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/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=True 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 } 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: 0.01s 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: 4.79, per 1000 atoms: 0.26 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: 6.57 Conformation dependent library (CDL) restraints added in 934.5 milliseconds 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. Time building geometry restraints manager: 7.53 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: 0.110 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: 0.160 Extract box with map and model: 0.450 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 27.910 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:25.000 Internal consistency checks: 0.000 Total: 54.030 ------------------------------------------------------------------------------- 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 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9487 Z= 0.213 Angle : 0.464 5.146 12842 Z= 0.248 Chirality : 0.050 0.197 1486 Planarity : 0.003 0.034 1608 Dihedral : 11.460 81.884 3417 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.49 % Allowed : 2.35 % Favored : 97.16 % 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: -0.85 (0.24), residues: 1163 helix: 1.03 (0.25), residues: 423 sheet: -1.60 (0.29), residues: 280 loop : -1.29 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 159 TYR 0.009 0.001 TYR E 178 PHE 0.009 0.001 PHE C 235 TRP 0.007 0.001 TRP A 168 HIS 0.002 0.001 HIS C 142 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 106 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 114 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 36 optimal weight: 0.7980 chunk 96 optimal weight: 8.9990 overall best weight: 7.1588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9487 Z= 0.252 Angle : 0.476 4.697 12842 Z= 0.255 Chirality : 0.051 0.210 1486 Planarity : 0.003 0.037 1608 Dihedral : 10.995 74.591 3417 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.88 % Allowed : 3.03 % Favored : 96.09 % 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: -0.62 (0.24), residues: 1163 helix: 1.11 (0.25), residues: 433 sheet: -1.54 (0.29), residues: 285 loop : -1.04 (0.28), residues: 445 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 0.010 0.001 PHE C 235 TRP 0.009 0.001 TRP C 339 HIS 0.002 0.001 HIS C 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9487 Z= 0.234 Angle : 0.456 4.738 12842 Z= 0.244 Chirality : 0.051 0.202 1486 Planarity : 0.003 0.034 1608 Dihedral : 10.710 71.819 3417 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.88 % Allowed : 3.03 % Favored : 96.09 % 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: -0.49 (0.24), residues: 1163 helix: 1.19 (0.25), residues: 435 sheet: -1.43 (0.30), residues: 291 loop : -0.95 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 159 TYR 0.009 0.001 TYR E 178 PHE 0.010 0.001 PHE C 235 TRP 0.009 0.001 TRP C 339 HIS 0.002 0.001 HIS C 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 9 optimal weight: 20.0000 chunk 108 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9487 Z= 0.198 Angle : 0.427 4.640 12842 Z= 0.226 Chirality : 0.050 0.199 1486 Planarity : 0.003 0.031 1608 Dihedral : 10.375 71.035 3417 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.98 % Allowed : 2.94 % Favored : 96.09 % 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: -0.27 (0.25), residues: 1163 helix: 1.41 (0.25), residues: 435 sheet: -1.34 (0.30), residues: 290 loop : -0.85 (0.29), residues: 438 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 0.008 0.001 PHE C 235 TRP 0.009 0.001 TRP C 339 HIS 0.002 0.001 HIS C 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 81 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 1 optimal weight: 40.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9487 Z= 0.238 Angle : 0.455 4.720 12842 Z= 0.244 Chirality : 0.051 0.198 1486 Planarity : 0.003 0.034 1608 Dihedral : 10.433 70.619 3417 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.17 % Allowed : 3.23 % Favored : 95.60 % 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: -0.29 (0.25), residues: 1163 helix: 1.36 (0.25), residues: 430 sheet: -1.33 (0.30), residues: 292 loop : -0.81 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 159 TYR 0.008 0.001 TYR E 163 PHE 0.009 0.001 PHE C 235 TRP 0.008 0.001 TRP C 339 HIS 0.002 0.001 HIS C 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 726.98 seconds wall clock time: 13 minutes 12.23 seconds (792.23 seconds total)