Starting phenix.real_space_refine on Sun May 19 16:30:35 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8ve0_43160.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8ve0_43160.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global+local_grid_search+nqh_flips resolution=3.1 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8ve0_43160.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8ve0_43160.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8ve0_43160.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8ve0_43160.map" } resolution = 3.1 refinement { run = *minimization_global rigid_body *local_grid_search morphing \ simulated_annealing adp occupancy *nqh_flips } 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= 0.002 sd= 0.007 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: 5 Type Number sf(0) Gaussians S 2 5.16 5 C 579 2.51 5 N 149 2.21 5 O 176 1.98 5 H 885 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 1791 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1791 Classifications: {'peptide': 117} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Time building chain proxies: 0.47, per 1000 atoms: 0.26 Number of scatterers: 1791 At special positions: 0 Unit cell: (43.274, 56.2, 48.894, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 2 16.00 O 176 8.00 N 149 7.00 C 579 6.00 H 885 1.00 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: 0.29 Conformation dependent library (CDL) restraints added in 87.6 milliseconds 230 Ramachandran restraints generated. 115 Oldfield, 0 Emsley, 115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 220 Finding SS restraints... Secondary structure from input PDB file: 1 helices and 2 sheets defined 6.8% alpha, 38.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'A' and resid 75 through 82 Processing sheet with id= A, first strand: chain 'A' and resid 12 through 18 removed outlier: 7.046A pdb=" N TYR A 105 " --> pdb=" O MET A 13 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N LYS A 15 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE A 107 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N LEU A 17 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA A 109 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 91 through 97 removed outlier: 3.605A pdb=" N GLY A 67 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ILE A 68 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ARG A 34 " --> pdb=" O PRO A 43 " (cutoff:3.500A) 28 hydrogen bonds defined for protein. 78 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: 0.26 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.14: 884 1.14 - 1.31: 152 1.31 - 1.47: 377 1.47 - 1.64: 399 1.64 - 1.80: 3 Bond restraints: 1815 Sorted by residual: bond pdb=" N THR A 96 " pdb=" H THR A 96 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" N SER A 85 " pdb=" H SER A 85 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.53e+01 bond pdb=" N VAL A 122 " pdb=" H VAL A 122 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" N TYR A 69 " pdb=" H TYR A 69 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.50e+01 bond pdb=" N SER A 52 " pdb=" H SER A 52 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.50e+01 ... (remaining 1810 not shown) Histogram of bond angle deviations from ideal: 100.94 - 107.54: 82 107.54 - 114.14: 2192 114.14 - 120.74: 523 120.74 - 127.34: 472 127.34 - 133.95: 14 Bond angle restraints: 3283 Sorted by residual: angle pdb=" N PHE A 95 " pdb=" CA PHE A 95 " pdb=" C PHE A 95 " ideal model delta sigma weight residual 108.76 110.67 -1.91 1.58e+00 4.01e-01 1.47e+00 angle pdb=" C VAL A 94 " pdb=" N PHE A 95 " pdb=" CA PHE A 95 " ideal model delta sigma weight residual 121.63 119.68 1.95 1.92e+00 2.71e-01 1.03e+00 angle pdb=" N PHE A 44 " pdb=" CA PHE A 44 " pdb=" C PHE A 44 " ideal model delta sigma weight residual 113.43 112.21 1.22 1.26e+00 6.30e-01 9.42e-01 angle pdb=" CB ILE A 26 " pdb=" CG2 ILE A 26 " pdb="HG22 ILE A 26 " ideal model delta sigma weight residual 109.00 111.85 -2.85 3.00e+00 1.11e-01 9.03e-01 angle pdb=" N ASP A 39 " pdb=" CA ASP A 39 " pdb=" C ASP A 39 " ideal model delta sigma weight residual 111.74 110.47 1.27 1.35e+00 5.49e-01 8.91e-01 ... (remaining 3278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.51: 769 11.51 - 23.01: 39 23.01 - 34.52: 34 34.52 - 46.02: 17 46.02 - 57.53: 7 Dihedral angle restraints: 866 sinusoidal: 456 harmonic: 410 Sorted by residual: dihedral pdb=" CA ASP A 38 " pdb=" CB ASP A 38 " pdb=" CG ASP A 38 " pdb=" OD1 ASP A 38 " ideal model delta sinusoidal sigma weight residual -30.00 -86.42 56.42 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA ASP A 39 " pdb=" CB ASP A 39 " pdb=" CG ASP A 39 " pdb=" OD1 ASP A 39 " ideal model delta sinusoidal sigma weight residual -30.00 -81.89 51.89 1 2.00e+01 2.50e-03 9.19e+00 dihedral pdb=" CB ARG A 34 " pdb=" CG ARG A 34 " pdb=" CD ARG A 34 " pdb=" NE ARG A 34 " ideal model