Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 2 18:47:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtk_33451/10_2023/7xtk_33451_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtk_33451/10_2023/7xtk_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_33451/10_2023/7xtk_33451.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtk_33451/10_2023/7xtk_33451.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtk_33451/10_2023/7xtk_33451_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtk_33451/10_2023/7xtk_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-1.21rc1-5097/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: 2.17, per 1000 atoms: 0.69 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: 1.23 Conformation dependent library (CDL) restraints added in 458.4 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: 0.23 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: 0.82 Time building geometry restraints manager: 1.36 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: 1.350 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: 0.000 Extract box with map and model: 6.750 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.410 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:11.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.240 ------------------------------------------------------------------------------- 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 *********************** 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 : 0.308 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.7177 time to fit residues: 26.4822 Evaluate side-chains 28 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.302 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4543 ------------------------------------------------------------------------------- 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 *********************** 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 : 0.336 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 36 average time/residue: 0.6838 time to fit residues: 26.0666 Evaluate side-chains 29 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.320 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4588 ------------------------------------------------------------------------------- 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 *********************** 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 : 0.302 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.7760 time to fit residues: 30.9981 Evaluate side-chains 33 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.324 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.4760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7886 moved from start: 0.1339 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 : 0.623 7.649 4423 Z= 0.321 Chirality : 0.039 0.182 519 Planarity : 0.005 0.056 534 Dihedral : 5.192 30.603 440 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.65 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: 0.31 (0.44), residues: 391 helix: 1.42 (0.31), residues: 304 sheet: None (None), residues: 0 loop : -4.44 (0.50), residues: 87 *********************** 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 : 0.309 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 36 average time/residue: 0.6811 time to fit residues: 25.9459 Evaluate side-chains 33 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.337 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.4647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7922 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 3245 Z= 0.272 Angle : 0.633 6.981 4423 Z= 0.326 Chirality : 0.040 0.180 519 Planarity : 0.005 0.055 534 Dihedral : 5.161 30.250 440 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.65 % Favored : 92.58 % Rotamer: Outliers : 1.47 % Allowed : 10.91 % Favored : 87.61 % 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: 0.32 (0.44), residues: 391 helix: 1.37 (0.30), residues: 306 sheet: None (None), residues: 0 loop : -4.31 (0.52), residues: 85 *********************** 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 36 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 31 time to evaluate : 0.315 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 36 average time/residue: 0.6487 time to fit residues: 24.8462 Evaluate side-chains 32 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.327 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.4865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.0980 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 7.9990 chunk 36 optimal weight: 0.0040 chunk 4 optimal weight: 0.0050 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.0040 overall best weight: 0.1418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 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 0.041 3245 Z= 0.164 Angle : 0.550 7.916 4423 Z= 0.285 Chirality : 0.037 0.172 519 Planarity : 0.005 0.052 534 Dihedral : 4.883 29.619 440 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.77 % Allowed : 5.88 % Favored : 93.35 % Rotamer: Outliers : 1.18 % Allowed : 11.21 % 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: 0.85 (0.45), residues: 391 helix: 1.71 (0.31), residues: 306 sheet: None (None), residues: 0 loop : -3.93 (0.57), residues: 85 *********************** 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: 4 poor density : 32 time to evaluate : 0.348 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 36 average time/residue: 0.6594 time to fit residues: 25.1554 Evaluate side-chains 31 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 0.255 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.4736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 0.0770 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3245 Z= 0.228 Angle : 0.597 9.659 4423 Z= 0.304 Chirality : 0.039 0.180 519 Planarity : 0.005 0.050 534 Dihedral : 4.870 29.286 440 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.77 % Allowed : 5.88 % Favored : 93.35 % Rotamer: Outliers : 1.47 % Allowed : 12.09 % 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: 0.79 (0.45), residues: 391 helix: 1.66 (0.31), residues: 305 sheet: None (None), residues: 0 loop : -3.88 (0.57), residues: 86 *********************** 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: 5 poor density : 30 time to evaluate : 0.351 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 34 average time/residue: 0.7330 time to fit residues: 26.3719 Evaluate side-chains 33 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.355 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1747 time to fit residues: 0.6806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.3980 chunk 29 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7900 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3245 Z= 0.250 Angle : 0.603 9.276 4423 Z= 0.307 Chirality : 0.039 0.173 519 Planarity : 0.005 0.050 534 Dihedral : 4.937 29.713 440 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.65 % Favored : 92.58 % Rotamer: Outliers : 1.47 % Allowed : 12.09 % 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: 0.70 (0.45), residues: 391 helix: 1.58 (0.31), residues: 305 sheet: None (None), residues: 0 loop : -3.86 (0.58), residues: 86 *********************** 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 35 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 30 time to evaluate : 0.342 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 34 average time/residue: 0.6864 time to fit residues: 24.8274 Evaluate side-chains 30 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 28 time to evaluate : 0.344 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.4725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 0.4980 chunk 3 optimal weight: 0.0770 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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: 0.7879 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3245 Z= 0.212 Angle : 0.577 10.021 4423 Z= 0.293 Chirality : 0.038 0.168 519 Planarity : 0.005 0.050 534 Dihedral : 4.828 29.342 440 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.14 % Favored : 93.09 % Rotamer: Outliers : 1.18 % Allowed : 13.27 % Favored : 85.55 % 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: 0.86 (0.45), residues: 391 helix: 1.71 (0.31), residues: 302 sheet: None (None), residues: 0 loop : -3.68 (0.58), residues: 89 *********************** 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 34 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.336 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 33 average time/residue: 0.7205 time to fit residues: 25.1366 Evaluate side-chains 32 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.311 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1808 time to fit residues: 0.6925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.2980 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 0.0870 chunk 28 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 31 optimal weight: 0.4980 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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: 0.7860 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3245 Z= 0.199 Angle : 0.561 8.320 4423 Z= 0.287 Chirality : 0.038 0.164 519 Planarity : 0.005 0.049 534 Dihedral : 4.768 29.085 440 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.65 % Favored : 92.58 % Rotamer: Outliers : 1.47 % Allowed : 12.98 % Favored : 85.55 % 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: 0.86 (0.45), residues: 391 helix: 1.71 (0.31), residues: 305 sheet: None (None), residues: 0 loop : -3.86 (0.58), residues: 86 ********************** 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 36 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 31 time to evaluate : 0.359 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 35 average time/residue: 0.8446 time to fit residues: 31.1732 Evaluate side-chains 34 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.344 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1949 time to fit residues: 0.7109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 0.0470 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 24 optimal weight: 0.2980 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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 = 0.3654 r_free = 0.3654 target = 0.144529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.121131 restraints weight = 3528.621| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.85 r_work: 0.3361 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3245 Z= 0.203 Angle : 0.570 10.158 4423 Z= 0.288 Chirality : 0.038 0.161 519 Planarity : 0.005 0.049 534 Dihedral : 4.742 28.977 440 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.65 % Favored : 92.58 % Rotamer: Outliers : 1.18 % Allowed : 13.57 % 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: 0.89 (0.45), residues: 391 helix: 1.73 (0.30), residues: 305 sheet: None (None), residues: 0 loop : -3.83 (0.58), residues: 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1256.73 seconds wall clock time: 23 minutes 11.16 seconds (1391.16 seconds total)