 39 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 64 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 74 optimal weight: 0.0870 chunk 37 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 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 = 0.3844 r_free = 0.3844 target = 0.143520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.129970 restraints weight = 8170.101| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.05 r_work: 0.3557 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5878 Z= 0.157 Angle : 0.722 11.992 8008 Z= 0.343 Chirality : 0.044 0.173 963 Planarity : 0.005 0.042 973 Dihedral : 5.355 43.424 868 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.76 % Allowed : 29.62 % Favored : 66.61 % 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: 1.47 (0.32), residues: 750 helix: 1.45 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -0.89 (0.51), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 421 TYR 0.008 0.001 TYR B 349 PHE 0.019 0.001 PHE B 28 TRP 0.010 0.001 TRP B 326 HIS 0.001 0.000 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 5878) covalent geometry : angle 0.72211 ( 8008) hydrogen bonds : bond 0.04501 ( 467) hydrogen bonds : angle 4.79636 ( 1371) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.208 Fit side-chains REVERT: A 151 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6508 (tt) REVERT: A 266 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7737 (mp) REVERT: A 279 GLN cc_start: 0.8544 (mp10) cc_final: 0.8186 (mp10) REVERT: A 280 PRO cc_start: 0.7836 (Cg_endo) cc_final: 0.7514 (Cg_exo) REVERT: A 359 LEU cc_start: 0.7773 (tt) cc_final: 0.7526 (tp) REVERT: A 376 VAL cc_start: 0.7465 (t) cc_final: 0.7223 (t) REVERT: A 405 MET cc_start: 0.7258 (mtp) cc_final: 0.7021 (ttm) REVERT: B 254 VAL cc_start: 0.7333 (m) cc_final: 0.7049 (p) REVERT: B 356 PHE cc_start: 0.7823 (m-80) cc_final: 0.7566 (m-80) REVERT: B 376 VAL cc_start: 0.7937 (OUTLIER) cc_final: 0.7702 (t) outliers start: 23 outliers final: 19 residues processed: 140 average time/residue: 0.0608 time to fit residues: 12.0201 Evaluate side-chains 148 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 439 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 0.3980 chunk 12 optimal weight: 0.5980 chunk 35 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 6 optimal weight: 0.0270 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN ** A 361 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 = 0.3837 r_free = 0.3837 target = 0.142948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.129024 restraints weight = 8049.580| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.16 r_work: 0.3542 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5878 Z= 0.170 Angle : 0.719 10.505 8008 Z= 0.343 Chirality : 0.044 0.168 963 Planarity : 0.005 0.043 973 Dihedral : 5.323 43.917 868 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.09 % Allowed : 28.97 % Favored : 66.94 % 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: 1.47 (0.32), residues: 750 helix: 1.45 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -0.89 (0.51), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 421 TYR 0.009 0.001 TYR B 349 PHE 0.052 0.002 PHE A 206 TRP 0.010 0.001 TRP B 326 HIS 0.001 0.000 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 5878) covalent geometry : angle 0.71922 ( 8008) hydrogen bonds : bond 0.04511 ( 467) hydrogen bonds : angle 4.80221 ( 1371) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1389.73 seconds wall clock time: 24 minutes 30.94 seconds (1470.94 seconds total)