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/8qk3_18455.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8qk3_18455.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/8qk3_18455.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8qk3_18455.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8qk3_18455.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8qk3_18455.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= 0.004 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 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 None 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: 0.62, per 1000 atoms: 0.20 Number of scatterers: 3038 At special positions: 0 Unit cell: (54.6, 57.12, 62.16, 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: 0.60 Conformation dependent library (CDL) restraints added in 117.5 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: 3 helices and 2 sheets defined 9.6% alpha, 30.5% 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 180 through 187 removed outlier: 4.178A pdb=" N LEU A 185 " --> pdb=" O ASN A 181 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N THR A 186 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 5.089A 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: 5.367A 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: 6.296A pdb=" N ASN A 297 " --> pdb=" O PRO A 270 " (cutoff:3.500A) 47 hydrogen bonds defined for protein. 120 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: 0.62 Time building geometry restraints manager: 0.71 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=" N PHE A 244 " pdb=" H PHE A 244 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.68e+01 bond pdb=" N THR A 298 " pdb=" H THR A 298 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" N SER A 287 " pdb=" H SER A 287 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.53e+01 bond pdb=" N CYS A 156 " pdb=" H CYS A 156 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.53e+01 bond pdb=" N ASN A 130 " pdb=" H ASN A 130 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.52e+01 ... (remaining 3066 not shown) Histogram of bond angle deviations from ideal: 100.63 - 107.29: 86 107.29 - 113.94: 3572 113.94 - 120.60: 980 120.60 - 127.26: 852 127.26 - 133.91: 15 Bond angle restraints: 5505 Sorted by residual: angle pdb=" C SER A 153 " pdb=" N ASN A 154 " pdb=" CA ASN A 154 " ideal model delta sigma weight residual 121.54 124.94 -3.40 1.91e+00 2.74e-01 3.16e+00 angle pdb=" C LEU A 277 " pdb=" N ASN A 278 " pdb=" CA ASN A 278 " ideal model delta sigma weight residual 121.54 124.86 -3.32 1.91e+00 2.74e-01 3.03e+00 angle pdb=" C TYR A 319 " pdb=" N TYR A 320 " pdb=" CA TYR A 320 " ideal model delta sigma weight residual 121.63 118.70 2.93 1.92e+00 2.71e-01 2.33e+00 angle pdb=" CA TRP A 296 " pdb=" CB TRP A 296 " pdb=" CG TRP A 296 " ideal model delta sigma weight residual 113.60 116.17 -2.57 1.90e+00 2.77e-01 1.83e+00 angle pdb=" C TRP A 294 " pdb=" N SER A 295 " pdb=" CA SER A 295 " ideal model delta sigma weight residual 121.62 119.27 2.35 1.83e+00 2.99e-01 1.64e+00 ... (remaining 5500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.21: 1378 13.21 - 26.43: 58 26.43 - 39.64: 23 39.64 - 52.86: 10 52.86 - 66.07: 6 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 -164.64 -15.36 0 5.00e+00 4.00e-02 9.43e+00 dihedral pdb=" CA ASN A 154 " pdb=" C ASN A 154 " pdb=" N ASP A 155 " pdb=" CA ASP A 155 " ideal model delta harmonic sigma weight residual -180.00 -164.84 -15.16 0 5.00e+00 4.00e-02 9.19e+00 dihedral pdb=" N ASN A 149 " pdb=" CA ASN A 149 " pdb=" CB ASN A 149 " pdb=" CG ASN A 149 " ideal model delta sinusoidal sigma weight residual -180.00 -134.58 -45.42 3 1.50e+01 4.44e-03 8.17e+00 ... (remaining 1472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 140 0.027 - 0.054: 79 0.054 - 0.081: 13 0.081 - 0.108: 7 0.108 - 0.134: 12 Chirality restraints: 251 Sorted by residual: 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 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 -0.13 2.00e-01 2.50e+01 4.48e-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 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 248 not shown) Planarity restraints: 467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 139 " 0.014 5.00e-02 4.00e+02 2.11e-02 7.13e-01 pdb=" N PRO A 140 