delta sinusoidal sigma weight residual 60.00 103.39 -43.39 3 1.50e+01 4.44e-03 7.80e+00 ... (remaining 863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 79 0.026 - 0.052: 42 0.052 - 0.078: 5 0.078 - 0.105: 4 0.105 - 0.131: 14 Chirality restraints: 144 Sorted by residual: chirality pdb=" CA ILE A 73 " pdb=" N ILE A 73 " pdb=" C ILE A 73 " pdb=" CB ILE A 73 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA VAL A 93 " pdb=" N VAL A 93 " pdb=" C VAL A 93 " pdb=" CB VAL A 93 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA ILE A 107 " pdb=" N ILE A 107 " pdb=" C ILE A 107 " pdb=" CB ILE A 107 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 141 not shown) Planarity restraints: 271 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 23 " -0.012 5.00e-02 4.00e+02 1.83e-02 5.36e-01 pdb=" N PRO A 24 " 0.032 5.00e-02 4.00e+02 pdb=" CA PRO A 24 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO A 24 " -0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 124 " -0.011 5.00e-02 4.00e+02 1.73e-02 4.81e-01 pdb=" N PRO A 125 " 0.030 5.00e-02 4.00e+02 pdb=" CA PRO A 125 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO A 125 " -0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 85 " 0.011 5.00e-02 4.00e+02 1.72e-02 4.75e-01 pdb=" N PRO A 86 " -0.030 5.00e-02 4.00e+02 pdb=" CA PRO A 86 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO A 86 " 0.010 5.00e-02 4.00e+02 ... (remaining 268 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 106 2.18 - 2.79: 3323 2.79 - 3.39: 4435 3.39 - 4.00: 6295 4.00 - 4.60: 9003 Nonbonded interactions: 23162 Sorted by model distance: nonbonded pdb=" O VAL A 65 " pdb=" HH TYR A 69 " model vdw 1.577 1.850 nonbonded pdb=" H ASN A 98 " pdb=" OH TYR A 105 " model vdw 1.593 1.850 nonbonded pdb=" HZ3 LYS A 76 " pdb=" OE1 GLU A 89 " model vdw 1.613 1.850 nonbonded pdb=" O VAL A 28 " pdb=" H THR A 49 " model vdw 1.648 1.850 nonbonded pdb=" O PRO A 102 " pdb="HH11 ARG A 103 " model vdw 1.648 1.850 ... (remaining 23157 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: 5 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.48 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will not be refined 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: 0.020 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: 0.070 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 3.310 Find NCS groups from input model: 0.010 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:0.770 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:1.250 Internal consistency checks: 0.000 Total: 5.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 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 : 0.002 0.015 930 Z= 0.112 Angle : 0.414 3.597 1269 Z= 0.217 Chirality : 0.047 0.131 144 Planarity : 0.004 0.018 162 Dihedral : 11.132 56.419 329 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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: 0.96 (0.73), residues: 115 helix: 0.17 (1.66), residues: 9 sheet: 1.60 (0.69), residues: 54 loop : -0.32 (0.74), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 34 TYR 0.005 0.001 TYR A 105 PHE 0.006 0.001 PHE A 44 TRP 0.004 0.001 TRP A 79 HIS 0.002 0.001 HIS A 31 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 230 Ramachandran restraints generated. 115 Oldfield, 0 Emsley, 115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 230 Ramachandran restraints generated. 115 Oldfield, 0 Emsley, 115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.043 Fit side-chains REVERT: A 89 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7108 (mp0) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1054 time to fit residues: 2.8998 Evaluate side-chains 22 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 11 random chunks: chunk 6 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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: 0.7612 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 930 Z= 0.213 Angle : 0.450 3.610 1269 Z= 0.229 Chirality : 0.047 0.136 144 Planarity : 0.004 0.020 162 Dihedral : 3.813 21.191 126 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.02 % Allowed : 7.14 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.75), residues: 115 helix: 0.83 (1.75), residues: 9 sheet: 1.35 (0.70), residues: 54 loop : 0.22 (0.80), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 34 TYR 0.003 0.001 TYR A 116 PHE 0.008 0.002 PHE A 33 TRP 0.008 0.002 TRP A 79 HIS 0.001 0.001 HIS A 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 230 Ramachandran restraints generated. 115 Oldfield, 0 Emsley, 115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 230 Ramachandran restraints generated. 