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/8dat_27275.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dat_27275.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global+local_grid_search+nqh_flips resolution=3.8 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dat_27275.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dat_27275.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dat_27275.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dat_27275.pdb" } resolution = 3.8 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= 3.872 sd= 7.650 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 1 5.16 5 C 375 2.51 5 N 105 2.21 5 O 120 1.98 5 H 625 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: 1226 Number of models: 1 Model: "" Number of chains: 1 Chain: "K" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1226 Classifications: {'peptide': 76} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 73} Time building chain proxies: 0.32, per 1000 atoms: 0.26 Number of scatterers: 1226 At special positions: 0 Unit cell: (47.88, 43.624, 42.56, 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 1 16.00 O 120 8.00 N 105 7.00 C 375 6.00 H 625 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: 0.22 Conformation dependent library (CDL) restraints added in 36.6 milliseconds 148 Ramachandran restraints generated. 74 Oldfield, 0 Emsley, 74 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 140 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 1 sheets defined 21.1% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.03 Creating SS restraints... Processing helix chain 'K' and resid 223 through 234 Processing helix chain 'K' and resid 256 through 259 No H-bonds generated for 'chain 'K' and resid 256 through 259' Processing sheet with id= A, first strand: chain 'K' and resid 212 through 216 removed outlier: 5.704A pdb=" N SER K 265 " --> pdb=" O PHE K 204 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LYS K 206 " --> pdb=" O SER K 265 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU K 267 " --> pdb=" O LYS K 206 " (cutoff:3.500A) 16 hydrogen bonds defined for protein. 45 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: 0.18 Time building geometry restraints manager: 0.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.14: 625 1.14 - 1.31: 107 1.31 - 1.47: 210 1.47 - 1.64: 287 1.64 - 1.80: 2 Bond restraints: 1231 Sorted by residual: bond pdb=" N GLY K 247 " pdb=" H GLY K 247 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.48e+01 bond pdb=" N LYS K 227 " pdb=" H LYS K 227 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.47e+01 bond pdb=" NH2 ARG K 274 " pdb="HH21 ARG K 274 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" NH2 ARG K 274 " pdb="HH22 ARG K 274 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N LYS K 229 " pdb=" H LYS K 229 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 1226 not shown) Histogram of bond angle deviations from ideal: 101.02 - 107.06: 17 107.06 - 113.11: 1536 113.11 - 119.15: 239 119.15 - 125.19: 439 125.19 - 131.23: 10 Bond angle restraints: 2241 Sorted by residual: angle pdb=" N ASN K 260 " pdb=" CA ASN K 260 " pdb=" CB ASN K 260 " ideal model delta sigma weight residual 112.63 110.95 1.68 1.61e+00 3.86e-01 1.08e+00 angle pdb=" C ILE K 236 " pdb=" N PRO K 237 " pdb=" CA PRO K 237 " ideal model delta sigma weight residual 119.66 120.42 -0.76 7.30e-01 1.88e+00 1.08e+00 angle pdb=" N ARG K 274 " pdb=" CA ARG K 274 " pdb=" C ARG K 274 " ideal model delta sigma weight residual 112.54 111.10 1.44 1.51e+00 4.39e-01 9.14e-01 angle pdb=" C PRO K 237 " pdb=" N PRO K 238 " pdb=" CD PRO K 238 " ideal model delta sigma weight residual 125.00 128.84 -3.84 4.10e+00 5.95e-02 8.77e-01 angle pdb=" N GLU K 234 " pdb=" CA GLU K 234 " pdb=" C GLU K 234 " ideal model delta sigma weight residual 114.75 113.61 1.14 1.26e+00 6.30e-01 8.23e-01 ... (remaining 2236 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.88: 511 13.88 - 27.76: 31 27.76 - 41.65: 13 41.65 - 55.53: 4 55.53 - 69.41: 3 Dihedral angle restraints: 562 sinusoidal: 329 harmonic: 233 Sorted by residual: dihedral pdb=" N LEU K 215 " pdb=" CA LEU K 215 " pdb=" CB LEU K 215 " pdb=" CG LEU K 215 " ideal model delta sinusoidal sigma weight residual -60.00 -97.18 37.18 3 1.50e+01 4.44e-03 6.48e+00 dihedral pdb=" N MET K 201 " pdb=" CA MET K 201 " pdb=" CB MET K 201 " pdb=" CG MET K 201 " ideal model delta sinusoidal sigma weight residual 60.00 95.58 -35.58 3 1.50e+01 4.44e-03 6.11e+00 dihedral pdb=" CB ARG K 274 " pdb=" CG ARG K 274 " pdb=" CD ARG K 274 " pdb=" NE ARG K 274 " ideal model delta sinusoidal sigma weight residual -60.00 -90.67 30.67 3 1.50e+01 4.44e-03 4.91e+00 ... (remaining 559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 65 0.025 - 0.051: 15 0.051 - 0.076: 8 0.076 - 0.101: 3 0.101 - 0.127: 6 Chirality restraints: 97 Sorted by residual: chirality pdb=" CA ILE K 236 " pdb=" N ILE K 236 " pdb=" C ILE K 236 " pdb=" CB ILE K 236 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA VAL K 270 " pdb=" N VAL K 270 " pdb=" C VAL K 270 " pdb=" CB VAL K 270 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.70e-01 chirality pdb=" CA