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/6xmx_22265.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6xmx_22265.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global+local_grid_search+nqh_flips resolution=3.7 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6xmx_22265.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6xmx_22265.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6xmx_22265.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6xmx_22265.pdb" } resolution = 3.7 refinement { run = *minimization_global rigid_body *local_grid_search morphing \ simulated_annealing adp occupancy *nqh_flips } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.009 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 11 5.16 5 C 618 2.51 5 N 170 2.21 5 O 177 1.98 5 H 1000 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: 1976 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1976 Classifications: {'peptide': 122} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 119} Time building chain proxies: 0.49, per 1000 atoms: 0.25 Number of scatterers: 1976 At special positions: 0 Unit cell: (58.575, 56.1, 56.925, 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 11 16.00 O 177 8.00 N 170 7.00 C 618 6.00 H 1000 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: 0.39 Conformation dependent library (CDL) restraints added in 62.4 milliseconds 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 238 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 1 sheets defined 57.4% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 14 through 27 Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 55 through 62 Processing helix chain 'A' and resid 64 through 67 No H-bonds generated for 'chain 'A' and resid 64 through 67' Processing helix chain 'A' and resid 80 through 92 Processing helix chain 'A' and resid 102 through 112 Processing helix chain 'A' and resid 115 through 127 Processing sheet with id= A, first strand: chain 'A' and resid 41 through 45 50 hydrogen bonds defined for protein. 144 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: 0.31 Time building geometry restraints manager: 0.45 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: 995 1.15 - 1.31: 163 1.31 - 1.48: 385 1.48 - 1.65: 430 1.65 - 1.81: 17 Bond restraints: 1990 Sorted by residual: bond pdb=" N PHE A 83 " pdb=" H PHE A 83 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.53e+01 bond pdb=" N LEU A 20 " pdb=" H LEU A 20 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" N ASP A 29 " pdb=" H ASP A 29 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.50e+01 bond pdb=" NH2 ARG A 44 " pdb="HH22 ARG A 44 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.49e+01 bond pdb=" N ILE A 30 " pdb=" H ILE A 30 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.49e+01 ... (remaining 1985 not shown) Histogram of bond angle deviations from ideal: 100.64 - 106.76: 20 106.76 - 112.88: 2339 112.88 - 119.00: 393 119.00 - 125.11: 796 125.11 - 131.23: 42 Bond angle restraints: 3590 Sorted by residual: angle pdb=" C ASP A 33 " pdb=" N VAL A 34 " pdb=" CA VAL A 34 " ideal model delta sigma weight residual 122.71 120.62 2.09 1.44e+00 4.82e-01 2.10e+00 angle pdb=" N THR A 62 " pdb=" CA THR A 62 " pdb=" C THR A 62 " ideal model delta sigma weight residual 112.90 111.01 1.89 1.31e+00 5.83e-01 2.09e+00 angle pdb=" N LEU A 31 " pdb=" CA LEU A 31 " pdb=" CB LEU A 31 " ideal model delta sigma weight residual 112.78 110.84 1.94 1.53e+00 4.27e-01 1.61e+00 angle pdb=" C SER A 93 " pdb=" CA SER A 93 " pdb=" CB SER A 93 " ideal model delta sigma weight residual 110.65 108.27 2.38 1.95e+00 2.63e-01 1.49e+00 angle pdb=" C PHE A 124 " pdb=" N ILE A 125 " pdb=" CA ILE A 125 " ideal model delta sigma weight residual 121.09 119.22 1.87 1.65e+00 3.67e-01 1.29e+00 ... (remaining 3585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.72: 852 15.72 - 31.43: 51 31.43 - 47.15: 18 47.15 - 62.86: 6 62.86 - 78.58: 2 Dihedral angle restraints: 929 sinusoidal: 510 harmonic: 419 Sorted by residual: dihedral pdb=" N GLU A 81 " pdb=" CA GLU A 81 " pdb=" CB GLU A 81 " pdb=" CG GLU A 81 " ideal model delta sinusoidal sigma weight residual 180.00 126.47 53.53 3 1.50e+01 4.44e-03 