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/8qjx_18453.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8qjx_18453.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global+local_grid_search+nqh_flips resolution=3.3 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8qjx_18453.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8qjx_18453.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8qjx_18453.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8qjx_18453.pdb" } resolution = 3.3 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= 0.009 sd= 0.018 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: 0.65, per 1000 atoms: 0.21 Number of scatterers: 3038 At special positions: 0 Unit cell: (63.7, 58.5, 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: 0.62 Conformation dependent library (CDL) restraints added in 96.6 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: 3 helices and 3 sheets defined 9.6% alpha, 32.0% 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 180 through 187 removed outlier: 4.382A pdb=" N LEU A 185 " --> pdb=" O ASN A 181 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N THR A 186 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N THR A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 235 Processing helix chain 'A' and resid 247 through 253 removed outlier: 5.337A 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: 6.204A 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: 4.624A pdb=" N HIS A 218 " --> pdb=" O ALA A 225 " (cutoff:3.500A) 50 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: 0.49 Time building geometry restraints manager: 0.73 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 - 1.47: 661 1.47 - 1.64: 648 1.64 - 1.81: 14 Bond restraints: 3071 Sorted by residual: bond pdb=" N ASN A 278 " pdb=" H ASN A 278 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.70e+01 bond pdb=" N ILE A 147 " pdb=" H ILE A 147 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.58e+01 bond pdb=" N ASN A 223 " pdb=" H ASN A 223 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.54e+01 bond pdb=" N ARG A 266 " pdb=" H ARG A 266 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.54e+01 bond pdb=" N SER A 179 " pdb=" H SER A 179 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.53e+01 ... (remaining 3066 not shown) Histogram of bond angle deviations from ideal: 100.83 - 107.46: 99 107.46 - 114.09: 3589 114.09 - 120.72: 1009 120.72 - 127.35: 793 127.35 - 133.98: 15 Bond angle restraints: 5505 Sorted by residual: angle pdb=" C ALA A 171 " pdb=" N PHE A 172 " pdb=" CA PHE A 172 " ideal model delta sigma weight residual 123.13 125.05 -1.92 1.51e+00 4.39e-01 1.62e+00 angle pdb=" C TYR A 319 " pdb=" N TYR A 320 " pdb=" CA TYR A 320 " ideal model delta sigma weight residual 121.94 119.83 2.11 1.76e+00 3.23e-01 1.43e+00 angle pdb=" N VAL A 304 " pdb=" CA VAL A 304 " pdb=" C VAL A 304 " ideal model delta sigma weight residual 109.46 107.88 1.58 1.38e+00 5.25e-01 1.31e+00 angle pdb=" CA TRP A 296 " pdb=" CB TRP A 296 " pdb=" CG TRP A 296 " ideal model delta sigma weight residual 113.60 115.65 -2.05 1.90e+00 2.77e-01 1.17e+00 angle pdb=" N VAL A 173 " pdb=" CA VAL A 173 " pdb=" C VAL A 173 " ideal model delta sigma weight residual 108.46 110.06 -1.60 1.49e+00 4.50e-01 1.15e+00 ... (remaining 5500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.22: 1383 15.22 - 30.44: 57 30.44 - 45.67: 19 45.67 - 60.89: 12 60.89 - 76.11: 4 Dihedral angle restraints: 1475 sinusoidal: 784 harmonic: 691 Sorted by residual: dihedral pdb=" CA LEU A 134 " pdb=" CB LEU A 134 " pdb=" CG LEU A 134 " pdb=" CD1 LEU A 134 " ideal model delta sinusoidal sigma weight residual 180.00 133.41 46.59 3 1.50e+01 4.44e-03 8.36e+00 dihedral pdb=" N ASN A 181 " pdb=" CA ASN A 181 " pdb=" CB ASN A 181 " pdb=" CG ASN A 181 " ideal model delta sinusoidal sigma weight residual -60.00 -102.72 42.72 3 1.50e+01 4.44e-03 7.67e+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 60.00 102.07 -42.07 3 1.50e+01 4.44e-03 7.54e+00 ... (remaining 1472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 138 0.027 - 0.054: 79 0.054 - 0.082: 15 0.082 - 0.109: 8 0.109 - 0.136: 11 Chirality restraints: 251 Sorted by residual: chirality pdb=" CA ILE A 290 " pdb=" N ILE A 290 " pdb=" C ILE A 290 " pdb=" CB ILE A 290 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ILE A 271 " pdb=" N ILE A 271 " pdb=" C ILE A 271 " pdb=" CB ILE A 271 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA ILE A 255 " pdb=" N ILE A 255 " pdb=" C ILE A 255 " pdb=" CB ILE A 255 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 248 not shown) Planarity restraints: 467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 172 " 0.010 2.00e-02 2.50e+03 5.22e-03 8.18e-01 