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/8qjy_18454.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8qjy_18454.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global+local_grid_search+nqh_flips resolution=3.5 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8qjy_18454.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8qjy_18454.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8qjy_18454.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8qjy_18454.map" } resolution = 3.5 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= 0.005 sd= 0.015 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 971 2.51 5 N 258 2.21 5 O 310 1.98 5 H 1490 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 318": "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: 3038 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3038 Classifications: {'peptide': 197} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 189} Time building chain proxies: 0.64, per 1000 atoms: 0.21 Number of scatterers: 3038 At special positions: 0 Unit cell: (61.1, 57.2, 66.3, 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 310 8.00 N 258 7.00 C 971 6.00 H 1490 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: 0.57 Conformation dependent library (CDL) restraints added in 96.5 milliseconds 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 376 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 3 sheets defined 11.7% alpha, 32.5% 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 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 180 through 187 removed outlier: 3.736A pdb=" N LEU A 185 " --> pdb=" O ASN A 181 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N THR A 186 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N THR A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 247 through 253 removed outlier: 5.160A pdb=" N LYS A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 133 through 135 Processing sheet with id= B, first strand: chain 'A' and resid 190 through 199 removed outlier: 6.315A pdb=" N ASN A 297 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 218 through 220 removed outlier: 4.646A pdb=" N HIS A 218 " --> pdb=" O ALA A 225 " (cutoff:3.500A) 51 hydrogen bonds defined for protein. 126 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: 0.47 Time building geometry restraints manager: 0.66 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: 1486 1.14 - 1.31: 262 1.31 - 1.48: 661 1.48 - 1.64: 648 1.64 - 1.81: 14 Bond restraints: 3071 Sorted by residual: bond pdb=" ND2 ASN A 139 " pdb="HD21 ASN A 139 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.74e+01 bond pdb=" N ASN A 192 " pdb=" H ASN A 192 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" N ASN A 139 " pdb=" H ASN A 139 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" NH1 ARG A 208 " pdb="HH12 ARG A 208 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" N PHE A 269 " pdb=" H PHE A 269 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.52e+01 ... (remaining 3066 not shown) Histogram of bond angle deviations from ideal: 100.79 - 107.42: 101 107.42 - 114.05: 3582 114.05 - 120.68: 982 120.68 - 127.31: 825 127.31 - 133.94: 15 Bond angle restraints: 5505 Sorted by residual: angle pdb=" C ASN A 278 " pdb=" CA ASN A 278 " pdb=" CB ASN A 278 " ideal model delta sigma weight residual 117.23 114.64 2.59 1.36e+00 5.41e-01 3.62e+00 angle pdb=" N GLY A 299 " pdb=" CA GLY A 299 " pdb=" C GLY A 299 " ideal model delta sigma weight residual 115.61 112.31 3.30 1.74e+00 3.30e-01 3.61e+00 angle pdb=" CA GLY A 299 " pdb=" C GLY A 299 " pdb=" N ASP A 300 " ideal model delta sigma weight residual 118.41 116.70 1.71 1.29e+00 6.01e-01 1.76e+00 angle pdb=" C ASN A 144 " pdb=" CA ASN A 144 " pdb=" CB ASN A 144 " ideal model delta sigma weight residual 110.44 108.26 2.18 1.68e+00 3.54e-01 1.68e+00 angle pdb=" N TYR A 260 " pdb=" CA TYR A 260 " pdb=" C TYR A 260 " ideal model delta sigma weight residual 108.76 110.72 -1.96 1.69e+00 3.50e-01 1.35e+00 ... (remaining 5500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.79: 1362 14.79 - 29.58: 77 29.58 - 44.37: 23 44.37 - 59.16: 10 59.16 - 73.95: 3 Dihedral angle restraints: 1475 sinusoidal: 784 harmonic: 691 Sorted by residual: dihedral pdb=" CA PHE A 172 " pdb=" C PHE A 172 " pdb=" N VAL A 173 " pdb=" CA VAL A 173 " ideal model delta harmonic sigma weight residual -180.00 -164.58 -15.42 0 5.00e+00 4.00e-02 9.51e+00 dihedral pdb=" CA ARG A 249 " pdb=" CB ARG A 249 " pdb=" CG ARG A 249 " pdb=" CD ARG A 249 " ideal model delta sinusoidal sigma weight residual -180.00 -125.55 -54.45 3 1.50e+01 4.44e-03 9.28e+00 dihedral pdb=" CB