Starting phenix.real_space_refine on Sun Mar 10 15:48:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtk_33451/03_2024/7xtk_33451_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtk_33451/03_2024/7xtk_33451.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtk_33451/03_2024/7xtk_33451.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtk_33451/03_2024/7xtk_33451.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtk_33451/03_2024/7xtk_33451_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtk_33451/03_2024/7xtk_33451_neut.pdb" } resolution = 2.89 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= 0.062 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 10 5.16 5 C 2105 2.51 5 N 516 2.21 5 O 528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 56": "OD1" <-> "OD2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3159 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3159 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 13, 'TRANS': 381} Chain breaks: 1 Time building chain proxies: 2.26, per 1000 atoms: 0.72 Number of scatterers: 3159 At special positions: 0 Unit cell: (72.165, 54.336, 73.014, 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 10 16.00 O 528 8.00 N 516 7.00 C 2105 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: 1.29 Conformation dependent library (CDL) restraints added in 592.7 milliseconds 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 80.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 28 through 38 Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 60 through 69 Processing helix chain 'A' and resid 69 through 91 removed outlier: 4.200A pdb=" N SER A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 4.672A pdb=" N LEU A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 112 removed outlier: 4.155A pdb=" N VAL A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 111 " --> pdb=" O TRP A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 133 removed outlier: 3.899A pdb=" N MET A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 144 Processing helix chain 'A' and resid 148 through 176 removed outlier: 3.510A pdb=" N LEU A 161 " --> pdb=" O ARG A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 200 removed outlier: 3.748A pdb=" N LEU A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN A 186 " --> pdb=" O PHE A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 263 Processing helix chain 'A' and resid 266 through 288 removed outlier: 3.802A pdb=" N TRP A 270 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TRP A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 296 removed outlier: 3.769A pdb=" N GLU A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 324 Processing helix chain 'A' and resid 336 through 355 removed outlier: 3.542A pdb=" N LEU A 352 " --> pdb=" O GLY A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 388 removed outlier: 3.835A pdb=" N CYS A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 369 " --> pdb=" O CYS A 365 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 371 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 380 " --> pdb=" O TYR A 376 " (cutoff:3.500A) Proline residue: A 381 - end of helix Processing helix chain 'A' and resid 392 through 419 removed outlier: 3.734A pdb=" N ALA A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 398 " --> pdb=" O GLU A 394 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 453 217 hydrogen bonds defined for protein. 651 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: 0.78 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 935 1.34 - 1.46: 745 1.46 - 1.58: 1549 1.58 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 3245 Sorted by residual: bond pdb=" C MET A 254 " pdb=" N LEU A 255 " ideal model delta sigma weight residual 1.332 1.294 0.038 1.40e-02 5.10e+03 7.37e+00 bond pdb=" CB ARG A 205 " pdb=" CG ARG A 205 " ideal model delta sigma weight residual 1.520 1.460 0.060 3.00e-02 1.11e+03 3.99e+00 bond pdb=" C VAL A 81 " pdb=" N PRO A 82 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.54e+00 bond pdb=" CG LEU A 258 " pdb=" CD2 LEU A 258 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.48e+00 bond pdb=" C LEU A 251 " pdb=" O LEU A 251 " ideal model delta sigma weight residual 1.233 1.250 -0.018 1.47e-02 4.63e+03 1.45e+00 ... (remaining 3240 not shown) Histogram of bond angle deviations from ideal: 100.42 - 107.14: 75 107.14 - 113.87: 1839 113.87 - 120.59: 1328 120.59 - 127.31: 1151 127.31 - 134.03: 30 Bond angle restraints: 4423 Sorted by residual: angle pdb=" N ARG A 333 " pdb=" CA ARG A 333 " pdb=" C ARG A 333 " ideal model delta sigma weight residual 114.64 103.10 11.54 1.52e+00 4.33e-01 5.76e+01 angle pdb=" N ARG A 205 " pdb=" CA ARG A 205 " pdb=" C ARG A 205 " ideal model delta sigma weight residual 110.13 