Starting phenix.real_space_refine on Fri Jul 19 02:12:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgl_41240/07_2024/8tgl_41240_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgl_41240/07_2024/8tgl_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgl_41240/07_2024/8tgl_41240.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgl_41240/07_2024/8tgl_41240.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgl_41240/07_2024/8tgl_41240_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgl_41240/07_2024/8tgl_41240_trim.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/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: 4.20, per 1000 atoms: 0.73 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 - 3.50 Amino acid : False - 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: 2.24 Conformation dependent library (CDL) restraints added in 935.6 milliseconds 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: 0.47 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: 1.58 Time building geometry restraints manager: 2.44 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: 98.91 - 106.37: 217 106.37 - 113.84: 3358 113.84 - 121.30: 3305 121.30 - 128.77: 1094 128.77 - 136.23: 34 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 2.440 nonbonded pdb=" O THR B 291 " pdb=" OG1 THR B 291 " model vdw 2.225 2.440 nonbonded pdb=" O VAL A 375 " pdb=" OG SER A 379 " model vdw 2.236 2.440 nonbonded pdb=" O ARG B 138 " pdb=" OH TYR B 190 " model vdw 2.238 2.440 nonbonded pdb=" O ILE A 277 " pdb=" NE2 GLN A 279 " model vdw 2.246 2.520 ... (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 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: 1.350 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.890 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.580 ------------------------------------------------------------------------------- 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= 0.330 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.005 0.001 TRP B 459 HIS 0.018 0.002 HIS B 387 PHE 0.024 0.001 PHE B 28 TYR 0.009 0.001 TYR A 426 ARG 0.002 0.000 ARG A 365 *********************** 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 fitting. rotamer outliers: 5 poor density : 122 time to evaluate : 0.571 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: 0.1422 time to fit residues: 24.0164 Evaluate side-chains 120 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 63 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 58 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN B 329 GLN B 468 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 5878 Z= 0.302 Angle : 0.707 10.096 8008 Z= 0.344 Chirality : 0.044 0.176 963 Planarity : 0.006 0.046 973 Dihedral : 7.471 59.845 871 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.56 % Allowed : 26.35 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.31), residues: 750 helix: 1.53 (0.22), residues: 600 sheet: None (None), residues: 0 loop : -0.98 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 326 HIS 0.006 0.001 HIS B 387 PHE 0.034 0.002 PHE A 206 TYR 0.011 0.002 TYR B 349 ARG 0.002 0.001 ARG B 479 *********************** 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 162 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 128 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 151 LEU cc_start: 0.6561 (OUTLIER) cc_final: 0.6312 (tt) REVERT: A 233 LEU cc_start: 0.7439 (mt) cc_final: 0.7149 (mp) REVERT: A 266 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7823 (mp) REVERT: A 410 MET cc_start: 0.6030 (mmm) cc_final: 0.5733 (mmp) REVERT: B 325 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7601 (mp) REVERT: B 356 PHE cc_start: 0.7780 (m-80) cc_final: 0.7489 (m-80) REVERT: B 410 MET cc_start: 0.6432 (mmp) cc_final: 0.6165 (tpp) outliers start: 34 outliers final: 15 residues processed: 148 average time/residue: 0.1379 time to fit residues: 28.1090 Evaluate side-chains 144 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 177 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 39 THR 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 392 LEU Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 0.3980 chunk 56 optimal weight: 0.3980 chunk 46 optimal weight: 0.5980 chunk 18 optimal weight: 0.0000 chunk 68 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 23 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.1431 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= 0.234 Angle : 0.673 10.631 8008 Z= 0.319 Chirality : 0.042 0.133 963 Planarity : 0.005 0.044 973 Dihedral : 6.078 46.965 868 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 5.24 % Allowed : 26.