Starting phenix.real_space_refine on Sun May 19 16:31:06 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=False secondary_structure.enabled=False resolution=3.0 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { 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" 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" } 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 ramachandran_plot_restraints { enabled = 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: 2.48, per 1000 atoms: 0.18 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: 4.14 Conformation dependent library (CDL) restraints added in 653.8 milliseconds Time building geometry restraints manager: 4.84 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: 0.070 Extract box with map and model: 0.350 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 14.710 Find NCS groups from input model: 0.090 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:13.560 Internal consistency checks: 0.000 Total: 28.870 ------------------------------------------------------------------------------- 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 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6870 Z= 0.232 Angle : 0.487 6.049 9354 Z= 0.249 Chirality : 0.050 0.178 1090 Planarity : 0.004 0.059 1166 Dihedral : 12.847 83.179 2413 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.69 % Allowed : 6.34 % Favored : 92.96 % Rotamer: Outliers : 1.08 % Allowed : 11.04 % Favored : 87.89 % 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: -3.09 (0.24), residues: 867 helix: -2.47 (0.19), residues: 394 sheet: -0.30 (0.38), residues: 192 loop : -2.36 (0.33), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 364 TYR 0.007 0.001 TYR D 113 PHE 0.011 0.001 PHE D 171 TRP 0.008 0.001 TRP C 183 HIS 0.008 0.001 HIS D 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 20.0000 chunk 64 optimal weight: 60.0000 chunk 17 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 79 optimal weight: 40.0000 chunk 32 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 overall best weight: 9.1998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6870 Z= 0.292 Angle : 0.489 6.301 9354 Z= 0.252 Chirality : 0.050 0.176 1090 Planarity : 0.004 0.040 1166 Dihedral : 11.767 82.325 2413 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 1.38 % Allowed : 11.65 % Favored : 86.97 % Rotamer: Outliers : 1.21 % Allowed : 8.88 % Favored : 89.91 % 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: -4.88 (0.22), residues: 867 helix: -3.96 (0.15), residues: 390 sheet: -1.40 (0.33), residues: 201 loop : -3.09 (0.30), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 117 TYR 0.011 0.001 TYR C 193 PHE 0.008 0.001 PHE C 107 TRP 0.008 0.001 TRP D 69 HIS 0.004 0.001 HIS D 224 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 12 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 60 optimal weight: 30.0000 chunk 71 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 78 optimal weight: 50.0000 chunk 81 optimal weight: 50.0000 chunk 26 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6870 Z= 0.274 Angle : 0.436 6.170 9354 Z= 0.224 Chirality : 0.048 0.162 1090 Planarity : 0.003 0.051 1166 Dihedral : 11.225 77.756 2413 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 1.73 % Allowed : 11.53 % Favored : 86.74 % Rotamer: Outliers : 1.21 % Allowed : 7.40 % Favored : 91.39 % 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: -4.99 (0.22), residues: 867 helix: -3.80 (0.16), residues: 390 sheet: -1.65 (0.34), residues: 203 loop : -3.43 (0.30), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 179 TYR 0.007 0.001 TYR C 160 PHE 0.007 0.001 PHE A 324 TRP 0.006 0.001 TRP A 470 HIS 0.006 0.001 HIS D 224 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 70 optimal weight: 10.0000 chunk 61 optimal weight: 30.0000 chunk 56 optimal weight: 60.0000 chunk 66 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 85 optimal weight: 30.0000 chunk 80 optimal weight: 20.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6870 Z= 0.297 Angle : 0.446 6.775 9354 Z= 0.229 Chirality : 0.048 0.164 1090 Planarity : 0.003 0.044 1166 Dihedral : 10.873 79.053 2413 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 2.08 % Allowed : 12.57 % Favored : 85.35 % Rotamer: Outliers : 1.88 % Allowed : 7.40 % Favored : 90.71 % 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: -5.47 (0.21), residues: 867 helix: -4.01 (0.14), residues: 386 sheet: -2.17 (0.33), residues: 202 loop : -3.72 (0.29), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 117 TYR 0.007 0.001 TYR C 111 PHE 0.006 0.001 PHE A 324 TRP 0.005 0.001 TRP D 69 HIS 0.004 0.001 HIS D 224 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 60.0000 chunk 63 optimal weight: 50.0000 chunk 42 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6870 Z= 0.284 Angle : 0.429 6.399 9354 Z= 0.222 Chirality : 0.048 0.153 1090 Planarity : 0.003 0.055 1166 Dihedral : 10.647 74.438 2413 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 2.42 % Allowed : 12.57 % Favored : 85.01 % Rotamer: Outliers : 1.62 % Allowed : 6.86 % 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: -5.58 (0.20), residues: 867 helix: -4.00 (0.14), residues: 387 sheet: -2.42 (0.31), residues: 209 loop : -3.79 (0.30), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 293 TYR 0.006 0.001 TYR C 160 PHE 0.007 0.001 PHE A 324 TRP 0.007 0.001 TRP A 470 HIS 0.005 0.001 HIS D 224 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 301.46 seconds wall clock time: 5 minutes 58.45 seconds (358.45 seconds total)