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/8dl8_27499.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dl8_27499.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=3.0 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dl8_27499.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dl8_27499.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dl8_27499.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dl8_27499.pdb" } resolution = 3.0 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= 0.069 sd= 0.195 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 42 5.16 5 C 4311 2.51 5 N 1096 2.21 5 O 1269 1.98 5 H 6701 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 190": "OD1" <-> "OD2" Residue "C TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 13419 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 6914 Inner-chain residues flagged as termini: ['pdbres="GLY A 238 "', 'pdbres="CYS A 284 "', 'pdbres="PRO A 397 "', 'pdbres="PRO A 451 "'] Classifications: {'peptide': 445} Modifications used: {'COO': 3, 'NH2': 1, 'NH3': 2} Link IDs: {'PTRANS': 11, 'TRANS': 433} Chain breaks: 2 Chain: "C" Number of atoms: 3220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3220 Classifications: {'peptide': 213} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203} Chain: "D" Number of atoms: 3285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3285 Classifications: {'peptide': 219} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 204} Time building chain proxies: 2.79, per 1000 atoms: 0.21 Number of scatterers: 13419 At special positions: 0 Unit cell: (73.44, 76.68, 147.96, 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 42 16.00 O 1269 8.00 N 1096 7.00 C 4311 6.00 H 6701 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 553 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " distance=2.03 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: 5.55 Conformation dependent library (CDL) restraints added in 858.8 milliseconds 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. Time building geometry restraints manager: 6.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.97 - 1.14: 6692 1.14 - 1.31: 1079 1.31 - 1.48: 2839 1.48 - 1.65: 2896 1.65 - 1.82: 65 Bond restraints: 13571 Sorted by residual: bond pdb=" N ALA C 150 " pdb=" H ALA C 150 " ideal model delta sigma weight residual 0.860 1.034 -0.174 2.00e-02 2.50e+03 7.54e+01 bond pdb=" N THR D 209 " pdb=" H THR D 209 " ideal model delta sigma weight residual 0.860 1.028 -0.168 2.00e-02 2.50e+03 7.07e+01 bond pdb=" N GLY C 149 " pdb=" H GLY C 149 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.78e+01 bond pdb=" N SER C 72 " pdb=" H SER C 72 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" N VAL D 161 " pdb=" H VAL D 161 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.75e+01 ... (remaining 13566 not shown) Histogram of bond angle deviations from ideal: 95.82 - 103.54: 76 103.54 - 111.25: 15074 111.25 - 118.97: 3530 118.97 - 126.68: 5708 126.68 - 134.40: 120 Bond angle restraints: 24508 Sorted by residual: angle pdb=" N GLY D 169 " pdb=" CA GLY D 169 " pdb=" C GLY D 169 " ideal model delta sigma weight residual 113.76 105.99 7.77 1.80e+00 3.09e-01 1.86e+01 angle pdb=" N THR D 209 " pdb=" CA THR D 209 " pdb=" C THR D 209 " ideal model delta sigma weight residual 111.07 114.52 -3.45 1.07e+00 8.73e-01 1.04e+01 angle pdb=" CB THR D 142 " pdb=" CG2 THR D 142 " pdb="HG22 THR D 142 " ideal model delta sigma weight residual 110.00 101.72 8.28 3.00e+00 1.11e-01 7.61e+00 angle pdb=" N PRO D 172 " pdb=" CA PRO D 172 " pdb=" C PRO D 172 " ideal model delta sigma weight residual 112.47 117.64 -5.17 2.06e+00 2.36e-01 6.29e+00 angle pdb=" CA TYR D 170 " pdb=" CB TYR D 170 " pdb=" CG TYR D 170 " ideal model delta sigma weight residual 113.90 118.38 -4.48 1.80e+00 3.09e-01 6.18e+00 ... (remaining 24503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 4081 17.39 - 34.78: 489 34.78 - 52.17: 196 52.17 - 69.56: 59 69.56 - 86.95: 5 Dihedral angle restraints: 4830 sinusoidal: 3443 harmonic: 1387 Sorted by residual: dihedral pdb=" CA GLY D 169 " pdb=" C GLY D 169 " pdb=" N TYR D 170 " pdb=" CA TYR D 170 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA SER C 194 " pdb=" C SER C 194 " pdb=" N MET C 195 " pdb=" CA MET C 195 " ideal model delta harmonic sigma weight residual -180.00 -159.10 -20.90 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA SER C 228 " pdb=" C SER C 228 " pdb=" N PHE C 229 " pdb=" CA PHE C 229 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 4827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 756 0.036 - 0.071: 236 0.071 - 0.107: 69 0.107 - 0.143: 26 0.143 - 0.179: 3 Chirality restraints: 1090 Sorted by residual: chirality pdb=" CA ILE C 164 " pdb=" N ILE C 164 " pdb=" C ILE C 164 " pdb=" CB ILE C 164 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.98e-01 chirality pdb=" CA PRO D 172 " pdb=" N PRO D 172 " pdb=" C PRO D 172 " pdb=" CB PRO D 172 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CB ILE D 235 " pdb=" CA ILE D 235 " pdb=" CG1 ILE D 235 " pdb=" CG2 ILE D 235 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.23e-01 ... (remaining 1087 not shown) Planarity restraints: 2005 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 143 " -0.042 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO D 144 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO D 144 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 144 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 516 " 0.039 5.00e-02 4.00e+02 5.90e-02 5.57e+00 pdb=" N PRO A 517 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 517 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 