115.16 -5.03 1.15e+00 7.56e-01 1.91e+01 angle pdb=" N VAL A 327 " pdb=" CA VAL A 327 " pdb=" C VAL A 327 " ideal model delta sigma weight residual 106.21 110.71 -4.50 1.07e+00 8.73e-01 1.77e+01 angle pdb=" N ARG A 148 " pdb=" CA ARG A 148 " pdb=" C ARG A 148 " ideal model delta sigma weight residual 114.64 108.47 6.17 1.52e+00 4.33e-01 1.65e+01 angle pdb=" CA ARG A 333 " pdb=" C ARG A 333 " pdb=" N TRP A 334 " ideal model delta sigma weight residual 119.58 114.22 5.36 1.39e+00 5.18e-01 1.48e+01 ... (remaining 4418 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.46: 1668 16.46 - 32.91: 160 32.91 - 49.37: 29 49.37 - 65.83: 6 65.83 - 82.28: 2 Dihedral angle restraints: 1865 sinusoidal: 703 harmonic: 1162 Sorted by residual: dihedral pdb=" CA ALA A 252 " pdb=" C ALA A 252 " pdb=" N ARG A 253 " pdb=" CA ARG A 253 " ideal model delta harmonic sigma weight residual 180.00 -145.79 -34.21 0 5.00e+00 4.00e-02 4.68e+01 dihedral pdb=" CA LEU A 255 " pdb=" C LEU A 255 " pdb=" N ARG A 256 " pdb=" CA ARG A 256 " ideal model delta harmonic sigma weight residual 180.00 152.93 27.07 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N TYR A 92 " pdb=" CA TYR A 92 " ideal model delta harmonic sigma weight residual 180.00 -156.56 -23.44 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 1862 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 397 0.046 - 0.092: 105 0.092 - 0.137: 16 0.137 - 0.183: 0 0.183 - 0.229: 1 Chirality restraints: 519 Sorted by residual: chirality pdb=" CA PHE A 202 " pdb=" N PHE A 202 " pdb=" C PHE A 202 " pdb=" CB PHE A 202 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA THR A 49 " pdb=" N THR A 49 " pdb=" C THR A 49 " pdb=" CB THR A 49 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA TRP A 107 " pdb=" N TRP A 107 " pdb=" C TRP A 107 " pdb=" CB TRP A 107 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.50e-01 ... (remaining 516 not shown) Planarity restraints: 534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 254 " 0.026 2.00e-02 2.50e+03 5.25e-02 2.76e+01 pdb=" C MET A 254 " -0.091 2.00e-02 2.50e+03 pdb=" O MET A 254 " 0.035 2.00e-02 2.50e+03 pdb=" N LEU A 255 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 81 " -0.056 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO A 82 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 69 " 0.045 5.00e-02 4.00e+02 6.75e-02 7.30e+00 pdb=" N PRO A 70 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " 0.038 5.00e-02 4.00e+02 ... (remaining 531 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 13 2.48 - 3.08: 2206 3.08 - 3.69: 4527 3.69 - 4.29: 7039 4.29 - 4.90: 11724 Nonbonded interactions: 25509 Sorted by model distance: nonbonded pdb=" O ARG A 253 " pdb=" N LEU A 255 " model vdw 1.873 2.520 nonbonded pdb=" O TYR A 139 " pdb=" NH2 ARG A 205 " model vdw 2.099 2.520 nonbonded pdb=" O PRO A 43 " pdb=" OG SER A 189 " model vdw 2.195 2.440 nonbonded pdb=" O ILE A 41 " pdb=" OG SER A 167 " model vdw 2.201 2.440 nonbonded pdb=" O LEU A 251 " pdb=" O ARG A 253 " model vdw 2.263 3.040 ... (remaining 25504 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 6.790 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.910 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:11.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 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 : 0.004 0.060 3245 Z= 0.267 Angle : 0.872 11.540 4423 Z= 0.539 Chirality : 0.041 0.229 519 Planarity : 0.008 0.087 534 Dihedral : 13.372 82.282 1119 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 1.28 % Allowed : 6.39 % Favored : 92.33 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -1.05 (0.43), residues: 391 helix: 0.43 (0.31), residues: 298 sheet: None (None), residues: 0 loop : -4.46 (0.50), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.002 0.001 HIS A 289 PHE 0.015 0.001 PHE A 84 TYR 0.025 0.002 TYR A 139 ARG 0.007 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.375 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.7558 time to fit residues: 27.9350 Evaluate side-chains 28 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 0.0570 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3245 Z= 0.214 Angle : 0.678 8.111 4423 Z= 0.350 Chirality : 0.039 0.196 519 Planarity : 0.007 0.065 534 Dihedral : 5.273 26.577 440 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 1.02 % Allowed : 6.39 % Favored : 92.58 % Rotamer: Outliers : 0.88 % Allowed : 5.90 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.03 (0.45), residues: 391 helix: 1.16 (0.31), residues: 302 sheet: None (None), residues: 0 loop : -4.36 (0.53), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 363 HIS 0.001 0.000 HIS A 355 PHE 0.010 0.001 PHE A 372 TYR 0.012 0.001 TYR A 139 ARG 0.004 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.351 