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/8g94_29861.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8g94_29861.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=3.15 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8g94_29861.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8g94_29861.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8g94_29861.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8g94_29861.map" } resolution = 3.15 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= 0.003 sd= 0.007 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 67 5.16 5 C 5939 2.51 5 N 1575 2.21 5 O 1727 1.98 5 H 9374 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 18682 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 4812 Inner-chain residues flagged as termini: ['pdbres="ILE A 37 "', 'pdbres="LYS A 46 "', 'pdbres="LYS A 239 "', 'pdbres="LYS A 250 "'] Classifications: {'peptide': 288} Modifications used: {'COO': 3, 'NH3': 3} Link IDs: {'PTRANS': 6, 'TRANS': 281} Chain breaks: 2 Chain: "B" Number of atoms: 3574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3574 Inner-chain residues flagged as termini: ['pdbres="ILE B 55 "', 'pdbres="THR B 182 "', 'pdbres="ALA B 235 "', 'pdbres="MET B 240 "'] Classifications: {'peptide': 221} Modifications used: {'COO': 3, 'NH3': 3} Link IDs: {'PTRANS': 2, 'TRANS': 218} Chain breaks: 2 Chain: "C" Number of atoms: 5095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 5095 Classifications: {'peptide': 337} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "D" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 902 Classifications: {'peptide': 58} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 3500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3500 Inner-chain residues flagged as termini: ['pdbres="SER E 120 "', 'pdbres="SER E 124 "'] Classifications: {'peptide': 231} Modifications used: {'COO': 2, 'NH3': 2} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "F" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 392 Classifications: {'peptide': 25} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'TRANS': 24} Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 407 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 26} Time building chain proxies: 3.43, per 1000 atoms: 0.18 Number of scatterers: 18682 At special positions: 0 Unit cell: (90.47, 119.52, 129.48, 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 67 16.00 O 1727 8.00 N 1575 7.00 C 5939 6.00 H 9374 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " 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: 4.82 Conformation dependent library (CDL) restraints added in 641.0 milliseconds Time building geometry restraints manager: 5.43 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: 9338 1.14 - 1.31: 1534 1.31 - 1.48: 3851 1.48 - 1.65: 4042 1.65 - 1.82: 96 Bond restraints: 18861 Sorted by residual: bond pdb=" N ILE F 55 " pdb=" H ILE F 55 " ideal model delta sigma weight residual 0.860 1.032 -0.172 2.00e-02 2.50e+03 7.42e+01 bond pdb=" N SER G 56 " pdb=" H SER G 56 " ideal model delta sigma weight residual 0.860 1.028 -0.168 2.00e-02 2.50e+03 7.09e+01 bond pdb=" N ASN C 119 " pdb=" H ASN C 119 " ideal model delta sigma weight residual 0.860 1.026 -0.166 2.00e-02 2.50e+03 6.91e+01 bond pdb=" N PHE C 335 " pdb=" H PHE C 335 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.81e+01 bond pdb=" N SER E 7 " pdb=" H SER E 7 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.77e+01 ... (remaining 18856 not shown) Histogram of bond angle deviations from ideal: 99.97 - 106.78: 279 106.78 - 113.59: 22369 113.59 - 120.41: 6110 120.41 - 127.22: 5172 127.22 - 134.03: 86 Bond angle restraints: 34016 Sorted by residual: angle pdb=" N ALA E 92 " pdb=" CA ALA E 92 " pdb=" C ALA E 92 " ideal model delta sigma weight residual 107.73 112.54 -4.81 1.61e+00 3.86e-01 8.94e+00 angle pdb=" N ASP C 291 " pdb=" CA ASP C 291 " pdb=" C ASP C 291 " ideal model delta sigma weight residual 112.93 109.95 2.98 1.12e+00 7.97e-01 7.09e+00 angle pdb=" C LEU A 290 " pdb=" N PHE A 291 " pdb=" CA PHE A 291 " ideal model delta sigma weight residual 121.54 126.12 -4.58 1.91e+00 2.74e-01 5.75e+00 angle pdb=" N SER C 277 " pdb=" CA SER C 277 " pdb=" C SER C 277 " ideal model delta sigma weight residual 108.32 111.93 -3.61 1.64e+00 3.72e-01 4.84e+00 angle pdb=" CB LYS G 58 " pdb=" CG LYS G 58 " pdb=" CD LYS G 58 " ideal model delta sigma weight residual 111.30 106.33 4.97 2.30e+00 1.89e-01 4.67e+00 ... (remaining 34011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 5935 16.96 - 33.92: 458 33.92 - 50.88: 175 50.88 - 67.84: 42 67.84 - 84.80: 11 Dihedral angle restraints: 6621 sinusoidal: 4750 harmonic: 1871 Sorted by residual: dihedral pdb=" CA GLN C 75 " pdb=" C GLN C 75 " pdb=" N ASP C 76 " pdb=" CA ASP C 76 " ideal model delta harmonic sigma weight residual 180.00 160.03 19.97 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ARG E 179 " pdb=" C ARG E 179 " pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta harmonic sigma weight residual 180.00 161.62 18.38 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 6618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 911 0.029 - 0.058: 400 0.058 - 0.087: 102 0.087 - 0.115: 59 0.115 - 0.144: 14 Chirality restraints: 1486 Sorted by residual: chirality pdb=" CA ILE B 265 " pdb=" N ILE B 265 " pdb=" C ILE B 265 " pdb=" CB ILE B 265 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA VAL C 327 " pdb=" N VAL C 327 " pdb=" C VAL C 327 " pdb=" CB VAL C 327 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA ILE C 58 " pdb=" N ILE C 58 " pdb=" C ILE C 58 " pdb=" CB ILE C 58 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 1483 not shown) Planarity restraints: 2756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 270 " -0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO A 271 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 58 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.74e+00 pdb=" C LYS G 58 " 0.023 2.00e-02 2.50e+03 pdb=" O LYS G 58 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP G 59 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 281 " -0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO B 282 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO B 282 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 282 " -0.015 5.00e-02 4.00e+02 ... (remaining 2753 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.08: 1332 2.08 - 2.71: 29252 2.71 - 3.34: 54497 3.34 - 3.97: 73983 3.97 - 4.60: 108739 Nonbonded interactions: 267803 Sorted by model distance: nonbonded pdb=" OE2 GLU B 8 " pdb=" HH TYR E 163 " model vdw 1.456 1.850 nonbonded pdb=" O LEU A 174 " pdb=" HH TYR A 202 " model vdw 1.463 1.850 nonbonded pdb=" O LYS B 277 " pdb=" H SER B 281 " model vdw 1.479 1.850 nonbonded pdb=" HG1 THR C 274 " pdb=" O VAL C 315 " model vdw 1.482 1.850 nonbonded pdb=" HZ1 LYS B 210 " pdb=" OD1 ASN C 230 " model vdw 1.498 1.850 ... (remaining 267798 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: 0.070 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: 0.110 Extract box with map and model: 0.340 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 18.900 Find NCS groups from input model: 0.130 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:20.700 Internal consistency checks: 0.000 Total: 40.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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 0.055 9487 Z= 0.128 Angle : 0.526 6.148 12842 Z= 0.286 Chirality : 0.039 0.144 1486 Planarity : 0.003 0.034 1608 Dihedral : 12.278 84.300 3417 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.16 % Favored : 94.75 % Rotamer: Outliers : 0.49 % Allowed : 2.45 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.85 (0.22), residues: 1163 helix: -0.10 (0.23), residues: 421 sheet: -1.69 (0.29), residues: 271 loop : -1.88 (0.25), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 159 TYR 0.010 0.001 TYR E 95 PHE 0.011 0.001 PHE B 189 TRP 0.010 0.001 TRP C 339 HIS 0.002 0.001 HIS C 142 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 9487 Z= 0.219 Angle : 0.468 6.104 12842 Z= 0.247 Chirality : 0.050 0.190 1486 Planarity : 0.002 0.036 1608 