517 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP D 213 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO D 214 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 214 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 214 " -0.029 5.00e-02 4.00e+02 ... (remaining 2002 not shown) Histogram of nonbonded interaction distances: 1.29 - 1.95: 442 1.95 - 2.61: 14329 2.61 - 3.28: 40764 3.28 - 3.94: 52985 3.94 - 4.60: 78058 Nonbonded interactions: 186578 Sorted by model distance: nonbonded pdb=" O SER C 141 " pdb=" H LEU C 145 " model vdw 1.288 1.850 nonbonded pdb=" HG1 THR C 184 " pdb=" O SER C 194 " model vdw 1.375 1.850 nonbonded pdb=" OG SER C 141 " pdb=" H GLN C 144 " model vdw 1.457 1.850 nonbonded pdb=" O GLY A 368 " pdb=" HG1 THR A 372 " model vdw 1.520 1.850 nonbonded pdb=" O ILE A 354 " pdb=" HG1 THR A 357 " model vdw 1.556 1.850 ... (remaining 186573 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=0.47 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: 0.000 Construct map_model_manager: 0.130 Extract box with map and model: 0.580 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 20.970 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:18.190 Internal consistency checks: 0.000 Total: 40.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 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 : 0.003 0.053 6870 Z= 0.223 Angle : 0.586 7.768 9354 Z= 0.316 Chirality : 0.041 0.179 1090 Planarity : 0.006 0.065 1166 Dihedral : 14.872 86.950 2413 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.19 % Favored : 94.69 % Rotamer: Outliers : 2.15 % Allowed : 19.92 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.69 (0.29), residues: 867 helix: 1.66 (0.25), residues: 394 sheet: 0.46 (0.38), residues: 207 loop : -1.38 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 74 TYR 0.014 0.001 TYR D 170 PHE 0.019 0.002 PHE D 191 TRP 0.015 0.001 TRP D 213 HIS 0.007 0.001 HIS D 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6870 Z= 0.237 Angle : 0.488 5.628 9354 Z= 0.257 Chirality : 0.050 0.209 1090 Planarity : 0.005 0.063 1166 Dihedral : 13.193 84.092 2413 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.42 % Favored : 97.46 % Rotamer: Outliers : 1.21 % Allowed : 11.84 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.63 (0.29), residues: 867 helix: 2.65 (0.26), residues: 393 sheet: 0.92 (0.39), residues: 193 loop : -1.18 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 293 TYR 0.008 0.001 TYR D 113 PHE 0.005 0.001 PHE A 324 TRP 0.005 0.001 TRP C 168 HIS 0.007 0.001 HIS D 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 79 optimal weight: 30.0000 chunk 32 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6870 Z= 0.205 Angle : 0.422 5.951 9354 Z= 0.218 Chirality : 0.048 0.200 1090 Planarity : 0.005 0.076 1166 Dihedral : 11.818 84.355 2413 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.46 % Favored : 96.42 % Rotamer: Outliers : 1.48 % Allowed : 7.40 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.02 (0.29), residues: 867 helix: 2.84 (0.25), residues: 395 sheet: 1.25 (0.39), residues: 194 loop : -0.91 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 117 TYR 0.007 0.001 TYR D 200 PHE 0.009 0.001 PHE D 171 TRP 0.006 0.001 TRP D 69 HIS 0.004 0.001 HIS D 224 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 chunk 55 optimal weight: 30.0000 chunk 40 optimal weight: 9.9990 chunk 78 optimal weight: 50.0000 chunk 81 optimal weight: 50.0000 chunk 26 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6870 Z= 0.270 Angle : 0.471 5.840 9354 Z= 0.247 Chirality : 0.048 0.171 1090 Planarity : 0.004 0.047 1166 Dihedral : 11.273 83.610 2413 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.35 % Allowed : 7.13 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.69 (0.28), residues: 867 helix: 2.46 (0.24), residues: 388 sheet: 1.06 (0.37), residues: 203 loop : -0.83 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 117 TYR 0.008 0.001 TYR C 160 PHE 0.011 0.001 PHE D 171 TRP 0.005 0.001 TRP D 69 HIS 0.006 0.001 HIS D 224 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 70 optimal weight: 6.9990 chunk 61 optimal weight: 30.0000 chunk 56 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 85 optimal weight: 40.0000 chunk 80 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6870 Z= 0.212 Angle : 0.400 5.765 9354 Z= 0.207 Chirality : 0.046 0.183 1090 Planarity : 0.004 0.052 1166 Dihedral : 10.840 83.479 2413 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.62 % Allowed : 6.06 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.78 (0.28), residues: 867 helix: 2.53 (0.24), residues: 388 sheet: 1.10 (0.37), residues: 201 loop : -0.76 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 81 TYR 0.005 0.001 TYR C 69 PHE 0.006 0.001 PHE D 171 TRP 0.005 0.001 TRP D 69 HIS 0.005 0.001 HIS D 224 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 40.0000 chunk 63 optimal weight: 40.0000 chunk 42 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 6870 Z= 0.277 Angle : 0.452 5.719 9354 Z= 0.237 Chirality : 0.047 0.171 1090 Planarity : 0.004 0.043 1166 Dihedral : 10.688 84.451 2413 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.75 % Allowed : 6.33 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.48 (0.28), residues: 867 helix: 2.21 (0.25), residues: 384 sheet: 1.05 (0.36), residues: 203 loop : -0.85 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 117 TYR 0.008 0.001 TYR C 160 PHE 0.009 0.001 PHE D 171 TRP 0.006 0.001 TRP A 470 HIS 0.006 0.001 HIS D 224 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 616.61 seconds wall clock time: 11 minutes 8.25 seconds (668.25 seconds total)