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 36 average time/residue: 0.6728 time to fit residues: 25.6573 Evaluate side-chains 29 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.1980 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 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 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3245 Z= 0.246 Angle : 0.656 8.319 4423 Z= 0.337 Chirality : 0.039 0.186 519 Planarity : 0.006 0.061 534 Dihedral : 5.247 31.802 440 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 1.02 % Allowed : 6.39 % Favored : 92.58 % Rotamer: Outliers : 1.18 % Allowed : 7.67 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: 0.24 (0.45), residues: 391 helix: 1.31 (0.31), residues: 304 sheet: None (None), residues: 0 loop : -4.20 (0.57), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.014 0.001 PHE A 202 TYR 0.016 0.001 TYR A 139 ARG 0.003 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 0.360 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.7907 time to fit residues: 31.5926 Evaluate side-chains 33 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 321 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3245 Z= 0.239 Angle : 0.626 8.368 4423 Z= 0.322 Chirality : 0.039 0.186 519 Planarity : 0.005 0.056 534 Dihedral : 5.199 30.701 440 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 1.02 % Allowed : 6.91 % Favored : 92.07 % Rotamer: Outliers : 1.77 % Allowed : 7.96 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: 0.38 (0.45), residues: 391 helix: 1.42 (0.31), residues: 304 sheet: None (None), residues: 0 loop : -4.19 (0.55), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.002 0.001 HIS A 358 PHE 0.012 0.001 PHE A 372 TYR 0.015 0.001 TYR A 139 ARG 0.003 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.320 Fit side-chains REVERT: A 67 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7730 (mt-10) outliers start: 6 outliers final: 3 residues processed: 36 average time/residue: 0.7232 time to fit residues: 27.5381 Evaluate side-chains 35 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 321 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 0.0170 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3245 Z= 0.222 Angle : 0.600 8.341 4423 Z= 0.309 Chirality : 0.038 0.174 519 Planarity : 0.005 0.054 534 Dihedral : 5.056 29.829 440 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.39 % Favored : 92.84 % Rotamer: Outliers : 1.77 % Allowed : 10.91 % Favored : 87.32 % 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: 0.54 (0.45), residues: 391 helix: 1.52 (0.31), residues: 304 sheet: None (None), residues: 0 loop : -4.07 (0.56), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.001 0.001 HIS A 358 PHE 0.011 0.001 PHE A 372 TYR 0.013 0.001 TYR A 139 ARG 0.003 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 29 time to evaluate : 0.358 Fit side-chains REVERT: A 67 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7743 (mt-10) outliers start: 6 outliers final: 2 residues processed: 34 average time/residue: 0.7617 time to fit residues: 27.3564 Evaluate side-chains 32 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 321 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.0670 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 4 optimal weight: 0.0770 chunk 21 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3245 Z= 0.197 Angle : 0.581 8.289 4423 Z= 0.298 Chirality : 0.038 0.173 519 Planarity : 0.005 0.052 534 Dihedral : 4.954 29.282 440 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.91 % Favored : 92.33 % Rotamer: Outliers : 1.77 % Allowed : 10.62 % Favored : 87.61 % 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: 0.71 (0.45), residues: 391 helix: 1.60 (0.31), residues: 306 sheet: None (None), residues: 0 loop : -3.95 (0.57), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.001 0.000 HIS A 358 PHE 0.010 0.001 PHE A 372 TYR 0.012 0.001 TYR A 139 ARG 0.006 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 30 time to evaluate : 0.362 Fit side-chains REVERT: A 67 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7729 (mt-10) outliers start: 6 outliers final: 3 residues processed: 34 average time/residue: 0.7359 time to fit residues: 26.4316 Evaluate side-chains 34 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 321 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3245 Z= 0.238 Angle : 0.610 9.406 4423 Z= 0.312 Chirality : 0.039 0.175 519 Planarity : 0.005 0.052 534 Dihedral : 4.947 29.578 440 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.65 % Favored : 92.58 % Rotamer: Outliers : 1.77 % Allowed : 11.80 % Favored : 86.43 % 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: 0.66 (0.45), residues: 391 helix: 1.56 (0.31), residues: 305 sheet: None (None), residues: 