Dihedral : 11.260 81.184 3417 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 1.20 % Allowed : 7.57 % Favored : 91.23 % Rotamer: Outliers : 0.49 % Allowed : 2.54 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -3.61 (0.20), residues: 1163 helix: -2.13 (0.19), residues: 424 sheet: -2.54 (0.26), residues: 286 loop : -2.28 (0.25), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 159 TYR 0.008 0.001 TYR E 178 PHE 0.011 0.001 PHE E 165 TRP 0.009 0.001 TRP A 168 HIS 0.002 0.001 HIS B 195 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 106 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 114 optimal weight: 40.0000 chunk 27 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 17 optimal weight: 30.0000 chunk 36 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 overall best weight: 8.7996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 9487 Z= 0.300 Angle : 0.508 6.175 12842 Z= 0.269 Chirality : 0.053 0.201 1486 Planarity : 0.003 0.027 1608 Dihedral : 11.198 73.163 3417 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 1.81 % Allowed : 11.26 % Favored : 86.93 % Rotamer: Outliers : 0.88 % Allowed : 3.82 % Favored : 95.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -5.16 (0.19), residues: 1163 helix: -3.75 (0.15), residues: 435 sheet: -2.93 (0.26), residues: 276 loop : -3.11 (0.24), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 159 TYR 0.010 0.001 TYR E 178 PHE 0.012 0.001 PHE C 235 TRP 0.007 0.001 TRP C 99 HIS 0.002 0.001 HIS A 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 overall best weight: 8.3992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 9487 Z= 0.267 Angle : 0.463 5.052 12842 Z= 0.246 Chirality : 0.051 0.186 1486 Planarity : 0.002 0.024 1608 Dihedral : 10.956 69.274 3417 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 1.81 % Allowed : 11.09 % Favored : 87.10 % Rotamer: Outliers : 0.88 % Allowed : 3.91 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -5.35 (0.18), residues: 1163 helix: -3.95 (0.14), residues: 434 sheet: -3.06 (0.26), residues: 266 loop : -3.17 (0.23), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 159 TYR 0.010 0.001 TYR E 178 PHE 0.010 0.001 PHE C 235 TRP 0.007 0.001 TRP C 339 HIS 0.002 0.001 HIS A 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 9 optimal weight: 20.0000 chunk 108 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 overall best weight: 8.7994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 9487 Z= 0.305 Angle : 0.496 5.036 12842 Z= 0.266 Chirality : 0.053 0.193 1486 Planarity : 0.003 0.026 1608 Dihedral : 11.032 67.456 3417 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 2.84 % Allowed : 11.95 % Favored : 85.21 % Rotamer: Outliers : 1.57 % Allowed : 4.31 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -5.77 (0.18), residues: 1163 helix: -4.30 (0.12), residues: 432 sheet: -3.28 (0.26), residues: 267 loop : -3.42 (0.23), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 159 TYR 0.011 0.001 TYR E 178 PHE 0.011 0.001 PHE C 235 TRP 0.008 0.001 TRP C 339 HIS 0.002 0.001 HIS B 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 81 optimal weight: 7.9990 chunk 26 optimal weight: 30.0000 chunk 70 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 7 optimal weight: 30.0000 chunk 103 optimal weight: 7.9990 chunk 1 optimal weight: 50.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9487 Z= 0.245 Angle : 0.445 4.446 12842 Z= 0.236 Chirality : 0.050 0.181 1486 Planarity : 0.002 0.025 1608 Dihedral : 10.707 67.042 3417 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 2.15 % Allowed : 11.35 % Favored : 86.50 % Rotamer: Outliers : 1.57 % Allowed : 3.91 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -5.65 (0.17), residues: 1163 helix: -4.18 (0.13), residues: 430 sheet: -3.35 (0.25), residues: 266 loop : -3.29 (0.23), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 159 TYR 0.010 0.001 TYR E 178 PHE 0.009 0.001 PHE C 235 TRP 0.008 0.001 TRP C 339 HIS 0.003 0.001 HIS B 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 365.67 seconds wall clock time: 7 minutes 21.43 seconds (441.43 seconds total)