Starting phenix.real_space_refine on Thu Dec 7 15:48:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p34_17383/12_2023/8p34_17383_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p34_17383/12_2023/8p34_17383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p34_17383/12_2023/8p34_17383.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p34_17383/12_2023/8p34_17383.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p34_17383/12_2023/8p34_17383_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p34_17383/12_2023/8p34_17383_neut.pdb" } resolution = 2.61 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= 0.000 sd= 0.002 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 1 5.16 5 C 445 2.51 5 N 132 2.21 5 O 133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 314": "OD1" <-> "OD2" Residue "A ASP 345": "OD1" <-> "OD2" Residue "A ASP 348": "OD1" <-> "OD2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 711 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 711 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Time building chain proxies: 0.96, per 1000 atoms: 1.35 Number of scatterers: 711 At special positions: 0 Unit cell: (116.25, 75.33, 30.69, 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 1 16.00 O 133 8.00 N 132 7.00 C 445 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: 0.20 Conformation dependent library (CDL) restraints added in 141.9 milliseconds 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 162 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 0.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 152 1.34 - 1.45: 163 1.45 - 1.57: 406 1.57 - 1.69: 0 1.69 - 1.81: 1 Bond restraints: 722 Sorted by residual: bond pdb=" CA SER A 262 " pdb=" CB SER A 262 " ideal model delta sigma weight residual 1.532 1.488 0.044 1.59e-02 3.96e+03 7.79e+00 bond pdb=" CE1 HIS A 362 " pdb=" NE2 HIS A 362 " ideal model delta sigma weight residual 1.321 1.295 0.026 1.00e-02 1.00e+04 6.54e+00 bond pdb=" CG HIS A 362 " pdb=" CD2 HIS A 362 " ideal model delta sigma weight residual 1.354 1.326 0.028 1.10e-02 8.26e+03 6.45e+00 bond pdb=" CA SER A 352 " pdb=" CB SER A 352 " ideal model delta sigma weight residual 1.534 1.495 0.039 1.72e-02 3.38e+03 5.02e+00 bond pdb=" C GLN A 269 " pdb=" O GLN A 269 " ideal model delta sigma weight residual 1.233 1.223 0.010 4.80e-03 4.34e+04 4.30e+00 ... (remaining 717 not shown) Histogram of bond angle deviations from ideal: 103.00 - 108.79: 84 108.79 - 114.58: 376 114.58 - 120.38: 248 120.38 - 126.17: 249 126.17 - 131.96: 7 Bond angle restraints: 964 Sorted by residual: angle pdb=" C HIS A 268 " pdb=" N GLN A 269 " pdb=" CA GLN A 269 " ideal model delta sigma weight residual 123.10 126.62 -3.52 9.60e-01 1.09e+00 1.35e+01 angle pdb=" CB GLU A 264 " pdb=" CG GLU A 264 " pdb=" CD GLU A 264 " ideal model delta sigma weight residual 112.60 118.31 -5.71 1.70e+00 3.46e-01 1.13e+01 angle pdb=" N LYS A 369 " pdb=" CA LYS A 369 " pdb=" C LYS A 369 " ideal model delta sigma weight residual 108.99 113.92 -4.93 1.57e+00 4.06e-01 9.87e+00 angle pdb=" C ASN A 359 " pdb=" CA ASN A 359 " pdb=" CB ASN A 359 " ideal model delta sigma weight residual 112.11 116.62 -4.51 1.46e+00 4.69e-01 9.53e+00 angle pdb=" CB GLU A 342 " pdb=" CG GLU A 342 " pdb=" CD GLU A 342 " ideal model delta sigma weight residual 112.60 117.71 -5.11 1.70e+00 3.46e-01 9.05e+00 ... (remaining 959 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 9.43: 351 9.43 - 18.85: 64 18.85 - 28.26: 23 28.26 - 37.68: 2 37.68 - 47.10: 2 Dihedral angle restraints: 442 sinusoidal: 186 harmonic: 256 Sorted by residual: dihedral pdb=" CA SER A 356 " pdb=" C SER A 356 " pdb=" N LEU A 357 " pdb=" CA LEU A 357 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA SER A 341 " pdb=" C SER A 341 " pdb=" N GLU A 342 " pdb=" CA GLU A 342 " ideal model delta harmonic sigma weight residual 180.00 -161.77 -18.23 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA GLU A 342 " pdb=" C GLU A 342 " pdb=" N LYS A 343 " pdb=" CA LYS A 343 " ideal model delta harmonic sigma weight residual 180.00 -165.15 -14.85 0 5.00e+00 4.00e-02 8.82e+00 ... (remaining 439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 54 0.057 - 0.115: 37 0.115 - 0.172: 13 0.172 - 0.230: 1 0.230 - 0.287: 2 Chirality restraints: 107 Sorted by residual: chirality pdb=" CA PRO A 270 " pdb=" N PRO A 270 " pdb=" C PRO A 270 " pdb=" CB PRO A 270 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA LEU A 357 " pdb=" N LEU A 357 " pdb=" C LEU A 357 " pdb=" CB LEU A 357 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA ILE A 360 " pdb=" N ILE A 360 " pdb=" C ILE A 360 " pdb=" CB ILE A 360 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.63e-01 ... (remaining 104 not shown) Planarity restraints: 123 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 311 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.93e+00 pdb=" C LYS A 311 " -0.034 2.00e-02 2.50e+03 pdb=" O LYS A 311 " 0.013 2.00e-02 2.50e+03 pdb=" N PRO A 312 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 273 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" C GLY A 273 " 0.031 2.00e-02 2.50e+03 pdb=" O GLY A 273 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS A 274 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 378 " 0.019 2.00e-02 2.50e+03 1.26e-02 2.77e+00 pdb=" CG PHE A 378 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE A 378 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 378 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 378 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 378 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 378 " 0.007 2.00e-02 2.50e+03 ... (remaining 120 