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/7kzn_23083.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7kzn_23083.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global+local_grid_search+nqh_flips resolution=4.0 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7kzn_23083.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7kzn_23083.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7kzn_23083.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7kzn_23083.map" } resolution = 4.0 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= 0.006 sd= 0.009 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 4 5.16 5 C 433 2.51 5 N 112 2.21 5 O 122 1.98 5 H 653 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K ASP 14": "OD1" <-> "OD2" Residue "K ASP 39": "OD1" <-> "OD2" Residue "K PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 1324 Number of models: 1 Model: "" Number of chains: 1 Chain: "K" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1324 Inner-chain residues flagged as termini: ['pdbres="GLU K 71 "'] Classifications: {'peptide': 82} Modifications used: {'NH3': 2} Link IDs: {'PTRANS': 1, 'TRANS': 80} Time building chain proxies: 0.40, per 1000 atoms: 0.30 Number of scatterers: 1324 At special positions: 0 Unit cell: (47.6, 51.68, 47.6, 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 4 16.00 O 122 8.00 N 112 7.00 C 433 6.00 H 653 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 39.5 milliseconds 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 158 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 1 sheets defined 36.6% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing helix chain 'K' and resid 17 through 33 removed outlier: 3.985A pdb=" N ASP K 22 " --> pdb=" O GLU K 18 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN K 29 " --> pdb=" O ASP K 25 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA K 30 " --> pdb=" O CYS K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 49 removed outlier: 4.294A pdb=" N ALA K 41 " --> pdb=" O GLU K 37 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N PHE K 48 " --> pdb=" O ILE K 44 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'K' and resid 57 through 61 removed outlier: 3.710A pdb=" N ILE K 85 " --> pdb=" O PHE K 78 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASN K 12 " --> pdb=" O TYR K 77 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TYR K 79 " --> pdb=" O ILE K 10 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ILE K 10 " --> pdb=" O TYR K 79 " (cutoff:3.500A) 27 hydrogen bonds defined for protein. 75 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: 0.19 Time building geometry restraints manager: 0.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 652 1.15 - 1.32: 112 1.32 - 1.48: 281 1.48 - 1.65: 289 1.65 - 1.82: 6 Bond restraints: 1340 Sorted by residual: bond pdb=" N HIS K 74 " pdb=" H HIS K 74 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" ND1 HIS K 70 " pdb=" HD1 HIS K 70 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.67e+01 bond pdb=" N ILE K 44 " pdb=" H ILE K 44 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" N TYR K 77 " pdb=" H TYR K 77 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.65e+01 bond pdb=" N THR K 69 " pdb=" H THR K 69 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.65e+01 ... (remaining 1335 not shown) Histogram of bond angle deviations from ideal: 101.13 - 107.69: 123 107.69 - 114.26: 1502 114.26 - 120.82: 444 120.82 - 127.39: 339 127.39 - 133.95: 6 Bond angle restraints: 2414 Sorted by residual: angle pdb=" C HIS K 52 " pdb=" N ASN K 53 " pdb=" CA ASN K 53 " ideal model delta sigma weight residual 123.96 120.03 3.93 1.44e+00 4.82e-01 7.45e+00 angle pdb=" N ASN K 53 " pdb=" CA ASN K 53 " pdb=" C ASN K 53 " ideal model delta sigma weight residual 109.06 113.56 -4.50 1.78e+00 3.16e-01 6.41e+00 angle pdb=" N HIS K 74 " pdb=" CA HIS K 74 " pdb=" C HIS K 74 " ideal model delta sigma weight residual 110.80 115.79 -4.99 2.13e+00 2.20e-01 5.49e+00 angle pdb=" N GLU K 71 " pdb=" CA GLU K 71 " pdb=" C GLU K 71 " ideal model delta sigma weight residual 109.18 105.90 3.28 1.42e+00 4.96e-01 5.32e+00 angle pdb=" N PHE K 78 " pdb=" CA PHE K 78 " pdb=" CB PHE K 78 " ideal model delta sigma weight residual 110.44 113.66 -3.22 1.43e+00 4.89e-01 5.08e+00 ... (remaining 2409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.87: 545 11.87 - 23.73: 51 23.73 - 35.60: 13 35.60 - 47.46: 9 47.46 - 59.33: 8 Dihedral angle restraints: 626 sinusoidal: 320 harmonic: 306 Sorted by residual: dihedral pdb=" CA GLU K 37 " pdb=" C GLU K 37 " pdb=" N LYS K 38 " pdb=" CA LYS K 38 " ideal model delta harmonic sigma weight residual 180.00 162.93 17.07 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ILE K 44 " pdb=" C ILE K 44 " pdb=" N LYS K 45 " pdb=" CA LYS K 45 " ideal model delta harmonic sigma weight residual 180.00 163.71 16.29 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA ILE K 36 " pdb=" C ILE K 36 " pdb=" N GLU K 37 " pdb=" CA GLU K 37 " ideal model delta