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/6j6j_0689.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6j6j_0689.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 { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6j6j_0689.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6j6j_0689.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6j6j_0689.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6j6j_0689.pdb" } 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= 0.007 sd= 0.067 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: 4 Type Number sf(0) Gaussians C 557 2.51 5 N 155 2.21 5 O 180 1.98 5 H 839 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: 1731 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1731 Classifications: {'peptide': 119} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 117} Time building chain proxies: 0.46, per 1000 atoms: 0.27 Number of scatterers: 1731 At special positions: 0 Unit cell: (47.385, 58.968, 57.915, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 180 8.00 N 155 7.00 C 557 6.00 H 839 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: 0.28 Conformation dependent library (CDL) restraints added in 55.7 milliseconds 234 Ramachandran restraints generated. 117 Oldfield, 0 Emsley, 117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 206 Finding SS restraints... Secondary structure from input PDB file: 1 helices and 1 sheets defined 2.5% alpha, 43.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing sheet with id= A, first strand: chain 'A' and resid 19 through 21 removed outlier: 3.672A pdb=" N GLY A 41 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N VAL A 55 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA A 78 " --> pdb=" O VAL A 55 " (cutoff:3.500A) 45 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: 0.26 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.09: 822 1.09 - 1.21: 17 1.21 - 1.32: 146 1.32 - 1.43: 288 1.43 - 1.55: 480 Bond restraints: 1753 Sorted by residual: bond pdb=" N THR A 66 " pdb=" H THR A 66 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.85e+01 bond pdb=" N THR A 106 " pdb=" H THR A 106 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" N THR A 40 " pdb=" H THR A 40 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.60e+01 bond pdb=" N ALA A 63 " pdb=" H ALA A 63 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.60e+01 bond pdb=" N LEU A 109 " pdb=" H LEU A 109 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.59e+01 ... (remaining 1748 not shown) Histogram of bond angle deviations from ideal: 102.78 - 109.02: 831 109.02 - 115.27: 1283 115.27 - 121.51: 582 121.51 - 127.75: 413 127.75 - 134.00: 14 Bond angle restraints: 3123 Sorted by residual: angle pdb=" C SER A 62 " pdb=" N ALA A 63 " pdb=" CA ALA A 63 " ideal model delta sigma weight residual 122.37 124.62 -2.25 9.30e-01 1.16e+00 5.83e+00 angle pdb=" N PRO A 64 " pdb=" CA PRO A 64 " pdb=" C PRO A 64 " ideal model delta sigma weight residual 112.47 116.28 -3.81 2.06e+00 2.36e-01 3.42e+00 angle pdb=" N TRP A 108 " pdb=" CA TRP A 108 " pdb=" C TRP A 108 " ideal model delta sigma weight residual 109.23 111.42 -2.19 1.55e+00 4.16e-01 1.99e+00 angle pdb=" N ALA A 63 " pdb=" CA ALA A 63 " pdb=" C ALA A 63 " ideal model delta sigma weight residual 108.76 106.73 2.03 1.44e+00 4.82e-01 1.99e+00 angle pdb=" N GLY A 99 " pdb=" CA GLY A 99 " pdb=" C GLY A 99 " ideal model delta sigma weight residual 113.18 109.94 3.24 2.37e+00 1.78e-01 1.87e+00 ... (remaining 3118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 759 17.44 - 34.87: 54 34.87 - 52.31: 14 52.31 - 69.75: 4 69.75 - 87.19: 1 Dihedral angle restraints: 832 sinusoidal: 426 harmonic: 406 Sorted by residual: dihedral pdb=" CA ALA A 63 " pdb=" C ALA A 63 " pdb=" N PRO A 64 " pdb=" CA PRO A 64 " ideal model delta harmonic sigma weight residual -180.00 -157.36 -22.64 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA ILE A 17 " pdb=" CB ILE A 17 " pdb=" CG1 ILE A 17 " pdb=" CD1 ILE A 17 " ideal model delta sinusoidal sigma weight residual 60.00 104.31 -44.31 3 1.50e+01 4.44e-03 7.97e+00 dihedral pdb=" CA GLN A 107 " pdb=" C GLN A 107 " pdb=" N TRP A 108 " pdb=" CA TRP A 108 " ideal model delta harmonic sigma weight residual -180.00 -166.68 -13.32 0 5.00e+00 4.00e-02 7.10e+00 ... (remaining 829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 76 0.027 - 0.054: 40 0.054 - 0.082: 14 0.082 - 0.109: 4 0.109 - 0.136: 5 Chirality restraints: 139 Sorted by residual: chirality pdb=" CA ILE A 30 " pdb=" N ILE A 30 " pdb=" C ILE A 30 " pdb=" CB ILE A 30 