9.21e+00 dihedral pdb=" CA ARG A 26 " pdb=" CB ARG A 26 " pdb=" CG ARG A 26 " pdb=" CD ARG A 26 " ideal model delta sinusoidal sigma weight residual -60.00 -104.56 44.56 3 1.50e+01 4.44e-03 8.01e+00 dihedral pdb=" CA ARG A 44 " pdb=" CB ARG A 44 " pdb=" CG ARG A 44 " pdb=" CD ARG A 44 " ideal model delta sinusoidal sigma weight residual -180.00 -136.67 -43.33 3 1.50e+01 4.44e-03 7.79e+00 ... (remaining 926 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 99 0.026 - 0.052: 33 0.052 - 0.078: 17 0.078 - 0.103: 3 0.103 - 0.129: 8 Chirality restraints: 160 Sorted by residual: chirality pdb=" CA ILE A 36 " pdb=" N ILE A 36 " pdb=" C ILE A 36 " pdb=" CB ILE A 36 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA ILE A 72 " pdb=" N ILE A 72 " pdb=" C ILE A 72 " pdb=" CB ILE A 72 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 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 2.55 -0.12 2.00e-01 2.50e+01 3.66e-01 ... (remaining 157 not shown) Planarity restraints: 288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 81 " 0.003 2.00e-02 2.50e+03 5.88e-03 3.46e-01 pdb=" C GLU A 81 " -0.010 2.00e-02 2.50e+03 pdb=" O GLU A 81 " 0.004 2.00e-02 2.50e+03 pdb=" N GLY A 82 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 81 " 0.003 2.00e-02 2.50e+03 5.27e-03 2.78e-01 pdb=" N GLY A 82 " -0.009 2.00e-02 2.50e+03 pdb=" CA GLY A 82 " 0.002 2.00e-02 2.50e+03 pdb=" H GLY A 82 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 79 " 0.008 5.00e-02 4.00e+02 1.28e-02 2.62e-01 pdb=" N PRO A 80 " -0.022 5.00e-02 4.00e+02 pdb=" CA PRO A 80 " 0.006 5.00e-02 4.00e+02 pdb=" CD PRO A 80 " 0.007 5.00e-02 4.00e+02 ... (remaining 285 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 96 2.14 - 2.75: 3493 2.75 - 3.37: 5454 3.37 - 3.98: 7051 3.98 - 4.60: 10317 Nonbonded interactions: 26411 Sorted by model distance: nonbonded pdb=" O TYR A 58 " pdb=" HG1 THR A 62 " model vdw 1.521 1.850 nonbonded pdb=" O PHE A 89 " pdb=" H SER A 93 " model vdw 1.525 1.850 nonbonded pdb=" HZ3 LYS A 47 " pdb=" O CYS A 67 " model vdw 1.596 1.850 nonbonded pdb=" O THR A 92 " pdb=" HG SER A 93 " model vdw 1.604 1.850 nonbonded pdb=" O ASP A 88 " pdb=" HG1 THR A 92 " model vdw 1.622 1.850 ... (remaining 26406 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: 0.010 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: 0.080 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.570 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:0.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:1.430 Internal consistency checks: 0.000 Total: 5.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5224 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 0.012 990 Z= 0.127 Angle : 0.429 3.615 1336 Z= 0.251 Chirality : 0.040 0.129 160 Planarity : 0.002 0.013 169 Dihedral : 13.694 78.578 370 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.89 % Allowed : 0.00 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.70), residues: 120 helix: 0.52 (0.54), residues: 73 sheet: None (None), residues: 0 loop : -0.42 (0.90), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 28 TYR 0.002 0.001 TYR A 58 PHE 0.004 0.001 PHE A 43 HIS 0.001 0.001 HIS A 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.049 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 34 average time/residue: 0.1293 time to fit residues: 4.7577 Evaluate side-chains 19 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 6 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5786 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 990 Z= 0.214 Angle : 0.519 3.736 1336 Z= 0.296 Chirality : 0.041 0.139 160 Planarity : 0.004 0.026 169 Dihedral : 4.593 28.500 134 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.79 % Allowed : 13.39 % Favored : 84.82 % 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 (0.76), residues: 120 helix: 1.15 (0.60), residues: 74 sheet: -2.16 (1.10), residues: 10 loop : -0.27 (1.11), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 44 TYR 0.012 0.003 TYR A 91 PHE 0.013 0.002 PHE A 124 HIS 0.005 0.001 HIS A 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 28 time to evaluate : 0.059 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 28 average time/residue: 0.2895 time