not shown) Histogram of nonbonded interaction distances: 2.65 - 3.10: 411 3.10 - 3.55: 539 3.55 - 4.00: 734 4.00 - 4.45: 595 4.45 - 4.90: 1174 Nonbonded interactions: 3453 Sorted by model distance: nonbonded pdb=" N ASP A 358 " pdb=" OD1 ASP A 358 " model vdw 2.651 2.520 nonbonded pdb=" N GLY A 365 " pdb=" O GLY A 365 " model vdw 2.660 2.496 nonbonded pdb=" N ASN A 368 " pdb=" O ASN A 368 " model vdw 2.680 2.496 nonbonded pdb=" O GLN A 269 " pdb=" CB GLN A 269 " model vdw 2.689 2.752 nonbonded pdb=" N ASN A 327 " pdb=" O ASN A 327 " model vdw 2.713 2.496 ... (remaining 3448 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: 2.640 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: 11.390 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.890 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 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 : 0.009 0.044 722 Z= 0.603 Angle : 1.323 5.713 964 Z= 0.853 Chirality : 0.084 0.287 107 Planarity : 0.006 0.023 123 Dihedral : 11.050 47.098 280 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.78), residues: 92 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.60), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS A 362 PHE 0.026 0.007 PHE A 378 TYR 0.013 0.007 TYR A 310 ARG 0.002 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 81 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.131 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 1.0656 time to fit residues: 18.3631 Evaluate side-chains 16 residues out of total 81 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.093 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 722 Z= 0.130 Angle : 0.613 6.159 964 Z= 0.306 Chirality : 0.053 0.137 107 Planarity : 0.002 0.011 123 Dihedral : 4.948 14.819 95 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.23 % Allowed : 3.70 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.79), residues: 92 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.61), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 362 PHE 0.003 0.001 PHE A 378 TYR 0.007 0.002 TYR A 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 81 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.088 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 19 average time/residue: 0.9536 time to fit residues: 18.3716 Evaluate side-chains 19 residues out of total 81 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.087 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 8 optimal weight: 0.4980 overall best weight: 1.5485 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 722 Z= 0.123 Angle : 0.573 5.805 964 Z= 0.285 Chirality : 0.052 0.134 107 Planarity : 0.002 0.016 123 Dihedral : 4.670 15.162 95 Min Nonbonded Distance : 2.679 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.70 (0.80), residues: 92 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.61), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 362 PHE 0.003 0.001 PHE A 378 TYR 0.006 0.002 TYR A 310 ARG 0.000 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 81 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.096 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 1.0013 time to fit residues: 18.2705 Evaluate side-chains 17 residues out of total 81 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.093 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 overall best weight: 0.8983 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 722 Z= 0.081 Angle : 0.503 4.316 964 Z= 0.250 Chirality : 0.050 0.129 107 Planarity : 0.002 0.016 123 Dihedral : 4.353 14.877 95 Min Nonbonded Distance : 2.685 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.23 % Allowed : 7.41 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.80), residues: 92 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.61), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.002 0.001 PHE A 346 TYR 0.005 0.001 TYR A 310 ARG 0.000 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 81 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.072 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 17 average time/residue: 1.0613 time to fit residues: 18.2817 Evaluate side-chains 17 residues out of total 81 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.090 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.0050 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.4003 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 722 Z= 0.112 Angle : 0.535 5.244 964 Z= 0.266 Chirality : 0.051 0.133 107 Planarity : 0.002 0.013 123 Dihedral : 4.374 15.027 95 Min Nonbonded Distance : 2.681 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.80), residues: 92 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.61), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 362 PHE 0.003 0.001 PHE A 378 TYR 0.007 0.002 TYR A 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 81 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.094 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 1.0558 time to fit residues: 18.1823 Evaluate side-chains 17 residues out of total 81 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.097 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 0.1980 chunk 8 optimal weight: 4.9990 overall best weight: 1.2985 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 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 0.022 722 Z= 0.106 Angle : 0.522 4.895 964 Z= 0.260 Chirality : 0.051 0.133 107 Planarity : 0.002 0.013 123 Dihedral : 4.337 15.096 95 Min Nonbonded Distance : 2.687 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.23 % Allowed : 8.64 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.80), residues: 92 