Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:36:15 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiu_26553/11_2022/7uiu_26553.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiu_26553/11_2022/7uiu_26553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiu_26553/11_2022/7uiu_26553.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiu_26553/11_2022/7uiu_26553.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiu_26553/11_2022/7uiu_26553.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiu_26553/11_2022/7uiu_26553.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= -0.007 sd= 0.024 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "x GLU 271": "OE1" <-> "OE2" Residue "x GLU 321": "OE1" <-> "OE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 607 Number of models: 1 Model: "" Number of chains: 1 Chain: "x" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 607 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 81} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 0.90, per 1000 atoms: 1.48 Number of scatterers: 607 At special positions: 0 Unit cell: (36.55, 62.05, 59.5, 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 3 16.00 O 116 8.00 N 106 7.00 C 382 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 109.7 milliseconds 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 158 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 2 sheets defined 44.7% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'x' and resid 269 through 276 Processing helix chain 'x' and resid 279 through 290 removed outlier: 3.512A pdb=" N MET x 290 " --> pdb=" O PHE x 286 " (cutoff:3.500A) Processing helix chain 'x' and resid 302 through 312 Processing helix chain 'x' and resid 322 through 328 removed outlier: 3.623A pdb=" N GLU x 326 " --> pdb=" O ASN x 322 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'x' and resid 260 through 261 Processing sheet with id=AA2, first strand: chain 'x' and resid 266 through 268 23 hydrogen bonds defined for protein. 69 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: 0.12 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: 1.23 - 1.34: 210 1.34 - 1.45: 51 1.45 - 1.57: 347 1.57 - 1.68: 0 1.68 - 1.80: 6 Bond restraints: 614 Sorted by residual: bond pdb=" CB VAL x 269 " pdb=" CG1 VAL x 269 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.16e+00 bond pdb=" CB GLN x 302 " pdb=" CG GLN x 302 " ideal model delta sigma weight residual 1.520 1.489 0.031 3.00e-02 1.11e+03 1.07e+00 bond pdb=" CG GLN x 302 " pdb=" CD GLN x 302 " ideal model delta sigma weight residual 1.516 1.496 0.020 2.50e-02 1.60e+03 6.23e-01 bond pdb=" CB VAL x 283 " pdb=" CG1 VAL x 283 " ideal model delta sigma weight residual 1.521 1.504 0.017 3.30e-02 9.18e+02 2.68e-01 bond pdb=" CA HIS x 248 " pdb=" C HIS x 248 " ideal model delta sigma weight residual 1.525 1.514 0.011 2.10e-02 2.27e+03 2.52e-01 ... (remaining 609 not shown) Histogram of bond angle deviations from ideal: 100.02 - 106.26: 16 106.26 - 112.51: 339 112.51 - 118.75: 160 118.75 - 125.00: 314 125.00 - 131.24: 5 Bond angle restraints: 834 Sorted by residual: angle pdb=" N GLU x 265 " pdb=" CA GLU x 265 " pdb=" C GLU x 265 " ideal model delta sigma weight residual 113.41 110.70 2.71 1.22e+00 6.72e-01 4.92e+00 angle pdb=" N GLN x 302 " pdb=" CA GLN x 302 " pdb=" C GLN x 302 " ideal model delta sigma weight residual 111.07 112.78 -1.71 1.07e+00 8.73e-01 2.54e+00 angle pdb=" N GLY x 291 " pdb=" CA GLY x 291 " pdb=" C GLY x 291 " ideal model delta sigma weight residual 113.18 116.91 -3.73 2.37e+00 1.78e-01 2.47e+00 angle pdb=" C LYS x 315 " pdb=" CA LYS x 315 " pdb=" CB LYS x 315 " ideal model delta sigma weight residual 109.75 112.24 -2.49 1.65e+00 3.67e-01 2.27e+00 angle pdb=" C ASP x 301 " pdb=" N GLN x 302 " pdb=" CA GLN x 302 " ideal model delta sigma weight residual 120.44 122.35 -1.91 1.30e+00 5.92e-01 2.16e+00 ... (remaining 829 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.39: 338 15.39 - 30.79: 27 30.79 - 46.18: 5 46.18 - 61.58: 2 61.58 - 76.97: 1 Dihedral angle restraints: 373 sinusoidal: 131 harmonic: 242 Sorted by residual: dihedral pdb=" CA GLY x 291 " pdb=" C GLY x 291 " pdb=" N SER x 292 " pdb=" CA SER x 292 " ideal model