Starting phenix.real_space_refine on Sun Mar 10 14:16:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiu_26553/03_2024/7uiu_26553.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiu_26553/03_2024/7uiu_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_26553/03_2024/7uiu_26553.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiu_26553/03_2024/7uiu_26553.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiu_26553/03_2024/7uiu_26553.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiu_26553/03_2024/7uiu_26553.pdb" } resolution = 2.8 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= -0.007 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 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. 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-5265/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: 0.88, per 1000 atoms: 1.45 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: 0.19 Conformation dependent library (CDL) restraints added in 125.8 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: 0.10 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: 0.22 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 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: 5.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 26.440 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.830 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:12.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 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 : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS x 314 PHE 0.008 0.002 PHE x 250 ARG 0.001 0.000 ARG x 259 *********************** 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 : 0.060 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 1.3492 time to fit residues: 35.3273 Evaluate side-chains 23 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.064 ------------------------------------------------------------------------------- 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: 4.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.1485 ------------------------------------------------------------------------------- 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: 0.8191 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 614 Z= 0.204 Angle : 0.649 5.757 834 Z= 0.342 Chirality : 0.043 0.103 103 Planarity : 0.003 0.012 110 Dihedral : 4.939 13.387 85 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.33 % Allowed : 15.00 % Favored : 81.67 % 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: -1.60 (0.85), residues: 83 helix: -0.50 (0.77), residues: 42 sheet: -2.27 (1.62), residues: 10 loop : -1.20 (0.96), residues: 31 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS x 314 PHE 0.009 0.002 PHE x 288 ARG 0.000 0.000 ARG x 259 *********************** 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: 2 poor density : 24 time to evaluate : 0.074 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 25 average time/residue: 1.3716 time to fit residues: 34.5570 Evaluate side-chains 25 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.073 ------------------------------------------------------------------------------- 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: 0.7980 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.6735 ------------------------------------------------------------------------------- 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: 0.8253 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 614 Z= 0.241 Angle : 0.671 6.529 834 Z= 0.348 Chirality : 0.042 0.102 103 Planarity : 0.003 0.014 110 Dihedral : 5.080 12.573 85 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 5.00 % Allowed : 20.00 % Favored : 75.00 % 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: -1.94 (0.84), residues: 83 helix: -0.82 (0.80), residues: 41 sheet: -2.09 (1.59), residues: 10 loop : -1.41 (0.89), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS x 314 PHE 0.007 0.001 PHE x 288 ARG 0.001 0.001 ARG x 259 *********************** 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 27 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.081 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 24 average time/residue: 1.2089 time to fit residues: 29.2643 Evaluate side-chains 24 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 304 THR 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: 0.9980 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.2485 ------------------------------------------------------------------------------- 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: 0.8241 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 614 Z= 0.205 Angle : 0.750 7.087 834 Z= 0.377 Chirality : 0.042 0.105 103 Planarity : 0.003 0.011 110 Dihedral : 5.155 13.027 85 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 6.67 % Allowed : 26.67 % Favored : 66.67 % 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: -1.95 (0.84), residues: 83 helix: -0.81 (0.81), residues: 41 sheet: -1.70 (1.65), residues: 10 loop : -1.62 (0.88), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS x 314 PHE 0.003 0.001 PHE x 288 ARG 0.001 0.000 ARG x 259 *********************** 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 26 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 22 time to evaluate : 0.075 Fit side-chains REVERT: x 318 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7808 (pp) outliers start: 4 outliers final: 0 residues processed: 23 average time/residue: 1.3291 time to fit residues: 30.8192 Evaluate side-chains 23 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 318 LEU 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: 0.8980 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.9230 ------------------------------------------------------------------------------- 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: 0.8211 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 614 Z= 0.192 Angle : 0.726 7.298 834 Z= 0.369 Chirality : 0.042 0.101 103 Planarity : 0.003 0.011 110 Dihedral : 5.106 12.368 85 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.33 % Allowed : 28.33 % Favored : 68.33 % 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: -1.48 (0.87), residues: 83 helix: -0.55 (0.84), residues: 39 sheet: -1.45 (1.68), residues: 10 loop : -1.18 (0.93), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS x 314 PHE 0.003 0.001 PHE x 288 ARG 0.000 0.000 ARG x 259 *********************** 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 26 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.073 Fit side-chains REVERT: x 318 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7753 (pp) outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 1.3135 time to fit residues: 31.7742 Evaluate side-chains 25 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 304 THR Chi-restraints excluded: chain x residue 318 LEU 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: 0.