harmonic sigma weight residual -180.00 -164.08 -15.92 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 52 0.028 - 0.056: 32 0.056 - 0.085: 3 0.085 - 0.113: 9 0.113 - 0.141: 3 Chirality restraints: 99 Sorted by residual: chirality pdb=" CA TYR K 77 " pdb=" N TYR K 77 " pdb=" C TYR K 77 " pdb=" CB TYR K 77 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA ILE K 10 " pdb=" N ILE K 10 " pdb=" C ILE K 10 " pdb=" CB ILE K 10 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA VAL K 83 " pdb=" N VAL K 83 " pdb=" C VAL K 83 " pdb=" CB VAL K 83 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 96 not shown) Planarity restraints: 196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN K 53 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO K 54 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO K 54 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO K 54 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 75 " 0.017 2.00e-02 2.50e+03 8.41e-03 2.12e+00 pdb=" CG PHE K 75 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 PHE K 75 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE K 75 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE K 75 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE K 75 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE K 75 " 0.011 2.00e-02 2.50e+03 pdb=" HD1 PHE K 75 " -0.005 2.00e-02 2.50e+03 pdb=" HD2 PHE K 75 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE K 75 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE K 75 " -0.000 2.00e-02 2.50e+03 pdb=" HZ PHE K 75 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 78 " 0.013 2.00e-02 2.50e+03 8.07e-03 1.96e+00 pdb=" CG PHE K 78 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE K 78 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE K 78 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE K 78 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE K 78 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE K 78 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE K 78 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE K 78 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE K 78 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE K 78 " 0.003 2.00e-02 2.50e+03 pdb=" HZ PHE K 78 " 0.001 2.00e-02 2.50e+03 ... (remaining 193 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.23: 155 2.23 - 2.82: 2660 2.82 - 3.41: 3377 3.41 - 4.01: 4292 4.01 - 4.60: 6194 Nonbonded interactions: 16678 Sorted by model distance: nonbonded pdb=" H PHE K 78 " pdb=" HD1 PHE K 78 " model vdw 1.635 2.100 nonbonded pdb=" H ARG K 62 " pdb=" HE2 PHE K 64 " model vdw 1.707 2.100 nonbonded pdb=" O PHE K 48 " pdb=" H LYS K 51 " model vdw 1.715 1.850 nonbonded pdb=" O HIS K 70 " pdb=" H2 GLU K 71 " model vdw 1.726 1.960 nonbonded pdb=" H THR K 28 " pdb=" HG1 THR K 28 " model vdw 1.751 2.100 ... (remaining 16673 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=0.33 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: 2.880 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:0.950 Internal consistency checks: 0.000 Total: 4.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6155 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 : 0.005 0.053 687 Z= 0.344 Angle : 0.746 4.989 926 Z= 0.438 Chirality : 0.048 0.141 99 Planarity : 0.005 0.042 117 Dihedral : 10.462 58.376 247 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 2.86 % Allowed : 8.57 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.81), residues: 80 helix: -1.71 (0.83), residues: 32 sheet: -3.23 (1.02), residues: 15 loop : -2.26 (0.97), residues: 33 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 62 TYR 0.011 0.003 TYR K 34 PHE 0.023 0.004 PHE K 78 TRP 0.001 0.000 TRP K 56 HIS 0.003 0.001 HIS K 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 34 is missing expected H atoms. Skipping. Evaluate side-chains 51 residues out of total 70 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 49 average time/residue: 0.0998 time to fit residues: 5.2247 Evaluate side-chains 39 residues out of total 70 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 76 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 29 GLN K 53 ASN K 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6287 moved from start: 0.8202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 687 Z= 0.285 Angle : 0.732 5.203 926 Z= 0.403 Chirality : 0.047 0.161 99 Planarity : 0.004 0.029 117 Dihedral : 7.275 19.133 90 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 5.71 % Allowed : 22.86 % Favored : 71.43 % 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: -2.76 (0.87), residues: 80 helix: -0.54 (0.94), residues: 31 sheet: -3.27 (1.14), residues: 15 loop : -2.26 (0.92), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 62 TYR 0.009 0.003 TYR K 34 PHE 0.011 0.003 PHE K 75 TRP 0.001 0.000 TRP K 56 HIS 0.003 0.001 HIS K 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 34 is missing expected H atoms. Skipping. Evaluate side-chains 39 residues out of total 70 