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/8vi5_43249.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi5_43249.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global+local_grid_search+nqh_flips resolution=3.2 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi5_43249.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi5_43249.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi5_43249.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8vi5_43249.map" } resolution = 3.2 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= 0.015 sd= 0.069 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 9 5.16 5 C 1662 2.51 5 N 380 2.21 5 O 402 1.98 5 H 2489 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 28": "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: 4942 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 4942 Classifications: {'peptide': 308} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 13, 'TRANS': 294} Time building chain proxies: 0.93, per 1000 atoms: 0.19 Number of scatterers: 4942 At special positions: 0 Unit cell: (62.826, 60.562, 62.826, 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 9 16.00 O 402 8.00 N 380 7.00 C 1662 6.00 H 2489 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: 1.17 Conformation dependent library (CDL) restraints added in 149.2 milliseconds 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 568 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 82.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 11 through 30 removed outlier: 3.639A pdb=" N PHE A 14 " --> pdb=" O THR A 11 " (cutoff:3.500A) Proline residue: A 17 - end of helix Processing helix chain 'A' and resid 35 through 65 removed outlier: 4.089A pdb=" N ARG A 38 " --> pdb=" O PRO A 35 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR A 65 " --> pdb=" O LYS A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 75 Processing helix chain 'A' and resid 79 through 99 removed outlier: 3.547A pdb=" N PHE A 82 " --> pdb=" O ARG A 79 " (cutoff:3.500A) Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 102 through 122 Processing helix chain 'A' and resid 126 through 129 Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 140 through 146 Proline residue: A 145 - end of helix Processing helix chain 'A' and resid 148 through 160 Processing helix chain 'A' and resid 163 through 191 Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 195 through 218 removed outlier: 4.434A pdb=" N ALA A 199 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N THR A 200 " --> pdb=" O GLN A 196 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET A 201 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLY A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ILE A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL A 204 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU A 205 " --> pdb=" O MET A 201 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) Proline residue: A 207 - end of helix removed outlier: 3.566A pdb=" N VAL A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 243 Processing helix chain 'A' and resid 245 through 248 No H-bonds generated for 'chain 'A' and resid 245 through 248' Processing helix chain 'A' and resid 255 through 276 removed outlier: 4.138A pdb=" N PHE A 262 " --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 308 174 hydrogen bonds defined for protein. 300 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: 0.88 Time building geometry restraints manager: 1.31 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: 2488 1.14 - 1.31: 356 1.31 - 1.48: 1110 1.48 - 1.64: 1052 1.64 - 1.81: 17 Bond restraints: 5023 Sorted by residual: bond pdb=" N GLY A 12 " pdb=" H GLY A 12 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.55e+01 bond pdb=" N GLY A 263 " pdb=" H GLY A 263 " 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 273 " pdb=" H ALA A 273 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.52e+01 bond pdb=" N ILE A 88 " pdb=" H ILE A 88 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.52e+01 bond pdb=" N ALA A 48 " pdb=" H ALA A 48 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.52e+01 ... (remaining 5018 not shown) Histogram of bond angle deviations from ideal: 100.70 - 107.35: 192 107.35 - 114.01: 5702 114.01 - 120.66: 1956 120.66 - 127.32: 1192 127.32 - 133.97: 38 Bond angle restraints: 9080 Sorted by residual: angle pdb=" N GLY A 94 " pdb=" CA GLY A 94 " pdb=" C GLY A 94 " ideal model delta sigma weight residual 112.64 110.30 2.34 1.21e+00 6.83e-01 3.74e+00 angle pdb=" C PHE A 260 " pdb=" N SER A 261 " pdb=" CA SER A 261 " ideal model delta sigma weight residual 121.54 124.08 -2.54 1.91e+00 2.74e-01 1.77e+00 angle pdb=" N ILE A 88 " pdb=" CA ILE A 88 " pdb=" C ILE A 88 " ideal model delta sigma weight residual 110.23 108.85 1.38 1.04e+00 9.25e-01 1.76e+00 angle pdb=" C ALA A 206 " pdb=" CA ALA A 206 " pdb=" CB ALA A 206 " ideal model delta sigma weight residual 113.49 111.21 2.28 1.82e+00 3.02e-01 1.56e+00 angle pdb=" N PRO A 17 " pdb=" CA PRO A 17 " pdb=" C PRO A 17 " ideal model delta sigma weight residual 113.47 111.70 1.77 1.43e+00 4.89e-01 1.54e+00 ... (remaining 9075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.32: 2158 14.32 - 28.64: 133 28.64 - 42.96: 44 42.96 - 57.28: 39 57.28 - 71.60: 3 Dihedral angle restraints: 2377 sinusoidal: 1211 harmonic: 1166 Sorted by residual: dihedral pdb=" CB MET A 294 " pdb=" CG MET A 294 " pdb=" SD MET A 294 " pdb=" CE MET A 294 " ideal model delta sinusoidal sigma weight residual 180.00 128.76 51.24 3 1.50e+01 4.44e-03 8.99e+00 dihedral pdb=" CA GLN A 196 " pdb=" CB GLN A 196 " pdb=" CG GLN A 196 " pdb=" CD GLN A 196 " ideal model delta sinusoidal sigma weight residual -60.00 -108.31 48.31 3 1.50e+01 4.44e-03 8.62e+00 dihedral pdb=" N TRP A 231 " pdb=" CA TRP A 231 " pdb=" CB TRP A 231 " pdb=" CG TRP A 231 " ideal model delta sinusoidal sigma weight residual -60.00 -107.22 47.22 3 1.50e+01 4.44e-03 8.46e+00 ... (remaining 2374 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 224 0.023 - 0.046: 102 0.046 - 0.070: 30 0.070 - 0.093: 25 0.093 - 0.116: 9 Chirality restraints: 390 Sorted by residual: chirality pdb=" CA PRO A 207 " pdb=" N PRO A 207 " pdb=" C PRO A 207 " pdb=" CB PRO A 207 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.37e-01 chirality pdb=" CA VAL A 279 " pdb=" N VAL A 279 " pdb=" C VAL A 279 " pdb=" CB VAL A 279 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.02e-01 chirality pdb=" CA VAL A 43 " pdb=" N VAL A 43 " pdb=" C VAL A 43 " pdb=" CB VAL A 43 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.96e-01 ... (remaining 387 not shown) Planarity restraints: 714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 24 " 0.005 2.00e-02 2.50e+03 1.00e-02 1.00e+00 pdb=" C SER A 24 " -0.017 2.00e-02 2.50e+03 pdb=" O SER A 24 " 0.007 2.00e-02 2.50e+03 pdb=" N LEU A 25 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 44 " -0.005 2.00e-02 2.50e+03 9.83e-03 9.67e-01 pdb=" C LEU A 44 " 0.017 2.00e-02 2.50e+03 pdb=" O LEU A 44 " -0.006 2.00e-02 2.50e+03 pdb=" N GLY A 45 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 22 " -0.005 2.00e-02 2.50e+03 9.66e-03 9.34e-01 pdb=" C ALA A 22 " 0.017 2.00e-02 2.50e+03 pdb=" O ALA A 22 " -0.006 2.00e-02 2.50e+03 pdb=" N LEU A 23 " -0.006 2.00e-02 2.50e+03 ... (remaining 711 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 477 2.19 - 2.79: 9652 2.79 - 3.40: 14669 3.40 - 4.00: 19081 4.00 - 4.60: 29037 Nonbonded interactions: 72916 Sorted by model distance: nonbonded pdb=" O PHE A 197 " pdb=" HG1 THR A 200 " model vdw 1.592 1.850 nonbonded pdb=" O PRO A 17 " pdb=" H ALA A 21 " model vdw 1.601 1.850 nonbonded pdb=" HH TYR A 13 " pdb=" O PHE A 311 " model vdw 1.609 1.850 nonbonded pdb=" O MET A 267 " pdb=" HG SER A 270 " model vdw 1.612 1.850 nonbonded pdb=" O ASN A 269 " pdb=" HG1 THR A 272 " model vdw 1.613 1.850 ... (remaining 72911 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=0.50 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: 0.040 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: 0.140 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 6.930 Find NCS groups from input model: 0.030 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: 0.000 Make a string to write initial .geo file:3.820 Internal consistency checks: 0.000 Total: 11.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 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 2534 Z= 0.111 Angle : 0.440 4.552 3457 Z= 0.242 Chirality : 0.036 0.116 390 Planarity : 0.004 0.023 420 Dihedral : 11.997 71.595 856 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.78 % Allowed : 0.39 % Favored : 98.82 % 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: -0.75 (0.50), residues: 306 helix: -0.55 (0.34), residues: 241 sheet: None (None), residues: 0 loop : 0.49 (0.89), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 198 TYR 0.005 0.001 TYR A 61 PHE 0.007 0.001 PHE A 260 TRP 0.006 0.001 TRP A 177 HIS 0.001 0.000 HIS A 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 31 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: A 243 ARG cc_start: 0.8024 (tpt90) cc_final: 0.6226 (ttm170) outliers start: 2 outliers final: 0 residues processed: 33 average time/residue: 0.1293 time to fit residues: 5.1851 Evaluate side-chains 27 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2534 