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.31), residues: 750 helix: 1.56 (0.22), residues: 605 sheet: None (None), residues: 0 loop : -0.98 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 326 HIS 0.006 0.001 HIS B 387 PHE 0.028 0.001 PHE A 206 TYR 0.010 0.001 TYR B 476 ARG 0.002 0.000 ARG B 225 *********************** 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 165 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 133 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 279 GLN cc_start: 0.8551 (mp10) cc_final: 0.8185 (mp10) REVERT: A 359 LEU cc_start: 0.7802 (tt) cc_final: 0.7463 (tp) REVERT: A 467 ILE cc_start: 0.7426 (mt) cc_final: 0.7216 (mp) REVERT: B 325 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7548 (mp) outliers start: 32 outliers final: 15 residues processed: 151 average time/residue: 0.1434 time to fit residues: 30.1468 Evaluate side-chains 145 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 294 PHE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 268 LEU 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 392 LEU Chi-restraints excluded: chain B residue 423 THR 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 67 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 45 optimal weight: 0.0670 chunk 68 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5878 Z= 0.276 Angle : 0.692 10.316 8008 Z= 0.332 Chirality : 0.043 0.137 963 Planarity : 0.005 0.043 973 Dihedral : 5.719 50.564 868 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.26 % Allowed : 27.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.31), residues: 750 helix: 1.44 (0.22), residues: 605 sheet: None (None), residues: 0 loop : -1.07 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 326 HIS 0.004 0.001 HIS B 387 PHE 0.025 0.002 PHE A 206 TYR 0.012 0.002 TYR B 476 ARG 0.001 0.000 ARG B 479 *********************** 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 157 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 266 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7813 (mp) REVERT: A 279 GLN cc_start: 0.8576 (mp10) cc_final: 0.8221 (mp10) REVERT: A 447 THR cc_start: 0.7432 (p) cc_final: 0.7170 (m) REVERT: B 254 VAL cc_start: 0.7443 (m) cc_final: 0.7148 (p) outliers start: 26 outliers final: 17 residues processed: 147 average time/residue: 0.1330 time to fit residues: 27.0928 Evaluate side-chains 147 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 218 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 438 CYS 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 371 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 439 MET 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 41 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 0.0970 chunk 29 optimal weight: 0.4980 chunk 61 optimal weight: 0.0270 chunk 50 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 37 optimal weight: 0.0470 chunk 65 optimal weight: 0.9990 chunk 18 optimal weight: 0.2980 chunk 24 optimal weight: 0.3980 overall best weight: 0.1734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5878 Z= 0.194 Angle : 0.656 10.684 8008 Z= 0.313 Chirality : 0.041 0.128 963 Planarity : 0.005 0.041 973 Dihedral : 5.472 52.201 868 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.26 % Allowed : 27.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.32), residues: 750 helix: 1.61 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -0.92 (0.50), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 326 HIS 0.003 0.000 HIS B 387 PHE 0.023 0.001 PHE A 206 TYR 0.009 0.001 TYR B 476 ARG 0.002 0.000 ARG B 421 *********************** 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 157 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 151 LEU cc_start: 0.6518 (OUTLIER) cc_final: 0.6280 (tt) REVERT: A 266 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7761 (mp) REVERT: A 359 LEU cc_start: 0.7756 (tt) cc_final: 0.7444 (tp) REVERT: A 447 THR cc_start: 0.7406 (p) cc_final: 0.7057 (m) REVERT: B 179 LEU cc_start: 0.8040 (mp) cc_final: 0.7754 (mp) REVERT: B 254 VAL cc_start: 0.7360 (m) cc_final: 0.7079 (p) REVERT: B 261 LEU cc_start: 0.7204 (mm) cc_final: 0.7002 (mm) REVERT: B 410 MET cc_start: 0.6352 (mmp) cc_final: 0.5918 (tpp) outliers start: 26 outliers final: 19 residues processed: 148 average time/residue: 0.1398 time to fit residues: 28.5978 Evaluate side-chains 153 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 132 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 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 236 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 438 CYS 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 208 SER 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 423 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 42 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN B 387 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5878 Z= 0.292 Angle : 0.681 11.004 8008 Z= 0.329 Chirality : 0.044 0.143 963 Planarity : 0.005 0.042 973 Dihedral : 5.565 53.082 868 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.75 % Allowed : 27.82 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.31), residues: 750 helix: 1.44 (0.22), residues: 607 