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO A 140 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 140 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 242 " 0.014 5.00e-02 4.00e+02 2.05e-02 6.71e-01 pdb=" N PRO A 243 " -0.035 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 172 " 0.009 2.00e-02 2.50e+03 4.61e-03 6.39e-01 pdb=" CG PHE A 172 " -0.013 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 " 0.004 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 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE A 172 " 0.000 2.00e-02 2.50e+03 pdb=" HZ PHE A 172 " 0.001 2.00e-02 2.50e+03 ... (remaining 464 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.08: 106 2.08 - 2.71: 4625 2.71 - 3.34: 8312 3.34 - 3.97: 11626 3.97 - 4.60: 16807 Nonbonded interactions: 41476 Sorted by model distance: nonbonded pdb=" H ASN A 278 " pdb=" O CYS A 289 " model vdw 1.456 1.850 nonbonded pdb=" H TYR A 260 " pdb=" OG SER A 314 " model vdw 1.552 1.850 nonbonded pdb=" HG SER A 264 " pdb=" OE2 GLU A 303 " model vdw 1.577 1.850 nonbonded pdb=" O TYR A 260 " pdb=" H SER A 314 " model vdw 1.589 1.850 nonbonded pdb=" O PHE A 235 " pdb=" HH TYR A 320 " model vdw 1.593 1.850 ... (remaining 41471 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: 0.010 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.900 Find NCS groups from input model: 0.020 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:2.660 Internal consistency checks: 0.000 Total: 8.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 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 0.013 1581 Z= 0.121 Angle : 0.464 3.396 2158 Z= 0.260 Chirality : 0.042 0.134 251 Planarity : 0.003 0.021 278 Dihedral : 9.849 66.071 559 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.62 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % 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: -0.91 (0.58), residues: 195 helix: -3.13 (0.81), residues: 12 sheet: 0.03 (0.61), residues: 70 loop : -0.68 (0.58), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 291 TYR 0.008 0.001 TYR A 320 PHE 0.013 0.001 PHE A 172 TRP 0.010 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 84 residues out of total 175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 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: A 156 CYS cc_start: 0.6852 (p) cc_final: 0.6542 (p) REVERT: A 184 MET cc_start: 0.8219 (ppp) cc_final: 0.7936 (ppp) REVERT: A 291 ARG cc_start: 0.8222 (mtp-110) cc_final: 0.7921 (mtt90) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1389 time to fit residues: 12.9325 Evaluate side-chains 54 residues out of total 175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.105 ------------------------------------------------------------------------------- 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: 6.9990 chunk 13 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 1581 Z= 0.231 Angle : 0.501 3.648 2158 Z= 0.267 Chirality : 0.042 0.137 251 Planarity : 0.003 0.025 278 Dihedral : 4.847 22.350 214 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.29 % Allowed : 14.29 % 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: -0.73 (0.59), residues: 195 helix: -2.49 (1.03), residues: 12 sheet: 0.16 (0.60), residues: 70 loop : -0.63 (0.59), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 279 TYR 0.006 0.001 TYR A 174 PHE 0.013 0.001 PHE A 172 TRP 0.010 0.001 TRP A 296 HIS 0.001 0.000 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 55 residues out of total 175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.258 Fit side-chains REVERT: A 184 MET cc_start: 0.8339 (ppp) cc_final: 0.8037 (ppp) REVERT: A 291 ARG cc_start: 0.8316 (mtp-110) cc_final: 0.7978 (mtm-85) outliers start: 4 outliers final: 2 residues processed: 54 average time/residue: 0.3361 time to fit residues: 19.8359 Evaluate side-chains 48 residues out of total 175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 250 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 9 optimal weight: 30.0000 chunk 4 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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: 0.8400 moved from start: 0.3929 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= 0.200 Angle : 0.500 3.500 2158 Z= 0.266 Chirality : 0.042 0.138 251 Planarity : 0.003 0.020 278 Dihedral : 4.766 