Z= 0.237 Angle : 0.476 4.990 3457 Z= 0.250 Chirality : 0.037 0.121 390 Planarity : 0.004 0.024 420 Dihedral : 3.786 34.837 331 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.78 % Allowed : 2.75 % Favored : 96.47 % 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: -0.66 (0.49), residues: 306 helix: -0.30 (0.34), residues: 246 sheet: None (None), residues: 0 loop : -0.32 (0.85), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 71 TYR 0.008 0.001 TYR A 233 PHE 0.008 0.001 PHE A 151 TRP 0.008 0.001 TRP A 231 HIS 0.001 0.001 HIS A 220 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 26 time to evaluate : 0.200 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 27 average time/residue: 0.2032 time to fit residues: 6.8413 Evaluate side-chains 27 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 25 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 231 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 26 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2534 Z= 0.244 Angle : 0.469 4.921 3457 Z= 0.246 Chirality : 0.037 0.120 390 Planarity : 0.004 0.025 420 Dihedral : 3.458 17.951 331 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.78 % Allowed : 4.31 % Favored : 94.90 % 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: -0.14 (0.49), residues: 306 helix: -0.08 (0.35), residues: 236 sheet: None (None), residues: 0 loop : 0.47 (0.79), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 198 TYR 0.008 0.001 TYR A 59 PHE 0.009 0.001 PHE A 151 TRP 0.009 0.001 TRP A 231 HIS 0.001 0.000 HIS A 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 26 time to evaluate : 0.201 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 27 average time/residue: 0.2075 time to fit residues: 6.9925 Evaluate side-chains 27 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 25 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 231 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2534 Z= 0.200 Angle : 0.453 4.853 3457 Z= 0.237 Chirality : 0.036 0.118 390 Planarity : 0.004 0.026 420 Dihedral : 3.358 14.704 331 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.78 % Allowed : 3.92 % Favored : 95.29 % 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: 0.03 (0.50), residues: 306 helix: 0.05 (0.35), residues: 236 sheet: None (None), residues: 0 loop : 0.51 (0.79), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 198 TYR 0.007 0.001 TYR A 59 PHE 0.007 0.001 PHE A 151 TRP 0.009 0.001 TRP A 231 HIS 0.001 0.000 HIS A 163 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 25 time to evaluate : 0.198 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 26 average time/residue: 0.1984 time to fit residues: 6.3918 Evaluate side-chains 27 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 25 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 231 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 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 281 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2534 Z= 0.216 Angle : 0.470 5.142 3457 Z= 0.243 Chirality : 0.037 0.119 390 Planarity : 0.004 0.026 420 Dihedral : 3.300 14.812 331 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.78 % Allowed : 3.92 % Favored : 95.29 % 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: 0.05 (0.49), residues: 306 helix: 0.11 (0.35), residues: 234 sheet: None (None), residues: 0 loop : 0.31 (0.76), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 38 TYR 0.008 0.001 TYR A 59 PHE 0.008 0.001 PHE A 151 TRP 0.009 0.001 TRP A 231 HIS 0.001 0.000 HIS A 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 27 time to evaluate : 0.130 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 28 average time/residue: 0.1312 time to fit residues: 4.5982 Evaluate side-chains 28 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 26 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 231 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS A 281 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2534 Z= 0.127 Angle : 0.437 4.737 3457 Z= 0.225 Chirality : 0.035 0.112 390 Planarity : 0.004 0.028 420 Dihedral : 3.122 14.088 331 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.39 % Allowed : 5.49 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.50), residues: 306 helix: 0.30 (0.36), residues: 233 sheet: None (None), residues: 0 loop : 0.54 (0.78), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 38 TYR 0.015 0.001 TYR A 275 PHE 0.006 0.001 PHE A 180 TRP 0.007 0.001 TRP A 231 HIS 0.002 0.000 HIS A 276 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 537.75 seconds wall clock time: 9 minutes 38.85 seconds (578.85 seconds total)