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA VAL A 77 " pdb=" N VAL A 77 " pdb=" C VAL A 77 " pdb=" CB VAL A 77 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA VAL A 97 " pdb=" N VAL A 97 " pdb=" C VAL A 97 " pdb=" CB VAL A 97 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 136 not shown) Planarity restraints: 275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 63 " -0.015 5.00e-02 4.00e+02 2.33e-02 8.71e-01 pdb=" N PRO A 64 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 29 " -0.008 2.00e-02 2.50e+03 4.17e-03 5.21e-01 pdb=" CG PHE A 29 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE A 29 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 29 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 29 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 29 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 29 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE A 29 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE A 29 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 29 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 29 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 29 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 63 " 0.003 2.00e-02 2.50e+03 6.34e-03 4.03e-01 pdb=" C ALA A 63 " -0.011 2.00e-02 2.50e+03 pdb=" O ALA A 63 " 0.004 2.00e-02 2.50e+03 pdb=" N PRO A 64 " 0.004 2.00e-02 2.50e+03 ... (remaining 272 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.16: 98 2.16 - 2.75: 2779 2.75 - 3.33: 3985 3.33 - 3.92: 5571 3.92 - 4.50: 7608 Nonbonded interactions: 20041 Sorted by model distance: nonbonded pdb=" OE1 GLN A 24 " pdb=" H GLN A 24 " model vdw 1.578 1.850 nonbonded pdb=" H3 GLY A 16 " pdb=" H ILE A 17 " model vdw 1.629 2.100 nonbonded pdb=" OD1 ASN A 23 " pdb=" HG SER A 27 " model vdw 1.645 1.850 nonbonded pdb=" HG1 THR A 18 " pdb=" O VAL A 31 " model vdw 1.700 1.850 nonbonded pdb=" HG1 THR A 114 " pdb=" O ASN A 118 " model vdw 1.710 1.850 ... (remaining 20036 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: 0.020 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.350 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:0.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:1.210 Internal consistency checks: 0.000 Total: 5.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 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 0.018 914 Z= 0.148 Angle : 0.535 3.807 1251 Z= 0.315 Chirality : 0.043 0.136 139 Planarity : 0.003 0.023 158 Dihedral : 11.854 62.010 294 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 1.71 % Allowed : 7.69 % Favored : 90.60 % Rotamer: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % 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: -3.04 (0.65), residues: 117 helix: None (None), residues: 0 sheet: -0.99 (0.61), residues: 57 loop : -3.17 (0.60), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 84 TYR 0.005 0.001 TYR A 60 PHE 0.011 0.002 PHE A 29 TRP 0.007 0.001 TRP A 92 HIS 0.001 0.001 HIS A 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 234 Ramachandran restraints generated. 117 Oldfield, 0 Emsley, 117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 234 Ramachandran restraints generated. 117 Oldfield, 0 Emsley, 117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.7822 (m-40) cc_final: 0.7614 (m110) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1443 time to fit residues: 3.6958 Evaluate side-chains 20 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 11 random chunks: chunk 6 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 10 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: 0.6601 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 914 Z= 0.262 Angle : 0.511 3.933 1251 Z= 0.289 Chirality : 0.043 0.132 139 Planarity : 0.004 0.036 158 Dihedral : 6.632 44.397 129 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.69 % Favored : 91.45 % Rotamer: Outliers : 1.14 % Allowed : 7.95 % Favored : 90.91 % 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: -2.89 (0.70), residues: 117 helix: None (None), residues: 0 sheet: -1.32 (0.55), residues: 72 loop : -2.77 (0.83), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 59 TYR 0.012 0.002 TYR A 43 PHE 0.012 0.003 PHE A 29 TRP 0.008 0.001 TRP A 75 HIS 0.001 0.001 HIS A 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 234 Ramachandran restraints generated. 117 Oldfield, 0 Emsley, 117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 234 Ramachandran restraints generated. 