sheet: None (None), residues: 0 loop : -1.02 (0.49), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.002 0.001 HIS B 422 PHE 0.024 0.002 PHE A 206 TYR 0.010 0.002 TYR B 349 ARG 0.001 0.000 ARG B 479 *********************** 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 162 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 151 LEU cc_start: 0.6532 (OUTLIER) cc_final: 0.6298 (tt) REVERT: A 266 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7815 (mp) REVERT: A 359 LEU cc_start: 0.7769 (tt) cc_final: 0.7489 (tp) REVERT: A 447 THR cc_start: 0.7414 (p) cc_final: 0.7193 (m) REVERT: B 254 VAL cc_start: 0.7394 (m) cc_final: 0.7160 (p) REVERT: B 327 MET cc_start: 0.7325 (mtt) cc_final: 0.7093 (mtt) REVERT: B 376 VAL cc_start: 0.8054 (OUTLIER) cc_final: 0.7820 (t) REVERT: B 410 MET cc_start: 0.6408 (mmp) cc_final: 0.6025 (tpp) outliers start: 29 outliers final: 20 residues processed: 149 average time/residue: 0.1332 time to fit residues: 27.7152 Evaluate side-chains 154 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 331 MET Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 438 CYS 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 368 CYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 376 VAL 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 8 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 40 optimal weight: 0.5980 chunk 72 optimal weight: 0.0870 chunk 45 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5878 Z= 0.258 Angle : 0.675 10.351 8008 Z= 0.326 Chirality : 0.043 0.148 963 Planarity : 0.005 0.042 973 Dihedral : 5.493 53.564 868 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.09 % Allowed : 28.81 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.31), residues: 750 helix: 1.42 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -1.03 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.001 0.000 HIS A 422 PHE 0.024 0.001 PHE A 206 TYR 0.008 0.001 TYR B 349 ARG 0.001 0.000 ARG B 225 *********************** 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 155 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: A 151 LEU cc_start: 0.6522 (OUTLIER) cc_final: 0.6283 (tt) REVERT: A 233 LEU cc_start: 0.7508 (mt) cc_final: 0.7230 (mp) REVERT: A 266 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7823 (mp) REVERT: A 447 THR cc_start: 0.7405 (p) cc_final: 0.7174 (m) REVERT: B 179 LEU cc_start: 0.8068 (mp) cc_final: 0.7788 (mp) REVERT: B 254 VAL cc_start: 0.7352 (m) cc_final: 0.7109 (p) REVERT: B 327 MET cc_start: 0.7337 (mtt) cc_final: 0.7127 (mtt) REVERT: B 376 VAL cc_start: 0.8040 (OUTLIER) cc_final: 0.7816 (t) REVERT: B 410 MET cc_start: 0.6419 (mmp) cc_final: 0.5997 (tpp) outliers start: 25 outliers final: 20 residues processed: 144 average time/residue: 0.1378 time to fit residues: 27.8221 Evaluate side-chains 152 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 331 MET Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 438 CYS 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 368 CYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 376 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 0.0980 chunk 56 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5878 Z= 0.270 Angle : 0.689 11.423 8008 Z= 0.331 Chirality : 0.043 0.144 963 Planarity : 0.005 0.042 973 Dihedral : 5.506 53.637 868 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.93 % Allowed : 29.62 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.31), residues: 750 helix: 1.41 (0.22), residues: 605 sheet: None (None), residues: 0 loop : -1.07 (0.48), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 326 HIS 0.001 0.000 HIS A 422 PHE 0.020 0.001 PHE B 28 TYR 0.009 0.002 TYR B 349 ARG 0.001 0.000 ARG B 225 *********************** 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 155 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 0.611 Fit side-chains REVERT: A 151 LEU cc_start: 0.6508 (OUTLIER) cc_final: 0.6280 (tt) REVERT: A 233 LEU cc_start: 0.7514 (mt) cc_final: 0.7227 (mp) REVERT: A 246 PHE cc_start: 0.6864 (t80) cc_final: 0.6664 (t80) REVERT: A 266 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7822 (mp) REVERT: A 359 LEU cc_start: 0.7762 (tt) cc_final: 0.7455 (tp) REVERT: A 447 THR cc_start: 0.7411 (p) cc_final: 0.7193 (m) REVERT: B 254 VAL cc_start: 0.7293 (m) cc_final: 0.7045 (p) REVERT: B 376 VAL cc_start: 0.8053 (OUTLIER) cc_final: 0.7834 (t) REVERT: B 410 MET cc_start: 0.6406 (mmp) cc_final: 0.6014 (tpp) outliers start: 24 outliers final: 20 residues processed: 144 average time/residue: 0.1295 time to fit residues: 26.1187 Evaluate side-chains 152 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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 331 MET Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 438 CYS 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 368 CYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 376 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 