delta harmonic sigma weight residual -180.00 -166.66 -13.34 0 5.00e+00 4.00e-02 7.12e+00 dihedral pdb=" CA MET x 290 " pdb=" C MET x 290 " pdb=" N GLY x 291 " pdb=" CA GLY x 291 " ideal model delta harmonic sigma weight residual 180.00 166.97 13.03 0 5.00e+00 4.00e-02 6.80e+00 dihedral pdb=" CA LEU x 328 " pdb=" C LEU x 328 " pdb=" N ALA x 329 " pdb=" CA ALA x 329 " ideal model delta harmonic sigma weight residual 180.00 167.45 12.55 0 5.00e+00 4.00e-02 6.30e+00 ... (remaining 370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 44 0.021 - 0.043: 29 0.043 - 0.064: 13 0.064 - 0.085: 8 0.085 - 0.106: 9 Chirality restraints: 103 Sorted by residual: chirality pdb=" CA VAL x 278 " pdb=" N VAL x 278 " pdb=" C VAL x 278 " pdb=" CB VAL x 278 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.80e-01 chirality pdb=" CA ILE x 263 " pdb=" N ILE x 263 " pdb=" C ILE x 263 " pdb=" CB ILE x 263 " both_signs ideal model delta sigma weight residual False 2.43 2.53 -0.10 2.00e-01 2.50e+01 2.50e-01 chirality pdb=" CA VAL x 299 " pdb=" N VAL x 299 " pdb=" C VAL x 299 " pdb=" CB VAL x 299 " both_signs ideal model delta sigma weight residual False 2.44 2.54 -0.10 2.00e-01 2.50e+01 2.50e-01 ... (remaining 100 not shown) Planarity restraints: 110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY x 264 " 0.005 2.00e-02 2.50e+03 1.03e-02 1.06e+00 pdb=" C GLY x 264 " -0.018 2.00e-02 2.50e+03 pdb=" O GLY x 264 " 0.007 2.00e-02 2.50e+03 pdb=" N GLU x 265 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN x 252 " 0.011 5.00e-02 4.00e+02 1.65e-02 4.37e-01 pdb=" N PRO x 253 " -0.029 5.00e-02 4.00e+02 pdb=" CA PRO x 253 " 0.008 5.00e-02 4.00e+02 pdb=" CD PRO x 253 " 0.009 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN x 252 " 0.003 2.00e-02 2.50e+03 6.55e-03 4.28e-01 pdb=" C ASN x 252 " -0.011 2.00e-02 2.50e+03 pdb=" O ASN x 252 " 0.004 2.00e-02 2.50e+03 pdb=" N PRO x 253 " 0.004 2.00e-02 2.50e+03 ... (remaining 107 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.86: 209 2.86 - 3.37: 598 3.37 - 3.88: 906 3.88 - 4.39: 938 4.39 - 4.90: 1570 Nonbonded interactions: 4221 Sorted by model distance: nonbonded pdb=" OG1 THR x 268 " pdb=" OE2 GLU x 271 " model vdw 2.356 2.440 nonbonded pdb=" N GLU x 326 " pdb=" OE1 GLU x 326 " model vdw 2.466 2.520 nonbonded pdb=" N GLU x 321 " pdb=" OE1 GLU x 321 " model vdw 2.486 2.520 nonbonded pdb=" O ASN x 252 " pdb=" OD1 ASN x 252 " model vdw 2.495 3.040 nonbonded pdb=" O ASN x 322 " pdb=" OE1 GLU x 326 " model vdw 2.569 3.040 ... (remaining 4216 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 3 5.16 5 C 382 2.51 5 N 106 2.21 5 O 116 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 4.890 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: 26.200 Check model and map are aligned: 0.010 Convert atoms to be neutral: 0.010 Process input model: 9.060 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 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:12.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 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 0.036 614 Z= 0.279 Angle : 0.622 4.300 834 Z= 0.364 Chirality : 0.044 0.106 103 Planarity : 0.003 0.017 110 Dihedral : 13.600 76.970 215 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 0.00 % 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: -2.09 (0.81), residues: 83 helix: -1.03 (0.71), residues: 41 sheet: -1.98 (1.80), residues: 10 loop : -1.42 (0.93), residues: 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.075 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 1.2145 time to fit residues: 31.8274 Evaluate side-chains 23 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.074 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.8485 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 327 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 614 Z= 0.254 Angle : 0.657 5.694 834 Z= 0.348 Chirality : 0.043 0.101 103 Planarity : 0.003 0.012 110 Dihedral : 5.081 13.443 85 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer Outliers : 5.00 % 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: -1.88 (0.83), residues: 83 helix: -0.80 (0.76), residues: 42 sheet: -2.35 (1.57), residues: 10 loop : -1.23 (0.95), residues: 