115 Oldfield, 0 Emsley, 115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.076 Fit side-chains REVERT: A 34 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7354 (ttt-90) outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 0.2178 time to fit residues: 5.6051 Evaluate side-chains 24 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 11 random chunks: chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 0 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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: 0.7607 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 930 Z= 0.140 Angle : 0.442 3.677 1269 Z= 0.218 Chirality : 0.047 0.135 144 Planarity : 0.004 0.021 162 Dihedral : 3.421 12.584 126 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.02 % Allowed : 9.18 % Favored : 89.80 % 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: 1.45 (0.76), residues: 115 helix: 1.51 (1.92), residues: 9 sheet: 1.40 (0.70), residues: 54 loop : 0.50 (0.80), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 21 TYR 0.003 0.001 TYR A 116 PHE 0.007 0.001 PHE A 33 TRP 0.005 0.001 TRP A 79 HIS 0.001 0.000 HIS A 88 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 230 Ramachandran restraints generated. 115 Oldfield, 0 Emsley, 115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 230 Ramachandran restraints generated. 115 Oldfield, 0 Emsley, 115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.082 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 23 average time/residue: 0.2695 time to fit residues: 6.6684 Evaluate side-chains 24 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 11 random chunks: chunk 8 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 0 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 overall best weight: 4.8388 ------------------------------------------------------------------------------- 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: 0.7622 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 930 Z= 0.153 Angle : 0.441 3.604 1269 Z= 0.220 Chirality : 0.047 0.134 144 Planarity : 0.004 0.021 162 Dihedral : 3.378 10.836 126 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.04 % Allowed : 12.24 % Favored : 85.71 % 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: 1.46 (0.76), residues: 115 helix: 1.64 (1.98), residues: 9 sheet: 1.33 (0.69), residues: 54 loop : 0.57 (0.81), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 34 TYR 0.004 0.001 TYR A 78 PHE 0.007 0.001 PHE A 33 TRP 0.006 0.002 TRP A 79 HIS 0.001 0.000 HIS A 88 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 230 Ramachandran restraints generated. 115 Oldfield, 0 Emsley, 115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 230 Ramachandran restraints generated. 115 Oldfield, 0 Emsley, 115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.077 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.2161 time to fit residues: 5.5999 Evaluate side-chains 24 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 56 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 11 random chunks: chunk 4 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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: 0.7642 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 930 Z= 0.171 Angle : 0.454 3.932 1269 Z= 0.229 Chirality : 0.047 0.135 144 Planarity : 0.004 0.021 162 Dihedral : 3.511 11.018 126 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.04 % Allowed : 12.24 % Favored : 85.71 % 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: 1.32 (0.76), residues: 115 helix: 1.42 (1.97), residues: 9 sheet: 1.27 (0.68), residues: 55 loop : 0.44 (0.83), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 34 TYR 0.005 0.001 TYR A 78 PHE 0.008 0.002 PHE A 33 TRP 0.007 0.002 TRP A 79 HIS 0.002 0.000 HIS A 88 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 230 Ramachandran restraints generated. 115 Oldfield, 0 Emsley, 115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 230 Ramachandran restraints generated. 115 Oldfield, 0 Emsley, 115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.045 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 23 average time/residue: 0.1723 time to fit residues: 4.2697 Evaluate side-chains 23 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 11 random chunks: chunk 1 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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: 0.7619 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 930 Z= 0.126 Angle : 0.438 3.903 1269 Z= 0.217 Chirality : 0.046 0.135 144 Planarity : 0.004 0.022 162 Dihedral : 3.365 10.601 126 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.04 % Allowed : 13.27 % Favored : 84.69 % 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: 1.42 (0.77), residues: 115 helix: 1.42 (1.98), residues: 9 sheet: 1.23 (0.69), residues: 54 loop : 0.68 (0.84), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 103 TYR 0.004 0.001 TYR A 78 PHE 0.006 0.001 PHE A 33 TRP 0.005 0.001 TRP A 79 HIS 0.001 0.000 HIS A 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 436.54 seconds wall clock time: 7 minutes 49.09 seconds (469.09 seconds total)