117 Oldfield, 0 Emsley, 117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.075 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 15 average time/residue: 0.2499 time to fit residues: 4.0147 Evaluate side-chains 14 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 13 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 11 random chunks: chunk 5 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 914 Z= 0.268 Angle : 0.497 2.975 1251 Z= 0.285 Chirality : 0.043 0.131 139 Planarity : 0.005 0.037 158 Dihedral : 6.963 50.526 129 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.14 % Allowed : 12.50 % Favored : 86.36 % 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: -2.66 (0.74), residues: 117 helix: None (None), residues: 0 sheet: -1.31 (0.54), residues: 71 loop : -2.32 (0.99), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 84 TYR 0.013 0.002 TYR A 43 PHE 0.009 0.002 PHE A 29 TRP 0.006 0.001 TRP A 75 HIS 0.002 0.001 HIS A 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 234 Ramachandran restraints generated. 117 Oldfield, 0 Emsley, 117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 234 Ramachandran restraints generated. 117 Oldfield, 0 Emsley, 117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.069 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 17 average time/residue: 0.3223 time to fit residues: 5.8573 Evaluate side-chains 16 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 11 random chunks: chunk 8 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 914 Z= 0.184 Angle : 0.440 2.371 1251 Z= 0.254 Chirality : 0.041 0.129 139 Planarity : 0.004 0.038 158 Dihedral : 6.487 47.299 129 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.14 % Allowed : 13.64 % Favored : 85.23 % 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: -2.81 (0.73), residues: 117 helix: None (None), residues: 0 sheet: -1.61 (0.52), residues: 74 loop : -2.03 (1.04), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 59 TYR 0.008 0.001 TYR A 43 PHE 0.009 0.002 PHE A 29 TRP 0.006 0.001 TRP A 75 HIS 0.001 0.001 HIS A 127 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 234 Ramachandran restraints generated. 117 Oldfield, 0 Emsley, 117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 234 Ramachandran restraints generated. 117 Oldfield, 0 Emsley, 117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.074 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 15 average time/residue: 0.2738 time to fit residues: 4.4092 Evaluate side-chains 16 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 11 random chunks: chunk 4 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 overall best weight: 5.5992 ------------------------------------------------------------------------------- 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: 0.6611 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 914 Z= 0.205 Angle : 0.452 2.633 1251 Z= 0.258 Chirality : 0.042 0.129 139 Planarity : 0.004 0.033 158 Dihedral : 6.435 47.696 129 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % 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: -2.98 (0.71), residues: 117 helix: None (None), residues: 0 sheet: -1.66 (0.51), residues: 74 loop : -2.27 (1.00), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 84 TYR 0.008 0.001 TYR A 43 PHE 0.008 0.002 PHE A 29 TRP 0.007 0.001 TRP A 75 HIS 0.001 0.001 HIS A 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 234 Ramachandran restraints generated. 117 Oldfield, 0 Emsley, 117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 234 Ramachandran restraints generated. 117 Oldfield, 0 Emsley, 117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.055 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.2241 time to fit residues: 3.3658 Evaluate side-chains 14 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 11 random chunks: chunk 1 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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: 0.6614 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 914 Z= 0.186 Angle : 0.431 2.550 1251 Z= 0.247 Chirality : 0.041 0.129 139 Planarity : 0.003 0.028 158 Dihedral : 6.488 50.891 129 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 14.77 % Favored : 85.23 % 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: -2.98 (0.70), residues: 117 helix: None (None), residues: 0 sheet: -1.65 (0.50), residues: 74 loop : -2.28 (0.98), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 59 TYR 0.008 0.001 TYR A 43 PHE 0.008 0.002 PHE A 29 TRP 0.007 0.001 TRP A 75 HIS 0.001 0.001 HIS A 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 399.65 seconds wall clock time: 7 minutes 15.72 seconds (435.72 seconds total)