Starting phenix.real_space_refine on Sun May 19 16:31:31 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8esa_28573.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8esa_28573.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global c_beta_restraints=False ramachandran_plot_restraints.enabled=True secondary_structure.enabled=False resolution=3.4 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8esa_28573.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8esa_28573.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8esa_28573.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8esa_28573.pdb" } resolution = 3.4 refinement { run = *minimization_global rigid_body local_grid_search morphing \ simulated_annealing adp occupancy nqh_flips } pdb_interpretation { secondary_structure { enabled = False } c_beta_restraints = False } 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= 0.770 sd= 7.430 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 72 atoms to isotropic. 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 14 5.16 5 C 1970 2.51 5 N 563 2.21 5 O 597 1.98 5 H 2957 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 63": "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: 6101 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 4308 Inner-chain residues flagged as termini: ['pdbres="GLN A 224 "', 'pdbres="THR A 228 "'] Classifications: {'peptide': 273} Modifications used: {'COO': 2, 'NH3': 2} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 260} Chain breaks: 1 Chain: "B" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1624 Classifications: {'peptide': 99} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Chain: "C" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 169 Classifications: {'peptide': 12} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 11} Time building chain proxies: 1.53, per 1000 atoms: 0.25 Number of scatterers: 6101 At special positions: 0 Unit cell: (85, 66.3, 68, 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 14 16.00 O 597 8.00 N 563 7.00 C 1970 6.00 H 2957 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS C 12 " distance=2.03 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 259 " distance=2.04 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 80 " distance=2.04 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: 2.34 Conformation dependent library (CDL) restraints added in 349.8 milliseconds 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. Time building geometry restraints manager: 2.56 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: 2957 1.15 - 1.31: 526 1.31 - 1.48: 1402 1.48 - 1.65: 1284 1.65 - 1.82: 20 Bond restraints: 6189 Sorted by residual: bond pdb=" N MET A 98 " pdb=" H MET A 98 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.73e+01 bond pdb=" N VAL A 12 " pdb=" H VAL A 12 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.71e+01 bond pdb=" N VAL B 27 " pdb=" H VAL B 27 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.70e+01 bond pdb=" N TYR A 27 " pdb=" H TYR A 27 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.68e+01 bond pdb=" N ILE B 92 " pdb=" H ILE B 92 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.67e+01 ... (remaining 6184 not shown) Histogram of bond angle deviations from ideal: 100.26 - 107.01: 127 107.01 - 113.77: 6998 113.77 - 120.52: 2039 120.52 - 127.27: 1871 127.27 - 134.02: 58 Bond angle restraints: 11093 Sorted by residual: angle pdb=" C CYS A 164 " pdb=" N VAL A 165 " pdb=" CA VAL A 165 " ideal model delta sigma weight residual 120.42 117.94 2.48 1.42e+00 4.96e-01 3.06e+00 angle pdb=" N TYR A 159 " pdb=" CA TYR A 159 " pdb=" CB TYR A 159 " ideal model delta sigma weight residual 109.82 112.42 -2.60 1.52e+00 4.33e-01 2.92e+00 angle pdb=" CA TYR A 159 " pdb=" CB TYR A 159 " pdb=" CG TYR A 159 " ideal model delta sigma weight residual 113.90 110.98 2.92 1.80e+00 3.09e-01 2.63e+00 angle pdb=" CA SER A 207 " pdb=" C SER A 207 " pdb=" N PHE A 208 " ideal model delta sigma weight residual 116.84 114.49 2.35 1.71e+00 3.42e-01 1.90e+00 angle pdb=" N ARG A 111 " pdb=" CA ARG A 111 " pdb=" C ARG A 111 " ideal model delta sigma weight residual 108.32 110.54 -2.22 1.64e+00 3.72e-01 1.84e+00 ... (remaining 11088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 1948 16.43 - 32.86: 189 32.86 - 49.29: 60 49.29 - 65.72: 26 65.72 - 82.15: 3 Dihedral angle restraints: 2226 sinusoidal: 1552 harmonic: 674 Sorted by residual: dihedral pdb=" CA TYR A 27 " pdb=" C TYR A 27 " pdb=" N VAL A 28 " pdb=" CA VAL A 28 " ideal model delta harmonic sigma weight residual 180.00 164.21 15.79 0 5.00e+00 4.00e-02 9.97e+00 dihedral pdb=" CA ARG B 81 " pdb=" CB ARG B 81 " pdb=" CG ARG B 81 " pdb=" CD ARG B 81 " ideal model delta sinusoidal sigma weight residual -60.00 -107.41 47.41 3 1.50e+01 4.44e-03 8.49e+00 dihedral pdb=" CA ARG A 256 " pdb=" CB ARG A 256 " pdb=" CG ARG A 256 " pdb=" CD ARG A 256 " ideal model delta sinusoidal sigma weight residual -180.00 -134.14 -45.86 3 1.50e+01 4.44e-03 8.24e+00 ... (remaining 2223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 275 0.029 - 0.059: 119 0.059 - 0.088: 25 0.088 - 0.117: 18 0.117 - 0.146: 7 Chirality restraints: 444 Sorted by residual: chirality pdb=" CA ILE A 213 " pdb=" N ILE A 213 " pdb=" C ILE A 213 " pdb=" CB ILE A 213 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA ILE A 23 " pdb=" N ILE A 23 " pdb=" C ILE A 23 " pdb=" CB ILE A 23 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA VAL A 261 " pdb=" N VAL A 261 " pdb=" C VAL A 261 " pdb=" CB VAL A 261 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.14e-01 ... (remaining 441 not shown) Planarity restraints: 938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 49 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO A 50 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 50 