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 37 average time/residue: 0.0954 time to fit residues: 3.8095 Evaluate side-chains 36 residues out of total 70 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 74 HIS Chi-restraints excluded: chain K residue 76 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 overall best weight: 6.4990 ------------------------------------------------------------------------------- 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: 0.6282 moved from start: 0.9672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 687 Z= 0.219 Angle : 0.669 5.438 926 Z= 0.366 Chirality : 0.046 0.143 99 Planarity : 0.003 0.025 117 Dihedral : 7.218 20.689 90 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 8.57 % Allowed : 22.86 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.90), residues: 80 helix: -0.55 (0.94), residues: 31 sheet: -2.31 (1.25), residues: 16 loop : -2.10 (1.02), residues: 33 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 62 TYR 0.013 0.002 TYR K 77 PHE 0.013 0.003 PHE K 78 TRP 0.002 0.001 TRP K 56 HIS 0.003 0.001 HIS K 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 34 is missing expected H atoms. Skipping. Evaluate side-chains 39 residues out of total 70 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 35 average time/residue: 0.2055 time to fit residues: 7.6603 Evaluate side-chains 34 residues out of total 70 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 74 HIS Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 83 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 overall best weight: 5.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6265 moved from start: 1.0105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 687 Z= 0.200 Angle : 0.633 4.482 926 Z= 0.347 Chirality : 0.046 0.138 99 Planarity : 0.003 0.026 117 Dihedral : 6.886 25.002 90 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 8.57 % Allowed : 25.71 % Favored : 65.71 % 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: -2.26 (0.93), residues: 80 helix: -0.51 (0.98), residues: 31 sheet: -1.89 (1.33), residues: 16 loop : -2.17 (1.02), residues: 33 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 50 TYR 0.008 0.002 TYR K 34 PHE 0.010 0.002 PHE K 78 TRP 0.003 0.001 TRP K 56 HIS 0.002 0.001 HIS K 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 34 is missing expected H atoms. Skipping. Evaluate side-chains 36 residues out of total 70 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 30 time to evaluate : 0.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 32 average time/residue: 0.2020 time to fit residues: 6.9225 Evaluate side-chains 36 residues out of total 70 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 31 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 74 HIS Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 88 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 overall best weight: 5.7490 ------------------------------------------------------------------------------- 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: 0.6300 moved from start: 1.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 687 Z= 0.198 Angle : 0.641 4.681 926 Z= 0.355 Chirality : 0.048 0.134 99 Planarity : 0.003 0.024 117 Dihedral : 6.659 25.253 90 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 7.14 % Allowed : 30.00 % Favored : 62.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.97), residues: 80 helix: 0.08 (1.12), residues: 28 sheet: -1.53 (1.39), residues: 16 loop : -2.25 (0.97), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 50 TYR 0.007 0.002 TYR K 79 PHE 0.008 0.002 PHE K 78 TRP 0.001 0.000 TRP K 56 HIS 0.004 0.001 HIS K 74 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 34 is missing expected H atoms. Skipping. Evaluate side-chains 35 residues out of total 70 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 30 time to evaluate : 0.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 31 average time/residue: 0.1790 time to fit residues: 5.9516 Evaluate side-chains 35 residues out of total 70 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 88 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 30.0000 chunk 7 optimal weight: 8.9990 overall best weight: 5.7488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 moved from start: 1.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 687 Z= 0.213 Angle : 0.675 5.040 926 Z= 0.376 Chirality : 0.048 0.132 99 Planarity : 0.003 0.023 117 Dihedral : 6.787 30.443 90 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 5.71 % Allowed : 32.86 % Favored : 61.43 % 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: -2.10 (0.92), residues: 80 helix: 0.17 (1.09), residues: 28 sheet: -1.70 (1.31), residues: 16 loop : -2.54 (0.89), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG K 62 TYR 0.006 0.002 TYR K 79 PHE 0.010 0.001 PHE K 78 TRP 0.001 0.001 TRP K 56 HIS 0.003 0.001 HIS K 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 290.46 seconds wall clock time: 5 minutes 29.79 seconds (329.79 seconds total)