pdb=" CG PHE A 172 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE A 172 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 172 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 172 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 172 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 172 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 PHE A 172 " -0.000 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 TRP A 296 " 0.007 2.00e-02 2.50e+03 3.70e-03 5.47e-01 pdb=" CG TRP A 296 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP A 296 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP A 296 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 296 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 296 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 296 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 296 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 296 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 296 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP A 296 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 TRP A 296 " 0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP A 296 " -0.000 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 296 " 0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 296 " -0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP A 296 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 139 " 0.010 5.00e-02 4.00e+02 1.48e-02 3.51e-01 pdb=" N PRO A 140 " -0.026 5.00e-02 4.00e+02 pdb=" CA PRO A 140 " 0.008 5.00e-02 4.00e+02 pdb=" CD PRO A 140 " 0.008 5.00e-02 4.00e+02 ... (remaining 464 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 167 2.14 - 2.76: 5314 2.76 - 3.37: 8147 3.37 - 3.99: 11352 3.99 - 4.60: 16514 Nonbonded interactions: 41494 Sorted by model distance: nonbonded pdb=" HZ2 LYS A 219 " pdb=" O GLY A 221 " model vdw 1.528 1.850 nonbonded pdb=" OD1 ASN A 278 " pdb=" H CYS A 289 " model vdw 1.576 1.850 nonbonded pdb="HH12 ARG A 322 " pdb=" OD1 ASP A 325 " model vdw 1.579 1.850 nonbonded pdb=" H TYR A 260 " pdb=" OG SER A 314 " model vdw 1.590 1.850 nonbonded pdb=" O PHE A 235 " pdb=" HH TYR A 320 " model vdw 1.632 1.850 ... (remaining 41489 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: 0.020 Extract box with map and model: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.680 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 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:0.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:2.280 Internal consistency checks: 0.000 Total: 7.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 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= 0.120 Angle : 0.429 3.511 2158 Z= 0.235 Chirality : 0.042 0.136 251 Planarity : 0.002 0.015 278 Dihedral : 10.696 76.109 559 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % 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: -0.77 (0.59), residues: 195 helix: -4.01 (0.67), residues: 6 sheet: -0.37 (0.57), residues: 72 loop : -0.31 (0.60), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 249 TYR 0.009 0.001 TYR A 174 PHE 0.014 0.001 PHE A 172 TRP 0.012 0.001 TRP A 296 HIS 0.002 0.001 HIS A 218 *********************** 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 60 residues out of total 175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.076 Fit side-chains revert: symmetry clash REVERT: A 254 TYR cc_start: 0.9157 (m-80) cc_final: 0.8923 (m-80) REVERT: A 260 TYR cc_start: 0.9053 (m-80) cc_final: 0.8803 (m-80) REVERT: A 273 ILE cc_start: 0.9232 (mt) cc_final: 0.8897 (mt) REVERT: A 324 ASP cc_start: 0.8169 (m-30) cc_final: 0.7966 (m-30) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1398 time to fit residues: 9.3039 Evaluate side-chains 43 residues out of total 175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 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: 8.9990 chunk 13 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 1581 Z= 0.237 Angle : 0.480 4.479 2158 Z= 0.251 Chirality : 0.043 0.135 251 Planarity : 0.003 0.025 278 Dihedral : 4.068 15.010 214 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 12.57 % Favored : 87.43 % 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: -0.35 (0.60), residues: 195 helix: -3.64 (0.87), residues: 6 sheet: -0.22 (0.57), residues: 72 loop : 0.08 (0.62), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 291 TYR 0.009 0.001 TYR A 320 PHE 0.014 0.001 PHE A 172 TRP 0.010 0.001 TRP A 296 HIS 0.001 0.001 HIS A 188 *********************** 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 47 residues out of total 175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.147 Fit side-chains REVERT: A 254 TYR cc_start: 0.9205 (m-80) cc_final: 0.8870 (m-80) REVERT: A 260 TYR