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 50 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 160 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" C LEU A 160 " -0.022 2.00e-02 2.50e+03 pdb=" O LEU A 160 " 0.008 2.00e-02 2.50e+03 pdb=" N GLU A 161 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 249 " 0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO A 250 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 250 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 250 " 0.015 5.00e-02 4.00e+02 ... (remaining 935 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 503 2.18 - 2.78: 10875 2.78 - 3.39: 15584 3.39 - 3.99: 21491 3.99 - 4.60: 31973 Nonbonded interactions: 80426 Sorted by model distance: nonbonded pdb=" OD1 ASN B 21 " pdb=" H PHE B 22 " model vdw 1.575 1.850 nonbonded pdb=" OE1 GLU A 58 " pdb=" H GLU A 58 " model vdw 1.578 1.850 nonbonded pdb=" HE ARG A 21 " pdb=" OD2 ASP A 39 " model vdw 1.628 1.850 nonbonded pdb=" H LYS B 41 " pdb=" O GLU B 44 " model vdw 1.656 1.850 nonbonded pdb=" OD1 ASP A 77 " pdb=" H VAL C 10 " model vdw 1.684 1.850 ... (remaining 80421 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=0.52 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: 0.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.050 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.830 Find NCS groups from input model: 0.050 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:0.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:6.520 Internal consistency checks: 0.000 Total: 17.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 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 0.028 3232 Z= 0.145 Angle : 0.446 3.633 4383 Z= 0.247 Chirality : 0.040 0.146 444 Planarity : 0.003 0.040 575 Dihedral : 12.874 82.146 1180 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.38 % Favored : 93.09 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -1.41 (0.41), residues: 376 helix: 0.82 (0.59), residues: 66 sheet: -0.63 (0.45), residues: 129 loop : -1.85 (0.41), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 21 TYR 0.011 0.001 TYR A 159 PHE 0.005 0.001 PHE A 208 TRP 0.007 0.001 TRP A 204 HIS 0.002 0.001 HIS A 70 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 24 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3232 Z= 0.258 Angle : 0.467 3.940 4383 Z= 0.240 Chirality : 0.057 0.159 444 Planarity : 0.003 0.030 575 Dihedral : 12.239 78.545 1180 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.60 % Allowed : 0.60 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -1.30 (0.41), residues: 376 helix: 1.07 (0.59), residues: 66 sheet: -0.69 (0.45), residues: 128 loop : -1.71 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 21 TYR 0.010 0.001 TYR A 99 PHE 0.015 0.002 PHE B 56 TRP 0.004 0.001 TRP B 95 HIS 0.003 0.001 HIS B 51 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 32 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 8.9990 chunk 19 optimal weight: 30.0000 chunk 4 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3232 Z= 0.223 Angle : 0.425 3.973 4383 Z= 0.217 Chirality : 0.056 0.153 444 Planarity : 0.003 0.028 575 Dihedral : 11.731 82.669 1180 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.60 % Allowed : 1.20 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -1.42 (0.42), residues: 376 helix: 0.53 (0.58), residues: 67 sheet: -0.73 (0.45), residues: 128 loop : -1.63 (0.44), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 21 TYR 0.011 0.001 TYR A 99 PHE 0.013 0.002 PHE B 56 TRP 0.004 0.001 TRP A 274 HIS 0.003 0.001 HIS B 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 35 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 30 optimal weight: 0.0000 chunk 28 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 overall best weight: 3.3390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3232 Z= 0.152 Angle : 0.378 3.755 4383 Z= 0.188 Chirality : 0.054 0.146 444 Planarity : 0.003 0.040 575 Dihedral : 10.923 76.892 1180 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.60 % Allowed : 0.90 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -1.04 (0.43), residues: 376 helix: 1.15 (0.60), residues: 67 sheet: -0.68 (0.45), residues: 130 loop : -1.37 (0.46), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 21 TYR 0.008 0.001 TYR A 99 PHE 0.009 0.001 PHE B 56 TRP 0.003 0.001 TRP A 60 HIS 0.002 0.001 HIS A 70 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 35 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3232 Z= 0.270 Angle : 0.454 4.076 4383 Z= 0.233 Chirality : 0.057 0.156 444 Planarity : 0.003 0.030 575 Dihedral : 11.521 87.862 1180 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.60 % Allowed : 1.51 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -1.38 (0.42), residues: 376 helix: 0.32 (0.59), residues: 67 sheet: -0.38 (0.50), residues: 108 loop : -1.68 (0.42), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 21 TYR 0.012 0.001 TYR A 99 PHE 0.014 0.002 PHE B 56 TRP 0.004 0.001 TRP B 95 HIS 0.003 0.001 HIS B 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 14 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 20.0000 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3232 Z= 0.121 Angle : 0.363 3.744 4383 Z= 0.180 Chirality : 0.053 0.143 444 Planarity : 0.003 0.042 575 Dihedral : 10.528 75.686 1180 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.60 % Allowed : 0.90 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -1.04 (0.43), residues: 376 helix: 1.01 (0.60), residues: 67 sheet: -0.57 (0.50), residues: 116 loop : -1.37 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 21 TYR 0.008 0.001 TYR A 99 PHE 0.007 0.001 PHE B 56 TRP 0.003 0.001 TRP A 244 HIS 0.002 0.001 HIS A 70 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 581.16 seconds wall clock time: 10 minutes 18.64 seconds (618.64 seconds total)