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.075 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 24 average time/residue: 1.2224 time to fit residues: 29.6100 Evaluate side-chains 24 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.075 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.9483 ------------------------------------------------------------------------------- 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: 0.8288 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 614 Z= 0.188 Angle : 0.665 6.564 834 Z= 0.348 Chirality : 0.041 0.102 103 Planarity : 0.003 0.014 110 Dihedral : 4.931 12.265 85 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer Outliers : 3.33 % 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 (0.84), residues: 83 helix: -0.61 (0.81), residues: 41 sheet: -1.78 (1.60), residues: 10 loop : -1.40 (0.88), residues: 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.061 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 1.1329 time to fit residues: 27.4164 Evaluate side-chains 24 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.075 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0152 time to fit residues: 0.1203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 327 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 614 Z= 0.166 Angle : 0.641 6.572 834 Z= 0.333 Chirality : 0.041 0.102 103 Planarity : 0.003 0.011 110 Dihedral : 4.860 11.485 85 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 6.67 % 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: -1.57 (0.84), residues: 83 helix: -0.50 (0.81), residues: 41 sheet: -1.51 (1.63), residues: 10 loop : -1.44 (0.86), residues: 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 24 time to evaluate : 0.070 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 24 average time/residue: 1.1481 time to fit residues: 27.7904 Evaluate side-chains 25 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.075 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0524 time to fit residues: 0.1575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.1738 ------------------------------------------------------------------------------- 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: 0.8288 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.025 614 Z= 0.204 Angle : 0.760 7.325 834 Z= 0.384 Chirality : 0.042 0.102 103 Planarity : 0.003 0.012 110 Dihedral : 5.081 11.794 85 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 1.67 % 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: -1.83 (0.84), residues: 83 helix: -0.71 (0.81), residues: 41 sheet: -1.42 (1.61), residues: 10 loop : -1.63 (0.86), residues: 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.075 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 1.1899 time to fit residues: 28.8008 Evaluate side-chains 23 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.075 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 overall best weight: 0.8733 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 614 Z= 0.189 Angle : 0.729 9.855 834 Z= 0.370 Chirality : 0.042 0.102 103 Planarity : 0.003 0.013 110 Dihedral : 5.009 12.369 85 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 1.67 % 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: -1.40 (0.86), residues: 83 helix: -0.50 (0.85), residues: 39 sheet: -1.16 (1.61), residues: 10 loop : -1.20 (0.90), residues: 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.079 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 23 average time/residue: 1.0976 time to fit residues: 25.4904 Evaluate side-chains 23 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.066 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 297 ASN ** x 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 614 Z= 0.227 Angle : 0.821 9.601 834 Z= 0.407 Chirality : 0.042 0.101 103 Planarity : 0.003 0.012 110 Dihedral : 5.140 11.919 85 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.87), residues: 83 helix: -0.71 (0.85), residues: 39 sheet: -1.15 (1.60), residues: 10 loop : -1.28 (0.93), residues: 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.073 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 1.1460 time