ILE K 244 " pdb=" N ILE K 244 " pdb=" C ILE K 244 " pdb=" CB ILE K 244 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.52e-01 ... (remaining 94 not shown) Planarity restraints: 178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE K 236 " 0.009 5.00e-02 4.00e+02 1.41e-02 3.20e-01 pdb=" N PRO K 237 " -0.024 5.00e-02 4.00e+02 pdb=" CA PRO K 237 " 0.007 5.00e-02 4.00e+02 pdb=" CD PRO K 237 " 0.008 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO K 237 " 0.006 5.00e-02 4.00e+02 8.87e-03 1.26e-01 pdb=" N PRO K 238 " -0.015 5.00e-02 4.00e+02 pdb=" CA PRO K 238 " 0.004 5.00e-02 4.00e+02 pdb=" CD PRO K 238 " 0.005 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 204 " -0.003 2.00e-02 2.50e+03 1.82e-03 9.97e-02 pdb=" CG PHE K 204 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 PHE K 204 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE K 204 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE K 204 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE K 204 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE K 204 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE K 204 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE K 204 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE K 204 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE K 204 " -0.000 2.00e-02 2.50e+03 pdb=" HZ PHE K 204 " -0.001 2.00e-02 2.50e+03 ... (remaining 175 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 133 2.18 - 2.78: 2534 2.78 - 3.39: 3401 3.39 - 3.99: 4540 3.99 - 4.60: 6687 Nonbonded interactions: 17295 Sorted by model distance: nonbonded pdb=" HZ3 LYS K 206 " pdb=" OG1 THR K 212 " model vdw 1.573 1.850 nonbonded pdb=" O GLN K 231 " pdb=" H GLY K 235 " model vdw 1.600 1.850 nonbonded pdb=" OE1 GLU K 218 " pdb=" H GLU K 218 " model vdw 1.638 1.850 nonbonded pdb=" OD1 ASP K 239 " pdb=" H GLN K 240 " model vdw 1.649 1.850 nonbonded pdb=" H ILE K 223 " pdb=" O ARG K 254 " model vdw 1.660 1.850 ... (remaining 17290 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 5 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.49 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will not be refined Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 2.790 Find NCS groups from input model: 0.010 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:0.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.850 Internal consistency checks: 0.000 Total: 4.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 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 0.012 606 Z= 0.128 Angle : 0.432 3.840 814 Z= 0.229 Chirality : 0.042 0.127 97 Planarity : 0.002 0.014 105 Dihedral : 10.908 69.410 239 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.45 % Allowed : 8.70 % Favored : 89.86 % 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: -0.74 (0.96), residues: 74 helix: 0.35 (1.39), residues: 12 sheet: -2.29 (0.78), residues: 25 loop : 0.88 (1.12), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG K 272 TYR 0.002 0.001 TYR K 259 PHE 0.005 0.001 PHE K 204 HIS 0.001 0.000 HIS K 268 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 148 Ramachandran restraints generated. 74 Oldfield, 0 Emsley, 74 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 148 Ramachandran restraints generated. 74 Oldfield, 0 Emsley, 74 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 69 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 21 average time/residue: 0.1831 time to fit residues: 4.0149 Evaluate side-chains 15 residues out of total 69 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 overall best weight: 7.6657 ------------------------------------------------------------------------------- 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: 0.7259 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 606 Z= 0.189 Angle : 0.477 4.033 814 Z= 0.241 Chirality : 0.043 0.129 97 Planarity : 0.003 0.018 105 Dihedral : 9.434 77.961 83 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.45 % Allowed : 13.04 % Favored : 85.51 % 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: -0.41 (1.01), residues: 74 helix: 1.11 (1.61), residues: 12 sheet: -2.55 (0.75), residues: 25 loop : 1.29 (1.15), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG K 272 TYR 0.001 0.001 TYR K 259 PHE 0.008 0.002 PHE K 204 HIS 0.001 0.001 HIS K 268 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 148 Ramachandran restraints generated. 74 Oldfield, 0 Emsley, 74 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 148 Ramachandran restraints generated. 74 Oldfield, 0 Emsley, 74 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 69 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 249 GLN cc_start: 0.6587 (tp-100) cc_final: 0.6357 (tp40) outliers start: 1 outliers final: 1 residues processed: 14 average time/residue: 0.1767 time to fit residues: 2.6131 Evaluate side-chains 13 residues out of total 69 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 30.0000 chunk 1 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 overall best weight: 6.3323 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 606 Z= 0.172 Angle : 0.479 3.974 814 Z= 0.239 Chirality : 0.042 0.129 97 Planarity : 0.003 0.021 105 Dihedral : 10.700 89.964 83 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.45 % Allowed : 14.49 % Favored : 84.06 % 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: -0.50 (1.00), residues: 74 helix: 1.14 (1.60), residues: 12 sheet: -2.62 (0.73), residues: 25 loop : 1.21 (1.13), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 272 TYR 0.001 0.000 TYR K 259 PHE 0.009 0.002 PHE K 204 HIS 0.001 0.000 HIS K 268 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 148 Ramachandran restraints generated. 