22.681 214 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.86 % Allowed : 14.86 % Favored : 82.29 % 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: -0.57 (0.59), residues: 195 helix: -1.89 (1.29), residues: 12 sheet: 0.20 (0.59), residues: 70 loop : -0.53 (0.60), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 208 TYR 0.005 0.001 TYR A 174 PHE 0.012 0.002 PHE A 172 TRP 0.009 0.001 TRP A 296 HIS 0.001 0.000 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 54 residues out of total 175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.8317 (ppp) cc_final: 0.8013 (ppp) REVERT: A 291 ARG cc_start: 0.8299 (mtp-110) cc_final: 0.7957 (ttm110) outliers start: 5 outliers final: 4 residues processed: 52 average time/residue: 0.3277 time to fit residues: 18.4821 Evaluate side-chains 52 residues out of total 175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 300 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 17 optimal weight: 8.9990 chunk 15 optimal weight: 30.0000 chunk 14 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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: 0.8411 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1581 Z= 0.180 Angle : 0.492 3.510 2158 Z= 0.261 Chirality : 0.042 0.138 251 Planarity : 0.003 0.026 278 Dihedral : 4.715 22.274 214 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.29 % Allowed : 16.00 % 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: -0.51 (0.59), residues: 195 helix: -1.40 (1.45), residues: 12 sheet: 0.18 (0.58), residues: 70 loop : -0.50 (0.60), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 189 TYR 0.008 0.001 TYR A 256 PHE 0.011 0.001 PHE A 172 TRP 0.009 0.001 TRP A 296 HIS 0.001 0.001 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 56 residues out of total 175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.8358 (ppp) cc_final: 0.8024 (ppp) REVERT: A 291 ARG cc_start: 0.8288 (mtp-110) cc_final: 0.8019 (ttm110) outliers start: 4 outliers final: 3 residues processed: 55 average time/residue: 0.2455 time to fit residues: 14.7212 Evaluate side-chains 53 residues out of total 175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 300 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 10 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 chunk 7 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1581 Z= 0.202 Angle : 0.513 4.145 2158 Z= 0.270 Chirality : 0.042 0.139 251 Planarity : 0.003 0.028 278 Dihedral : 4.687 21.769 214 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.29 % Allowed : 18.86 % Favored : 78.86 % 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: -0.44 (0.59), residues: 195 helix: -1.02 (1.49), residues: 12 sheet: 0.16 (0.57), residues: 70 loop : -0.44 (0.61), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 280 TYR 0.005 0.001 TYR A 174 PHE 0.011 0.001 PHE A 172 TRP 0.009 0.001 TRP A 296 HIS 0.001 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 55 residues out of total 175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.8406 (ppp) cc_final: 0.8112 (ppp) REVERT: A 291 ARG cc_start: 0.8308 (mtp-110) cc_final: 0.8068 (ttm110) outliers start: 4 outliers final: 4 residues processed: 54 average time/residue: 0.2347 time to fit residues: 13.9928 Evaluate side-chains 52 residues out of total 175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 300 ASP 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: 10.0000 chunk 3 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 2 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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: 0.8440 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1581 Z= 0.217 Angle : 0.525 4.613 2158 Z= 0.278 Chirality : 0.042 0.138 251 Planarity : 0.003 0.032 278 Dihedral : 4.743 21.571 214 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.29 % Allowed : 20.00 % Favored : 77.71 % 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: -0.43 (0.59), residues: 195 helix: -0.68 (1.54), residues: 12 sheet: 0.18 (0.58), residues: 70 loop : -0.49 (0.61), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 189 TYR 0.006 0.001 TYR A 174 PHE 0.011 0.001 PHE A 172 TRP 0.009 0.001 TRP A 296 HIS 0.002 0.001 HIS A 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 528.71 seconds wall clock time: 9 minutes 27.64 seconds (567.64 seconds total)