to fit residues: 26.6000 Evaluate side-chains 23 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.078 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 overall best weight: 2.2488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.030 614 Z= 0.297 Angle : 0.864 10.124 834 Z= 0.444 Chirality : 0.044 0.100 103 Planarity : 0.003 0.010 110 Dihedral : 5.440 13.257 85 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer Outliers : 5.00 % 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: -2.24 (0.82), residues: 83 helix: -1.01 (0.80), residues: 41 sheet: -1.67 (1.37), residues: 10 loop : -1.87 (0.87), residues: 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.073 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 23 average time/residue: 1.1256 time to fit residues: 26.1203 Evaluate side-chains 24 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.067 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0104 time to fit residues: 0.0992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 overall best weight: 1.0733 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 614 Z= 0.219 Angle : 0.833 9.153 834 Z= 0.430 Chirality : 0.043 0.106 103 Planarity : 0.003 0.013 110 Dihedral : 5.135 13.302 85 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 0.00 % 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: -1.96 (0.86), residues: 83 helix: -0.82 (0.82), residues: 41 sheet: -1.56 (1.46), residues: 10 loop : -1.68 (0.95), residues: 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.081 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 1.1728 time to fit residues: 27.2189 Evaluate side-chains 23 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.075 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.2238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.031 614 Z= 0.303 Angle : 0.911 12.008 834 Z= 0.463 Chirality : 0.044 0.101 103 Planarity : 0.003 0.012 110 Dihedral : 5.561 15.165 85 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 3.33 % 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: -2.42 (0.84), residues: 83 helix: -1.15 (0.79), residues: 42 sheet: -2.35 (1.41), residues: 10 loop : -1.74 (0.96), residues: 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.076 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 24 average time/residue: 1.1126 time to fit residues: 26.9553 Evaluate side-chains 24 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.074 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 overall best weight: 0.6985 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 298 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.078760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.067518 restraints weight = 1736.333| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 3.54 r_work: 0.3160 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work: 0.3143 rms_B_bonded: 3.22 restraints_weight: 0.1250 r_work: 0.3134 rms_B_bonded: 3.26 restraints_weight: 0.0625 r_work: 0.3125 rms_B_bonded: 3.33 restraints_weight: 0.0312 r_work: 0.3116 rms_B_bonded: 3.43 restraints_weight: 0.0156 r_work: 0.3107 rms_B_bonded: 3.55 restraints_weight: 0.0078 r_work: 0.3097 rms_B_bonded: 3.69 restraints_weight: 0.0039 r_work: 0.3087 rms_B_bonded: 3.85 restraints_weight: 0.0020 r_work: 0.3076 rms_B_bonded: 4.03 restraints_weight: 0.0010 r_work: 0.3066 rms_B_bonded: 4.23 restraints_weight: 0.0005 r_work: 0.3055 rms_B_bonded: 4.45 restraints_weight: 0.0002 r_work: 0.3043 rms_B_bonded: 4.70 restraints_weight: 0.0001 r_work: 0.3031 rms_B_bonded: 4.97 restraints_weight: 0.0001 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 614 Z= 0.227 Angle : 0.894 11.638 834 Z= 0.451 Chirality : 0.043 0.116 103 Planarity : 0.003 0.013 110 Dihedral : 4.951 14.568 85 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer Outliers : 1.67 % 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: -1.79 (0.89), residues: 83 helix: -0.60 (0.82), residues: 42 sheet: -1.85 (1.49), residues: 10 loop : -1.58 (1.02), residues: 31 =============================================================================== Job complete usr+sys time: 1065.19 seconds wall clock time: 19 minutes 22.12 seconds (1162.12 seconds total)