74 Oldfield, 0 Emsley, 74 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 148 Ramachandran restraints generated. 74 Oldfield, 0 Emsley, 74 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 69 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 249 GLN cc_start: 0.6593 (tp-100) cc_final: 0.6363 (tp40) outliers start: 1 outliers final: 1 residues processed: 12 average time/residue: 0.3950 time to fit residues: 5.0144 Evaluate side-chains 12 residues out of total 69 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 11 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 30.0000 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 overall best weight: 7.6657 ------------------------------------------------------------------------------- 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: 0.7340 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 606 Z= 0.175 Angle : 0.490 4.067 814 Z= 0.246 Chirality : 0.041 0.127 97 Planarity : 0.003 0.021 105 Dihedral : 9.428 76.987 83 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.90 % Allowed : 13.04 % Favored : 84.06 % 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: -0.58 (0.96), residues: 74 helix: 1.27 (1.61), residues: 12 sheet: -2.66 (0.76), residues: 23 loop : 0.83 (1.02), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 272 TYR 0.001 0.000 TYR K 259 PHE 0.011 0.002 PHE K 204 HIS 0.001 0.001 HIS K 268 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 148 Ramachandran restraints generated. 74 Oldfield, 0 Emsley, 74 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 148 Ramachandran restraints generated. 74 Oldfield, 0 Emsley, 74 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 69 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 12 time to evaluate : 0.071 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 13 average time/residue: 0.3146 time to fit residues: 4.3247 Evaluate side-chains 10 residues out of total 69 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 9 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 30.0000 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 30.0000 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 overall best weight: 6.3323 ------------------------------------------------------------------------------- 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: 0.7328 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 606 Z= 0.170 Angle : 0.536 4.032 814 Z= 0.264 Chirality : 0.043 0.146 97 Planarity : 0.003 0.022 105 Dihedral : 8.295 64.857 83 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.45 % Allowed : 14.49 % Favored : 84.06 % 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: -1.33 (0.91), residues: 74 helix: -0.15 (1.28), residues: 18 sheet: -2.45 (0.85), residues: 18 loop : -0.24 (0.98), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG K 274 TYR 0.001 0.000 TYR K 259 PHE 0.011 0.002 PHE K 204 HIS 0.001 0.001 HIS K 268 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 148 Ramachandran restraints generated. 74 Oldfield, 0 Emsley, 74 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 148 Ramachandran restraints generated. 74 Oldfield, 0 Emsley, 74 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 69 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 11 time to evaluate : 0.056 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 11 average time/residue: 0.2017 time to fit residues: 2.4068 Evaluate side-chains 11 residues out of total 69 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 10 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 267 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 30.0000 chunk 1 optimal weight: 20.0000 chunk 2 optimal weight: 0.0470 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 overall best weight: 4.0150 ------------------------------------------------------------------------------- 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: 0.7314 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 606 Z= 0.148 Angle : 0.502 3.967 814 Z= 0.247 Chirality : 0.042 0.136 97 Planarity : 0.003 0.022 105 Dihedral : 7.740 59.510 83 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.45 % Allowed : 14.49 % Favored : 84.06 % 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: -1.10 (0.98), residues: 74 helix: 1.46 (1.62), residues: 12 sheet: -3.09 (0.69), residues: 27 loop : 0.84 (1.13), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 274 TYR 0.001 0.000 TYR K 259 PHE 0.011 0.002 PHE K 204 HIS 0.001 0.000 HIS K 268 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 302.29 seconds wall clock time: 5 minutes 41.89 seconds (341.89 seconds total)