MET A 236 " pdb=" CG MET A 236 " pdb=" SD MET A 236 " pdb=" CE MET A 236 " ideal model delta sinusoidal sigma weight residual 60.00 107.33 -47.33 3 1.50e+01 4.44e-03 8.48e+00 ... (remaining 1472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 152 0.031 - 0.061: 71 0.061 - 0.092: 12 0.092 - 0.123: 10 0.123 - 0.153: 6 Chirality restraints: 251 Sorted by residual: chirality pdb=" CA ILE A 176 " pdb=" N ILE A 176 " pdb=" C ILE A 176 " pdb=" CB ILE A 176 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA ILE A 292 " pdb=" N ILE A 292 " pdb=" C ILE A 292 " pdb=" CB ILE A 292 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA ILE A 229 " pdb=" N ILE A 229 " pdb=" C ILE A 229 " pdb=" CB ILE A 229 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 248 not shown) Planarity restraints: 467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 139 " 0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO A 140 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 140 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 140 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 172 " 0.010 2.00e-02 2.50e+03 5.36e-03 8.62e-01 pdb=" CG PHE A 172 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 PHE A 172 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 172 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 172 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 172 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 172 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 PHE A 172 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 172 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE A 172 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 172 " 0.001 2.00e-02 2.50e+03 pdb=" HZ PHE A 172 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 318 " -0.009 2.00e-02 2.50e+03 4.31e-03 5.57e-01 pdb=" CG PHE A 318 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE A 318 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 318 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 318 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 318 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 318 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE A 318 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 318 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 318 " -0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE A 318 " -0.000 2.00e-02 2.50e+03 pdb=" HZ PHE A 318 " -0.001 2.00e-02 2.50e+03 ... (remaining 464 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 176 2.14 - 2.76: 5336 2.76 - 3.37: 8204 3.37 - 3.99: 11501 3.99 - 4.60: 16596 Nonbonded interactions: 41813 Sorted by model distance: nonbonded pdb=" H SER A 264 " pdb=" OE2 GLU A 303 " model vdw 1.530 1.850 nonbonded pdb=" O PHE A 235 " pdb=" HH TYR A 320 " model vdw 1.582 1.850 nonbonded pdb=" O MET A 236 " pdb=" H GLU A 323 " model vdw 1.664 1.850 nonbonded pdb=" H ASN A 278 " pdb=" O CYS A 289 " model vdw 1.671 1.850 nonbonded pdb=" HZ2 LYS A 219 " pdb=" O GLY A 221 " model vdw 1.676 1.850 ... (remaining 41808 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=0.51 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: 0.010 Extract box with map and model: 0.020 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.610 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:0.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:2.260 Internal consistency checks: 0.000 Total: 7.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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 0.012 1581 Z= 0.125 Angle : 0.443 3.508 2158 Z= 0.249 Chirality : 0.043 0.153 251 Planarity : 0.003 0.030 278 Dihedral : 10.786 73.952 559 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % 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: -1.34 (0.62), residues: 195 helix: -0.35 (1.76), residues: 6 sheet: -0.65 (0.57), residues: 77 loop : -1.06 (0.65), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 280 TYR 0.010 0.001 TYR A 320 PHE 0.015 0.002 PHE A 172 TRP 0.008 0.001 TRP A 296 HIS 0.002 0.001 HIS A 188 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1189 time to fit residues: 10.8602 Evaluate side-chains 56 residues out of total 175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1581 Z= 0.221 Angle : 0.477 3.622 2158 Z= 0.251 Chirality : 0.042 0.139 251 Planarity : 0.004 0.049 278 Dihedral : 4.341 17.201 214 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.71 % Allowed : 13.14 % Favored : 85.14 % 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: -0.60 (0.64), residues: 195 helix: 0.46 (2.06), residues: 6 sheet: -0.09 (0.62), residues: 72 loop : -0.60 (0.64), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 280 TYR 0.008 0.001 TYR A 320 PHE 0.014 0.002 PHE A 172 TRP 0.006 0.001 TRP A 296 HIS 0.006 0.002 HIS A 218 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 52 average time/residue: 0.2890 time to fit residues: 16.7154 Evaluate side-chains 48 residues out of total 175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 9 optimal weight: 40.0000 chunk 4 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 30.0000 chunk 11 optimal weight: 7.9990 chunk 13 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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: 0.8233 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1581 Z= 0.203 Angle : 0.460 3.544 2158 Z= 0.243 Chirality : 0.043 0.138 251 Planarity : 0.004 0.047 278 Dihedral : 4.317 16.777 214 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.71 % Allowed : 13.14 % Favored : 85.14 % 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: -0.39 (0.65), residues: 195 helix: 0.21 (2.18), residues: 6 sheet: 0.04 (0.64), residues: 72 loop : -0.42 (0.65), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 279 TYR 0.008 0.001 TYR A 320 PHE 0.019 0.002 PHE A 172 TRP 0.006 0.001 TRP A 296 HIS 0.005 0.002 HIS A 218 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 51 average time/residue: 0.2311 time to fit residues: 13.2382 Evaluate side-chains 49 residues out of total 175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 274 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 17 optimal weight: 0.4980 chunk 15 optimal weight: 20.0000 chunk 14 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- 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: 0.8218 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 1581 Z= 0.159 Angle : 0.450 3.590 2158 Z= 0.237 Chirality : 0.043 0.139 251 Planarity : 0.004 0.046 278 Dihedral : 4.199 16.139 214 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.14 % Allowed : 14.29 % Favored : 84.57 % 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: -0.27 (0.65), residues: 195 helix: 0.43 (2.49), residues: 6 sheet: 0.07 (0.64), residues: 72 loop : -0.30 (0.65), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 208 TYR 0.008 0.001 TYR A 320 PHE 0.010 0.001 PHE A 318 TRP 0.006 0.001 TRP A 296 HIS 0.003 0.001 HIS A 218 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 52 average time/residue: 0.1826 time to fit residues: 10.7381 Evaluate side-chains 51 residues out of total 175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 185 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 10 optimal weight: 0.9990 chunk 2 optimal weight: 30.0000 chunk 6 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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: 0.8229 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1581 Z= 0.167 Angle : 0.449 3.619 2158 Z= 0.235 Chirality : 0.043 0.137 251 Planarity : 0.003 0.046 278 Dihedral : 4.136 15.093 214 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.14 % Allowed : 15.43 % Favored : 83.43 % 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: -0.33 (0.64), residues: 195 helix: 0.52 (2.55), residues: 6 sheet: 0.08 (0.63), residues: 72 loop : -0.40 (0.62), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 208 TYR 0.008 0.001 TYR A 320 PHE 0.009 0.001 PHE A 318 TRP 0.005 0.001 TRP A 296 HIS 0.003 0.001 HIS A 218 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.8166 (mmp) cc_final: 0.7830 (mmt) outliers start: 2 outliers final: 2 residues processed: 51 average time/residue: 0.2101 time to fit residues: 11.7923 Evaluate side-chains 50 residues out of total 175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 290 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 9 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 2 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- 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: 0.8235 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1581 Z= 0.171 Angle : 0.473 5.249 2158 Z= 0.248 Chirality : 0.043 0.140 251 Planarity : 0.004 0.047 278 Dihedral : 4.068 15.131 214 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.14 % Allowed : 17.14 % Favored : 81.71 % 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: -0.42 (0.63), residues: 195 helix: 0.55 (2.59), residues: 6 sheet: 0.02 (0.63), residues: 72 loop : -0.47 (0.62), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 322 TYR 0.007 0.001 TYR A 320 PHE 0.009 0.001 PHE A 318 TRP 0.005 0.001 TRP A 296 HIS 0.003 0.001 HIS A 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 505.26 seconds wall clock time: 9 minutes 6.27 seconds (546.27 seconds total)