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 overall best weight: 1.4488 ------------------------------------------------------------------------------- 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: 0.8248 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 614 Z= 0.220 Angle : 0.781 10.548 834 Z= 0.400 Chirality : 0.043 0.101 103 Planarity : 0.003 0.011 110 Dihedral : 5.310 13.092 85 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 5.00 % Allowed : 28.33 % Favored : 66.67 % 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: -1.70 (0.85), residues: 83 helix: -0.78 (0.82), residues: 39 sheet: -1.40 (1.60), residues: 10 loop : -1.26 (0.92), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS x 314 PHE 0.006 0.001 PHE x 288 ARG 0.001 0.000 ARG x 259 *********************** 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 26 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.066 Fit side-chains REVERT: x 318 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7758 (pp) outliers start: 3 outliers final: 1 residues processed: 23 average time/residue: 1.2607 time to fit residues: 29.2258 Evaluate side-chains 25 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 304 THR Chi-restraints excluded: chain x residue 318 LEU 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: 4.9990 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 overall best weight: 1.3233 ------------------------------------------------------------------------------- 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: 0.8240 moved from start: 0.4031 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= 0.219 Angle : 0.815 9.160 834 Z= 0.407 Chirality : 0.043 0.102 103 Planarity : 0.003 0.012 110 Dihedral : 5.256 12.535 85 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.33 % Allowed : 33.33 % Favored : 63.33 % 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: -2.27 (0.82), residues: 83 helix: -1.03 (0.80), residues: 41 sheet: -1.81 (1.50), residues: 10 loop : -1.86 (0.86), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS x 314 PHE 0.002 0.001 PHE x 250 ARG 0.000 0.000 ARG x 259 *********************** 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 25 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.073 Fit side-chains REVERT: x 318 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7730 (pp) outliers start: 2 outliers final: 1 residues processed: 23 average time/residue: 1.1860 time to fit residues: 27.5016 Evaluate side-chains 25 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 304 THR Chi-restraints excluded: chain x residue 318 LEU 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: 0.8980 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.4738 ------------------------------------------------------------------------------- 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: 0.8249 moved from start: 0.4016 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= 0.242 Angle : 0.824 9.128 834 Z= 0.438 Chirality : 0.043 0.102 103 Planarity : 0.003 0.010 110 Dihedral : 5.192 13.207 85 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 5.00 % Allowed : 30.00 % Favored : 65.00 % 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: -2.29 (0.82), residues: 83 helix: -0.91 (0.79), residues: 41 sheet: -1.92 (1.51), residues: 10 loop : -2.03 (0.87), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS x 314 PHE 0.007 0.001 PHE x 288 ARG 0.001 0.000 ARG x 259 *********************** 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 27 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.071 Fit side-chains REVERT: x 318 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7743 (pp) outliers start: 3 outliers final: 1 residues processed: 24 average time/residue: 1.1777 time to fit residues: 28.4974 Evaluate side-chains 26 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 304 THR Chi-restraints excluded: chain x residue 318 LEU 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: 4.9990 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 overall best weight: 0.9733 ------------------------------------------------------------------------------- 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: 0.8212 moved from start: 0.4256 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= 0.191 Angle : 0.822 7.984 834 Z= 0.420 Chirality : 0.042 0.102 103 Planarity : 0.003 0.013 110 Dihedral : 4.967 13.717 85 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.33 % Allowed : 33.33 % Favored : 63.33 % 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: -1.95 (0.85), residues: 83 helix: -0.69 (0.81), residues: 41 sheet: -1.81 (1.59), residues: 10 loop : -1.76 (0.92), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS x 314 PHE 0.002 0.001 PHE x 250 ARG 0.000 0.000 ARG x 259 *********************** 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 25 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.072 Fit side-chains REVERT: x 318 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7755 (pp) outliers start: 2 outliers final: 1 residues processed: 23 average time/residue: 1.1690 time to fit residues: 27.1170 Evaluate side-chains 25 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 304 THR Chi-restraints excluded: chain x residue 318 LEU 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: 5.9990 chunk 2 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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: 0.8298 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 614 Z= 0.309 Angle : 0.907 9.965 834 Z= 0.471 Chirality : 0.046 0.109 103 Planarity : 0.003 0.011 110 Dihedral : 5.536 14.021 85 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 5.00 % Allowed : 30.00 % Favored : 65.00 % 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: -2.39 (0.82), residues: 83 helix: -1.13 (0.79), residues: 41 sheet: -2.11 (1.38), residues: 10 loop : -1.82 (0.92), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS x 314 PHE 0.003 0.001 PHE x 250 ARG 0.001 0.001 ARG x 259 ********************** 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 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 REVERT: x 318 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7831 (pp) outliers start: 3 outliers final: 1 residues processed: 24 average time/residue: 1.1978 time to fit residues: 28.9868 Evaluate side-chains 25 residues out of total 71 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 304 THR Chi-restraints excluded: chain x residue 318 LEU 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: 0.7980 chunk 3 optimal weight: 0.2980 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 overall best weight: 1.2733 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.076556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.065350 restraints weight = 1806.350| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.60 r_work: 0.3016 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 614 Z= 0.238 Angle : 0.905 11.828 834 Z= 0.460 Chirality : 0.043 0.102 103 Planarity : 0.003 0.013 110 Dihedral : 5.229 14.780 85 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.33 % Allowed : 33.33 % Favored : 63.33 % 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: -2.09 (0.86), residues: 83 helix: -0.91 (0.79), residues: 42 sheet: -2.02 (1.48), residues: 10 loop : -1.61 (1.00), residues: 31 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS x 314 PHE 0.003 0.001 PHE x 250 ARG 0.001 0.000 ARG x 259 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1112.47 seconds wall clock time: 21 minutes 26.69 seconds (1286.69 seconds total)