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.61), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.003 0.001 PHE A 346 TYR 0.006 0.002 TYR A 310 ARG 0.000 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 81 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.131 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 17 average time/residue: 1.0540 time to fit residues: 18.1518 Evaluate side-chains 17 residues out of total 81 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.083 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 0.3980 chunk 8 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 722 Z= 0.068 Angle : 0.466 3.590 964 Z= 0.233 Chirality : 0.049 0.126 107 Planarity : 0.002 0.013 123 Dihedral : 4.085 14.269 95 Min Nonbonded Distance : 2.670 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.23 % Allowed : 8.64 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.82), residues: 92 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.63), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 362 PHE 0.002 0.001 PHE A 378 TYR 0.004 0.001 TYR A 310 ARG 0.000 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 81 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.090 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.8688 time to fit residues: 17.6246 Evaluate side-chains 18 residues out of total 81 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.093 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 0.0370 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 0.3980 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 0.1980 overall best weight: 1.1580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 722 Z= 0.095 Angle : 0.505 4.617 964 Z= 0.253 Chirality : 0.051 0.132 107 Planarity : 0.002 0.014 123 Dihedral : 4.129 14.521 95 Min Nonbonded Distance : 2.688 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.70 (0.81), residues: 92 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.62), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.003 0.001 PHE A 346 TYR 0.006 0.002 TYR A 310 ARG 0.000 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 81 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.099 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.9875 time to fit residues: 18.0020 Evaluate side-chains 18 residues out of total 81 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.068 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.0270 chunk 2 optimal weight: 0.5980 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 0.0020 chunk 8 optimal weight: 0.4980 overall best weight: 0.2813 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.013 722 Z= 0.056 Angle : 0.436 3.438 964 Z= 0.221 Chirality : 0.049 0.122 107 Planarity : 0.002 0.014 123 Dihedral : 3.811 13.693 95 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.23 % Allowed : 11.11 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.83), residues: 92 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.63), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 362 PHE 0.002 0.000 PHE A 346 TYR 0.003 0.001 TYR A 310 ARG 0.000 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 81 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 18 time to evaluate : 0.094 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 19 average time/residue: 0.9483 time to fit residues: 18.2716 Evaluate side-chains 17 residues out of total 81 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.091 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 0.0870 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 0.0050 overall best weight: 1.0225 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 722 Z= 0.086 Angle : 0.485 4.331 964 Z= 0.245 Chirality : 0.050 0.130 107 Planarity : 0.002 0.014 123 Dihedral : 3.945 14.084 95 Min Nonbonded Distance : 2.681 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.23 % Allowed : 9.88 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.62 (0.81), residues: 92 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.62), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.002 0.001 PHE A 346 TYR 0.006 0.002 TYR A 310 ARG 0.000 0.000 ARG A 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 184 Ramachandran restraints generated. 92 Oldfield, 0 Emsley, 92 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 81 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 18 time to evaluate : 0.090 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 18 average time/residue: 1.0035 time to fit residues: 18.3126 Evaluate side-chains 18 residues out of total 81 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.089 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 0.0570 chunk 8 optimal weight: 0.0170 overall best weight: 0.9178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 307 GLN A 374 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.121464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.109807 restraints weight = 834.370| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.79 r_work: 0.3440 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 722 Z= 0.081 Angle : 0.479 3.897 964 Z= 0.242 Chirality : 0.050 0.128 107 Planarity : 0.002 0.014 123 Dihedral : 3.938 14.244 95 Min Nonbonded Distance : 2.694 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.63 (0.81), residues: 92 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.62), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.002 0.001 PHE A 346 TYR 0.005 0.001 TYR A 310 ARG 0.000 0.000 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 914.39 seconds wall clock time: 22 minutes 22.21 seconds (1342.21 seconds total)