to fit residues: 8.5492 Evaluate side-chains 22 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 9 optimal weight: 0.5980 chunk 2 optimal weight: 20.0000 chunk 4 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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: 0.5750 moved from start: 0.5248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 990 Z= 0.132 Angle : 0.438 3.473 1336 Z= 0.246 Chirality : 0.041 0.129 160 Planarity : 0.003 0.024 169 Dihedral : 3.937 19.171 134 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.89 % Allowed : 13.39 % Favored : 85.71 % 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: 1.16 (0.77), residues: 120 helix: 1.46 (0.61), residues: 74 sheet: None (None), residues: 0 loop : -0.29 (0.92), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 28 TYR 0.003 0.001 TYR A 91 PHE 0.003 0.001 PHE A 43 HIS 0.001 0.000 HIS A 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.088 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 22 average time/residue: 0.2842 time to fit residues: 6.6937 Evaluate side-chains 21 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 8 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5856 moved from start: 0.5878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 990 Z= 0.149 Angle : 0.449 3.365 1336 Z= 0.256 Chirality : 0.041 0.129 160 Planarity : 0.003 0.029 169 Dihedral : 3.776 15.474 134 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.79 % Allowed : 15.18 % Favored : 83.04 % 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: 1.19 (0.77), residues: 120 helix: 1.41 (0.61), residues: 74 sheet: None (None), residues: 0 loop : -0.13 (0.93), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 28 TYR 0.008 0.001 TYR A 91 PHE 0.005 0.001 PHE A 83 HIS 0.003 0.001 HIS A 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 18 time to evaluate : 0.083 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 19 average time/residue: 0.2461 time to fit residues: 5.0756 Evaluate side-chains 19 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 17 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 128 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 11 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5911 moved from start: 0.6258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 990 Z= 0.171 Angle : 0.491 5.894 1336 Z= 0.267 Chirality : 0.041 0.129 160 Planarity : 0.003 0.029 169 Dihedral : 3.821 14.247 134 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.79 % Allowed : 16.96 % Favored : 81.25 % 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: 1.02 (0.76), residues: 120 helix: 1.23 (0.61), residues: 74 sheet: None (None), residues: 0 loop : -0.13 (0.90), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 122 TYR 0.007 0.002 TYR A 91 PHE 0.005 0.001 PHE A 83 HIS 0.002 0.001 HIS A 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 18 time to evaluate : 0.059 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 19 average time/residue: 0.2737 time to fit residues: 5.5704 Evaluate side-chains 20 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 18 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 128 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 9 optimal weight: 0.0970 chunk 10 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 overall best weight: 5.8186 ------------------------------------------------------------------------------- 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: 0.5967 moved from start: 0.6796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 990 Z= 0.186 Angle : 0.515 5.225 1336 Z= 0.282 Chirality : 0.042 0.129 160 Planarity : 0.004 0.029 169 Dihedral : 3.933 13.472 134 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.79 % Allowed : 16.96 % Favored : 81.25 % 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: 0.75 (0.76), residues: 120 helix: 1.10 (0.61), residues: 73 sheet: None (None), residues: 0 loop : -0.36 (0.88), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 122 TYR 0.009 0.002 TYR A 91 PHE 0.007 0.001 PHE A 83 HIS 0.003 0.001 HIS A 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 453.26 seconds wall clock time: 8 minutes 8.59 seconds (488.59 seconds total)