Starting phenix.real_space_refine on Sun May 19 16:30:36 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6ezj_3999.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6ezj_3999.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 { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6ezj_3999.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6ezj_3999.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6ezj_3999.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6ezj_3999.pdb" } 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= 0.011 sd= 0.110 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 894 2.51 5 N 265 2.21 5 O 276 1.98 5 H 1414 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 126": "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: 2851 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2851 Classifications: {'peptide': 185} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 179} Time building chain proxies: 0.61, per 1000 atoms: 0.21 Number of scatterers: 2851 At special positions: 0 Unit cell: (62.35, 50.525, 60.2, 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 276 8.00 N 265 7.00 C 894 6.00 H 1414 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: 0.55 Conformation dependent library (CDL) restraints added in 91.0 milliseconds 366 Ramachandran restraints generated. 183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 336 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 2 sheets defined 30.3% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 43 through 49 Processing helix chain 'A' and resid 51 through 54 No H-bonds generated for 'chain 'A' and resid 51 through 54' Processing helix chain 'A' and resid 74 through 90 removed outlier: 3.652A pdb=" N ASP A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL A 79 " --> pdb=" O THR A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 154 removed outlier: 3.540A pdb=" N THR A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 183 removed outlier: 3.568A pdb=" N ALA A 180 " --> pdb=" O PHE A 176 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 12 through 18 removed outlier: 3.736A pdb=" N ASP A 37 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 62 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 64 " --> pdb=" O SER A 39 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 101 through 107 removed outlier: 3.509A pdb=" N ILE A 112 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A 164 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N HIS A 113 " --> pdb=" O GLN A 162 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLN A 162 " --> pdb=" O HIS A 113 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N SER A 115 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ILE A 160 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N TYR A 123 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE A 160 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLY A 125 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLN A 162 " --> pdb=" O GLY A 125 " (cutoff:3.500A) 55 hydrogen bonds defined for protein. 153 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: 0.48 Time building geometry restraints manager: 0.64 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: 1414 1.14 - 1.31: 247 1.31 - 1.47: 588 1.47 - 1.64: 625 1.64 - 1.81: 4 Bond restraints: 2878 Sorted by residual: bond pdb=" N HIS A 169 " pdb=" H HIS A 169 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.73e+01 bond pdb=" N ALA A 174 " pdb=" H ALA A 174 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" N PHE A 146 " pdb=" H PHE A 146 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" ND2 ASN A 98 " pdb="HD22 ASN A 98 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.55e+01 bond pdb=" N ALA A 178 " pdb=" H ALA A 178 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.55e+01 ... (remaining 2873 not shown) Histogram of bond angle deviations from ideal: 100.94 - 107.01: 62 107.01 - 113.09: 3324 113.09 - 119.16: 571 119.16 - 125.23: 1123 125.23 - 131.31: 106 Bond angle restraints: 5186 Sorted by residual: angle pdb=" N LEU A 107 " pdb=" CA LEU A 107 " pdb=" C LEU A 107 " ideal model delta sigma weight residual 109.96 106.61 3.35 1.58e+00 4.01e-01 4.50e+00 angle pdb=" N GLY A 136 " pdb=" CA GLY A 136 " pdb=" C GLY A 136 " ideal model delta sigma weight residual 113.18 109.07 4.11 2.37e+00 1.78e-01 3.00e+00 angle pdb=" N ALA A 105 " pdb=" CA ALA A 105 " pdb=" C ALA A 105 " ideal model delta sigma weight residual 107.91 111.43 -3.52 2.05e+00 2.38e-01 2.96e+00 angle pdb=" N GLY A 125 " pdb=" CA GLY A 125 " pdb=" C GLY A 125 " ideal model delta sigma weight residual 113.18 110.03 3.15 2.37e+00 1.78e-01 1.76e+00 angle pdb=" CA GLU A 109 " pdb=" CB GLU A 109 " pdb=" CG GLU A 109 " ideal model delta sigma weight residual 114.10 116.73 -2.63 2.00e+00 2.50e-01 1.73e+00 ... (remaining 5181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.01: 1238 15.01 - 30.02: 62 30.02 - 45.02: 29 45.02 - 60.03: 15 60.03 - 75.04: 2 Dihedral angle restraints: 1346 sinusoidal: 733 harmonic: 613 Sorted by residual: dihedral pdb=" CA PRO A 106 " pdb=" C PRO A 106 " pdb=" N LEU A 107 " pdb=" CA