0 loop : -3.89 (0.58), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.013 0.001 PHE A 202 TYR 0.016 0.001 TYR A 139 ARG 0.007 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 29 time to evaluate : 0.357 Fit side-chains REVERT: A 58 ASN cc_start: 0.8750 (m-40) cc_final: 0.8442 (m-40) REVERT: A 67 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7742 (mt-10) outliers start: 6 outliers final: 3 residues processed: 33 average time/residue: 0.7393 time to fit residues: 25.8841 Evaluate side-chains 32 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 321 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 0.0170 chunk 27 optimal weight: 0.0770 chunk 10 optimal weight: 0.4980 chunk 31 optimal weight: 0.5980 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3245 Z= 0.190 Angle : 0.564 9.533 4423 Z= 0.287 Chirality : 0.037 0.162 519 Planarity : 0.005 0.050 534 Dihedral : 4.827 29.210 440 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.65 % Favored : 92.58 % Rotamer: Outliers : 1.47 % Allowed : 12.39 % Favored : 86.14 % 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: 0.85 (0.45), residues: 391 helix: 1.70 (0.31), residues: 305 sheet: None (None), residues: 0 loop : -3.87 (0.58), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.001 0.000 HIS A 358 PHE 0.010 0.001 PHE A 372 TYR 0.011 0.001 TYR A 438 ARG 0.005 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 31 time to evaluate : 0.370 Fit side-chains REVERT: A 67 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7707 (mt-10) outliers start: 5 outliers final: 3 residues processed: 34 average time/residue: 0.7594 time to fit residues: 27.2841 Evaluate side-chains 34 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 321 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 30 optimal weight: 0.0870 chunk 3 optimal weight: 0.0980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3245 Z= 0.190 Angle : 0.564 9.829 4423 Z= 0.286 Chirality : 0.038 0.159 519 Planarity : 0.005 0.050 534 Dihedral : 4.732 28.958 440 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.14 % Favored : 93.09 % Rotamer: Outliers : 1.47 % Allowed : 12.68 % Favored : 85.84 % 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: 0.89 (0.45), residues: 391 helix: 1.73 (0.31), residues: 305 sheet: None (None), residues: 0 loop : -3.85 (0.57), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.001 0.000 HIS A 355 PHE 0.010 0.001 PHE A 372 TYR 0.015 0.001 TYR A 126 ARG 0.005 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.320 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 38 average time/residue: 0.6851 time to fit residues: 27.5458 Evaluate side-chains 35 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 321 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3245 Z= 0.257 Angle : 0.602 8.280 4423 Z= 0.307 Chirality : 0.039 0.163 519 Planarity : 0.005 0.050 534 Dihedral : 4.884 29.299 440 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.77 % Allowed : 8.18 % Favored : 91.05 % Rotamer: Outliers : 1.47 % Allowed : 13.27 % Favored : 85.25 % 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: 0.74 (0.45), residues: 391 helix: 1.62 (0.31), residues: 305 sheet: None (None), residues: 0 loop : -3.87 (0.57), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.014 0.001 PHE A 202 TYR 0.017 0.002 TYR A 139 ARG 0.006 0.000 ARG A 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 29 time to evaluate : 0.352 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 33 average time/residue: 0.7904 time to fit residues: 27.5149 Evaluate side-chains 32 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 321 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 0.0980 chunk 22 optimal weight: 0.5980 chunk 35 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 0.0000 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.148840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.125658 restraints weight = 3503.539| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.82 r_work: 0.3352 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3245 Z= 0.191 Angle : 0.564 10.161 4423 Z= 0.286 Chirality : 0.038 0.154 519 Planarity : 0.005 0.050 534 Dihedral : 4.761 29.125 440 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.39 % Favored : 92.84 % Rotamer: Outliers : 1.77 % Allowed : 12.98 % Favored : 85.25 % 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: 0.94 (0.45), residues: 391 helix: 1.76 (0.31), residues: 306 sheet: None (None), residues: 0 loop : -3.86 (0.58), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.001 0.000 HIS A 358 PHE 0.010 0.001 PHE A 372 TYR 0.014 0.001 TYR A 126 ARG 0.005 0.000 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1333.90 seconds wall clock time: 24 minutes 27.07 seconds (1467.07 seconds total)