20 optimal weight: 0.0970 chunk 60 optimal weight: 0.0980 chunk 63 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 44 optimal weight: 0.3980 chunk 71 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5878 Z= 0.226 Angle : 0.682 10.743 8008 Z= 0.326 Chirality : 0.043 0.138 963 Planarity : 0.005 0.052 973 Dihedral : 5.457 53.624 868 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.60 % Allowed : 30.77 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.31), residues: 750 helix: 1.51 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -1.03 (0.48), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 326 HIS 0.002 0.000 HIS A 422 PHE 0.033 0.001 PHE A 206 TYR 0.008 0.001 TYR A 430 ARG 0.002 0.000 ARG B 421 *********************** 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 154 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 151 LEU cc_start: 0.6514 (OUTLIER) cc_final: 0.6286 (tt) REVERT: A 246 PHE cc_start: 0.6752 (t80) cc_final: 0.6528 (t80) REVERT: A 266 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7821 (mp) REVERT: A 359 LEU cc_start: 0.7741 (tt) cc_final: 0.7431 (tp) REVERT: A 447 THR cc_start: 0.7398 (p) cc_final: 0.7138 (m) REVERT: B 179 LEU cc_start: 0.8035 (mp) cc_final: 0.7792 (mp) REVERT: B 254 VAL cc_start: 0.7316 (m) cc_final: 0.7074 (p) REVERT: B 327 MET cc_start: 0.7287 (mtt) cc_final: 0.7074 (mtt) REVERT: B 376 VAL cc_start: 0.8050 (OUTLIER) cc_final: 0.7819 (t) REVERT: B 410 MET cc_start: 0.6400 (mmp) cc_final: 0.5996 (tpp) outliers start: 22 outliers final: 17 residues processed: 144 average time/residue: 0.1332 time to fit residues: 26.8925 Evaluate side-chains 152 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 378 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 438 CYS 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 371 ILE 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 33 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 59 optimal weight: 0.2980 chunk 6 optimal weight: 0.0570 chunk 45 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5878 Z= 0.266 Angle : 0.707 10.727 8008 Z= 0.339 Chirality : 0.044 0.167 963 Planarity : 0.005 0.045 973 Dihedral : 5.465 53.439 868 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.76 % Allowed : 30.77 % Favored : 65.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.31), residues: 750 helix: 1.44 (0.22), residues: 605 sheet: None (None), residues: 0 loop : -1.10 (0.48), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 326 HIS 0.002 0.000 HIS A 422 PHE 0.036 0.002 PHE A 206 TYR 0.009 0.001 TYR B 349 ARG 0.001 0.000 ARG B 421 ********************** 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 156 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 133 time to evaluate : 0.528 Fit side-chains REVERT: A 151 LEU cc_start: 0.6505 (OUTLIER) cc_final: 0.6271 (tt) REVERT: A 233 LEU cc_start: 0.7479 (mt) cc_final: 0.7278 (mp) REVERT: A 246 PHE cc_start: 0.6781 (t80) cc_final: 0.6536 (t80) REVERT: A 266 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7842 (mp) REVERT: A 359 LEU cc_start: 0.7742 (tt) cc_final: 0.7469 (tp) REVERT: A 447 THR cc_start: 0.7403 (p) cc_final: 0.7176 (m) REVERT: B 179 LEU cc_start: 0.8040 (mp) cc_final: 0.7792 (mp) REVERT: B 254 VAL cc_start: 0.7260 (m) cc_final: 0.7015 (p) REVERT: B 376 VAL cc_start: 0.8056 (OUTLIER) cc_final: 0.7825 (t) REVERT: B 410 MET cc_start: 0.6402 (mmp) cc_final: 0.6007 (tpp) outliers start: 23 outliers final: 20 residues processed: 145 average time/residue: 0.1288 time to fit residues: 26.0514 Evaluate side-chains 154 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 331 MET Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 438 CYS 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 368 CYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 376 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.0020 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 61 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3846 r_free = 0.3846 target = 0.143681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.129822 restraints weight = 8028.521| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.07 r_work: 0.3549 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.2049 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= 0.234 Angle : 0.704 10.708 8008 Z= 0.336 Chirality : 0.043 0.154 963 Planarity : 0.005 0.042 973 Dihedral : 5.393 51.148 868 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.76 % Allowed : 30.93 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.31), residues: 750 helix: 1.47 (0.22), residues: 605 sheet: None (None), residues: 0 loop : -1.07 (0.48), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 326 HIS 0.002 0.000 HIS A 422 PHE 0.017 0.001 PHE B 28 TYR 0.008 0.001 TYR B 349 ARG 0.002 0.000 ARG B 421 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1526.21 seconds wall clock time: 27 minutes 53.87 seconds (1673.87 seconds total)