LEU A 107 " ideal model delta harmonic sigma weight residual 180.00 156.11 23.89 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA ILE A 28 " pdb=" C ILE A 28 " pdb=" N ASN A 29 " pdb=" CA ASN A 29 " ideal model delta harmonic sigma weight residual 180.00 159.78 20.22 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLU A 109 " pdb=" CB GLU A 109 " pdb=" CG GLU A 109 " pdb=" CD GLU A 109 " ideal model delta sinusoidal sigma weight residual -180.00 -121.53 -58.47 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 1343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 107 0.025 - 0.050: 74 0.050 - 0.075: 19 0.075 - 0.099: 11 0.099 - 0.124: 14 Chirality restraints: 225 Sorted by residual: chirality pdb=" CA ILE A 42 " pdb=" N ILE A 42 " pdb=" C ILE A 42 " pdb=" CB ILE A 42 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA ILE A 160 " pdb=" N ILE A 160 " pdb=" C ILE A 160 " pdb=" CB ILE A 160 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.57e-01 chirality pdb=" CA ILE A 70 " pdb=" N ILE A 70 " pdb=" C ILE A 70 " pdb=" CB ILE A 70 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.40e-01 ... (remaining 222 not shown) Planarity restraints: 441 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 105 " 0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO A 106 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 106 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 106 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 168 " -0.005 2.00e-02 2.50e+03 9.68e-03 9.38e-01 pdb=" C SER A 168 " 0.017 2.00e-02 2.50e+03 pdb=" O SER A 168 " -0.006 2.00e-02 2.50e+03 pdb=" N HIS A 169 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 121 " -0.015 5.00e-02 4.00e+02 2.24e-02 7.99e-01 pdb=" N PRO A 122 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 122 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 122 " -0.012 5.00e-02 4.00e+02 ... (remaining 438 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 208 2.18 - 2.78: 5396 2.78 - 3.39: 7432 3.39 - 3.99: 10464 3.99 - 4.60: 15160 Nonbonded interactions: 38660 Sorted by model distance: nonbonded pdb=" HG1 THR A 22 " pdb=" OD2 ASP A 78 " model vdw 1.571 1.850 nonbonded pdb=" OD1 ASN A 76 " pdb=" HH TYR A 138 " model vdw 1.593 1.850 nonbonded pdb=" O SER A 119 " pdb=" H ARG A 121 " model vdw 1.600 1.850 nonbonded pdb=" OG1 THR A 132 " pdb=" HG SER A 168 " model vdw 1.619 1.850 nonbonded pdb="HD21 ASN A 76 " pdb=" HD1 PHE A 146 " model vdw 1.700 2.100 ... (remaining 38655 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=0.49 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: 0.000 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: 0.020 Extract box with map and model: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.550 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:0.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:2.250 Internal consistency checks: 0.000 Total: 7.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 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 : 0.003 0.025 1464 Z= 0.169 Angle : 0.564 4.108 1981 Z= 0.312 Chirality : 0.044 0.124 225 Planarity : 0.004 0.048 262 Dihedral : 11.089 72.094 532 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer: Outliers : 1.30 % Allowed : 3.90 % Favored : 94.81 % 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: -3.98 (0.51), residues: 183 helix: -2.70 (0.49), residues: 66 sheet: -1.01 (0.69), residues: 51 loop : -3.78 (0.57), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 121 TYR 0.009 0.002 TYR A 138 PHE 0.005 0.001 PHE A 100 HIS 0.003 0.001 HIS A 145 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 366 Ramachandran restraints generated. 183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 366 Ramachandran restraints generated. 183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.069 Fit side-chains REVERT: A 30 LEU cc_start: 0.8592 (tt) cc_final: 0.8324 (tp) REVERT: A 109 GLU cc_start: 0.5748 (OUTLIER) cc_final: 0.4032 (mm-30) REVERT: A 166 LYS cc_start: 0.7827 (ptpt) cc_final: 0.7556 (pttp) outliers start: 2 outliers final: 0 residues processed: 43 average time/residue: 0.2084 time to fit residues: 9.6204 Evaluate side-chains 24 residues out of total 154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1464 Z= 0.209 Angle : 0.574 3.905 1981 Z= 0.308 Chirality : 0.044 0.131 225 Planarity : 0.004 0.034 262 Dihedral : 7.928 58.522 203 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 3.25 % Allowed : 7.14 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.55), residues: 183 helix: -1.24 (0.57), residues: 65 sheet: -1.19 (0.64), residues: 61 loop : -3.75 (0.63), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 134 TYR 0.011 0.003 TYR A 126 PHE 0.008 0.001 PHE A 176 HIS 0.006 0.001 HIS A 145 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 366 Ramachandran restraints generated. 183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 366 Ramachandran restraints generated. 