cc_start: 0.9119 (m-80) cc_final: 0.8862 (m-80) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.3233 time to fit residues: 16.6430 Evaluate side-chains 45 residues out of total 175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 9 optimal weight: 20.0000 chunk 4 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 15 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1581 Z= 0.202 Angle : 0.455 3.618 2158 Z= 0.240 Chirality : 0.042 0.130 251 Planarity : 0.004 0.044 278 Dihedral : 4.006 13.908 214 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 13.14 % Favored : 86.86 % 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: -0.14 (0.60), residues: 195 helix: -2.58 (1.61), residues: 6 sheet: -0.21 (0.57), residues: 72 loop : 0.26 (0.61), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 280 TYR 0.009 0.001 TYR A 242 PHE 0.013 0.001 PHE A 172 TRP 0.010 0.001 TRP A 296 HIS 0.001 0.001 HIS A 188 *********************** 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 45 residues out of total 175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.136 Fit side-chains REVERT: A 260 TYR cc_start: 0.9055 (m-80) cc_final: 0.8811 (m-80) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.3049 time to fit residues: 15.1361 Evaluate side-chains 45 residues out of total 175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 17 optimal weight: 20.0000 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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: 0.8731 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1581 Z= 0.207 Angle : 0.468 3.654 2158 Z= 0.244 Chirality : 0.042 0.131 251 Planarity : 0.004 0.041 278 Dihedral : 3.991 13.524 214 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.57 % Allowed : 11.43 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.61), residues: 195 helix: -2.09 (2.10), residues: 6 sheet: -0.11 (0.57), residues: 72 loop : 0.38 (0.63), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 280 TYR 0.008 0.001 TYR A 174 PHE 0.013 0.002 PHE A 172 TRP 0.010 0.001 TRP A 296 HIS 0.001 0.000 HIS A 188 *********************** 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 47 residues out of total 175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.094 Fit side-chains REVERT: A 260 TYR cc_start: 0.9066 (m-80) cc_final: 0.8801 (m-80) outliers start: 1 outliers final: 1 residues processed: 47 average time/residue: 0.2568 time to fit residues: 13.1401 Evaluate side-chains 45 residues out of total 175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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: 0.8718 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1581 Z= 0.157 Angle : 0.458 3.642 2158 Z= 0.237 Chirality : 0.042 0.132 251 Planarity : 0.004 0.059 278 Dihedral : 3.892 13.767 214 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.14 % Allowed : 12.00 % Favored : 86.86 % 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: 0.07 (0.62), residues: 195 helix: -2.00 (2.23), residues: 6 sheet: -0.15 (0.56), residues: 72 loop : 0.46 (0.64), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 280 TYR 0.008 0.001 TYR A 320 PHE 0.012 0.001 PHE A 172 TRP 0.009 0.001 TRP A 296 HIS 0.001 0.000 HIS A 188 *********************** 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 47 residues out of total 175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.081 Fit side-chains REVERT: A 260 TYR cc_start: 0.9020 (m-80) cc_final: 0.8765 (m-80) outliers start: 2 outliers final: 1 residues processed: 47 average time/residue: 0.2035 time to fit residues: 10.4385 Evaluate side-chains 45 residues out of total 175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 9 optimal weight: 30.0000 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 10 optimal weight: 0.0050 chunk 6 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 overall best weight: 3.9800 ------------------------------------------------------------------------------- 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: 0.8714 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 1581 Z= 0.156 Angle : 0.472 3.936 2158 Z= 0.246 Chirality : 0.042 0.133 251 Planarity : 0.005 0.067 278 Dihedral : 3.971 13.716 214 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.57 % Allowed : 12.00 % Favored : 87.43 % 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: 0.12 (0.62), residues: 195 helix: -1.90 (2.31), residues: 6 sheet: -0.07 (0.57), residues: 72 loop : 0.45 (0.64), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 280 TYR 0.008 0.001 TYR A 320 PHE 0.011 0.001 PHE A 172 TRP 0.009 0.001 TRP A 296 HIS 0.001 0.000 HIS A 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 535.72 seconds wall clock time: 9 minutes 35.74 seconds (575.74 seconds total)