183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 26 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8631 (tt) cc_final: 0.8352 (tp) REVERT: A 89 LYS cc_start: 0.6733 (mtmt) cc_final: 0.6466 (mtmt) outliers start: 5 outliers final: 3 residues processed: 29 average time/residue: 0.5199 time to fit residues: 16.2278 Evaluate side-chains 27 residues out of total 154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 137 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 8 optimal weight: 30.0000 chunk 17 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1464 Z= 0.202 Angle : 0.571 4.344 1981 Z= 0.306 Chirality : 0.044 0.122 225 Planarity : 0.004 0.034 262 Dihedral : 5.896 25.078 200 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 3.25 % Allowed : 11.04 % 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: -2.59 (0.58), residues: 183 helix: -0.49 (0.62), residues: 65 sheet: -1.10 (0.66), residues: 60 loop : -3.72 (0.65), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 184 TYR 0.009 0.002 TYR A 126 PHE 0.006 0.001 PHE A 176 HIS 0.006 0.001 HIS A 145 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 366 Ramachandran restraints generated. 183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 366 Ramachandran restraints generated. 183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 26 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8573 (tt) cc_final: 0.8339 (tp) REVERT: A 37 ASP cc_start: 0.6056 (p0) cc_final: 0.5846 (p0) REVERT: A 109 GLU cc_start: 0.6472 (OUTLIER) cc_final: 0.4779 (pm20) outliers start: 5 outliers final: 4 residues processed: 29 average time/residue: 0.4751 time to fit residues: 14.6603 Evaluate side-chains 26 residues out of total 154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 137 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 17 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 8 optimal weight: 0.0020 chunk 1 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 overall best weight: 4.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1464 Z= 0.179 Angle : 0.559 6.439 1981 Z= 0.297 Chirality : 0.043 0.121 225 Planarity : 0.004 0.030 262 Dihedral : 5.552 20.604 200 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 3.25 % Allowed : 12.99 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.59), residues: 183 helix: 0.11 (0.62), residues: 65 sheet: -0.91 (0.67), residues: 60 loop : -3.77 (0.64), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 192 TYR 0.007 0.002 TYR A 138 PHE 0.006 0.001 PHE A 176 HIS 0.005 0.001 HIS A 145 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 366 Ramachandran restraints generated. 183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 366 Ramachandran restraints generated. 183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.128 Fit side-chains REVERT: A 30 LEU cc_start: 0.8599 (tt) cc_final: 0.8315 (tp) REVERT: A 109 GLU cc_start: 0.6071 (OUTLIER) cc_final: 0.4688 (pm20) outliers start: 5 outliers final: 4 residues processed: 24 average time/residue: 0.3372 time to fit residues: 8.7535 Evaluate side-chains 26 residues out of total 154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 137 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 9.9990 chunk 2 optimal weight: 40.0000 chunk 6 optimal weight: 20.0000 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1464 Z= 0.189 Angle : 0.568 5.512 1981 Z= 0.307 Chirality : 0.044 0.122 225 Planarity : 0.004 0.028 262 Dihedral : 5.356 20.595 200 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 3.25 % Allowed : 12.99 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.60), residues: 183 helix: 0.40 (0.63), residues: 65 sheet: -0.87 (0.67), residues: 61 loop : -3.68 (0.65), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 192 TYR 0.007 0.002 TYR A 126 PHE 0.006 0.001 PHE A 176 HIS 0.005 0.001 HIS A 145 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 366 Ramachandran restraints generated. 183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 366 Ramachandran restraints generated. 183 Oldfield, 0 Emsley, 183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 22 time to evaluate : 0.090 Fit side-chains REVERT: A 30 LEU cc_start: 0.8595 (tt) cc_final: 0.8322 (tp) REVERT: A 109 GLU cc_start: 0.6041 (OUTLIER) cc_final: 0.4534 (pm20) outliers start: 5 outliers final: 4 residues processed: 25 average time/residue: 0.2519 time to fit residues: 6.8539 Evaluate side-chains 26 residues out of total 154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 137 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 17 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 2 optimal weight: 30.0000 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1464 Z= 0.193 Angle : 0.579 5.612 1981 Z= 0.315 Chirality : 0.044 0.122 225 Planarity : 0.004 0.028 262 Dihedral : 5.315 20.212 200 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 3.25 % Allowed : 14.94 % Favored : 81.82 % 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: -1.72 (0.60), residues: 183 helix: 0.57 (0.65), residues: 65 sheet: -0.38 (0.75), residues: 51 loop : -3.60 (0.58), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 192 TYR 0.008 0.002 TYR A 138 PHE 0.006 0.001 PHE A 176 HIS 0.004 0.001 HIS A 145 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 482.17 seconds wall clock time: 8 minutes 41.18 seconds (521.18 seconds total)