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/7vvn_32145.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vvn_32145.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=3.8 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vvn_32145.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vvn_32145.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vvn_32145.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vvn_32145.map" } resolution = 3.8 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= 0.001 sd= 0.008 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 56 5.16 5 C 5549 2.51 5 N 1528 2.21 5 O 1595 1.98 5 H 8610 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ASP 30": "OD1" <-> "OD2" Residue "P PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 443": "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: 17338 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3832 Inner-chain residues flagged as termini: ['pdbres="ILE A 62 "', 'pdbres="GLY A 206 "'] Classifications: {'peptide': 230} Modifications used: {'COO': 2, 'NH3': 2} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Chain: "B" Number of atoms: 5107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5107 Classifications: {'peptide': 338} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 874 Classifications: {'peptide': 56} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "N" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1912 Classifications: {'peptide': 128} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "P" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 578 Classifications: {'peptide': 34} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 33} Chain: "R" Number of atoms: 5035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 5035 Inner-chain residues flagged as termini: ['pdbres="GLU R 49 "', 'pdbres="GLU R 111 "', 'pdbres="CYS R 117 "', 'pdbres="VAL R 129 "', 'pdbres="ILE R 135 "', 'pdbres="PHE R 138 "', 'pdbres="ARG R 146 "', 'pdbres="ARG R 162 "', 'pdbres="LEU R 174 "', 'pdbres="ARG R 181 "', 'pdbres="LEU R 244 "', 'pdbres="TYR R 278 "', 'pdbres="TRP R 352 "', 'pdbres="TRP R 361 "', 'pdbres="THR R 392 "', 'pdbres="ARG R 400 "', 'pdbres="THR R 430 "', 'pdbres="LEU R 436 "'] Classifications: {'peptide': 300} Modifications used: {'COO': 10, 'NH3': 10} Link IDs: {'PTRANS': 6, 'TRANS': 293} Chain breaks: 9 Time building chain proxies: 4.74, per 1000 atoms: 0.27 Number of scatterers: 17338 At special positions: 0 Unit cell: (123.947, 108.454, 117.307, 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 56 16.00 O 1595 8.00 N 1528 7.00 C 5549 6.00 H 8610 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.02 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " 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: 6.54 Conformation dependent library (CDL) restraints added in 821.9 milliseconds 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. Time building geometry restraints manager: 7.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.16: 8590 1.16 - 1.34: 2860 1.34 - 1.52: 3548 1.52 - 1.70: 2447 1.70 - 1.89: 80 Bond restraints: 17525 Sorted by residual: bond pdb=" NE ARG R 282 " pdb=" HE ARG R 282 " ideal model delta sigma weight residual 0.860 1.042 -0.182 2.00e-02 2.50e+03 8.27e+01 bond pdb=" NH2 ARG R 181 " pdb="HH21 ARG R 181 " ideal model delta sigma weight residual 0.860 1.030 -0.170 2.00e-02 2.50e+03 7.23e+01 bond pdb=" N ALA R 426 " pdb=" H ALA R 426 " ideal model delta sigma weight residual 0.860 1.030 -0.170 2.00e-02 2.50e+03 7.19e+01 bond pdb=" N PHE R 424 " pdb=" H PHE R 424 " ideal model delta sigma weight residual 0.860 1.026 -0.166 2.00e-02 2.50e+03 6.92e+01 bond pdb=" N PHE R 315 " pdb=" H PHE R 315 " ideal model delta sigma weight residual 0.860 1.026 -0.166 2.00e-02 2.50e+03 6.89e+01 ... (remaining 17520 not shown) Histogram of bond angle deviations from ideal: 96.44 - 104.04: 82 104.04 - 111.64: 19081 111.64 - 119.24: 4624 119.24 - 126.84: 7576 126.84 - 134.44: 135 Bond angle restraints: 31498 Sorted by residual: angle pdb=" N VAL R 455 " pdb=" CA VAL R 455 " pdb=" C VAL R 455 " ideal model delta sigma weight residual 112.12 106.28 5.84 8.40e-01 1.42e+00 4.83e+01 angle pdb=" N ILE R 222 " pdb=" CA ILE R 222 " pdb=" C ILE R 222 " ideal model delta sigma weight residual 112.12 107.41 4.71 8.40e-01 1.42e+00 3.14e+01 angle pdb=" C GLN R 47 " pdb=" N CYS R 48 " pdb=" CA CYS R 48 " ideal model delta sigma weight residual 122.38 114.15 8.23 1.81e+00 3.05e-01 2.07e+01 angle pdb=" C ALA R 347 " pdb=" N ASN R 348 " pdb=" CA ASN R 348 " ideal model delta sigma weight residual 121.54 127.80 -6.26 1.91e+00 2.74e-01 1.07e+01 angle pdb=" C GLU R 317 " pdb=" N LYS R 318 " pdb=" CA LYS R 318 " ideal model delta sigma weight residual 121.54 127.07 -5.53 1.91e+00 2.74e-01 8.38e+00 ... (remaining 31493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5404 17.93 - 35.86: 559 35.86 - 53.79: 168 53.79 - 71.72: 40 71.72 - 89.65: 8 Dihedral angle restraints: 6179 sinusoidal: 4377 harmonic: 1802 Sorted by residual: dihedral pdb=" CA ASN R 220 " pdb=" C ASN R 220 " pdb=" N TYR R 221 " pdb=" CA TYR R 221 " ideal model delta harmonic sigma weight residual 180.00 159.43 20.57 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 159.43 20.57 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA TYR R 421 " pdb=" C TYR R 421 " pdb=" N ILE R 422 " pdb=" CA ILE R 422 " ideal model delta harmonic sigma weight residual -180.00 -160.90 -19.10 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 6176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 847 0.032 - 0.065: 346 0.065 - 0.097: 86 0.097 - 0.129: 41 0.129 - 0.161: 8 Chirality restraints: 1328 Sorted by residual: chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA ILE B 123 " pdb=" N ILE B 123 " pdb=" C ILE B 123 " pdb=" CB ILE B 123 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 1325 not shown) Planarity restraints: 2582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 343 " 0.200 9.50e-02 1.11e+02 8.21e-02 5.39e+00 pdb=" NE ARG R 343 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG R 343 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG R 343 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG R 343 " 0.004 2.00e-02 2.50e+03 pdb="HH21 ARG R 343 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 315 " 0.018 2.00e-02 2.50e+03 1.13e-02 3.82e+00 pdb=" CG PHE R 315 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE R 315 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE R 315 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE R 315 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE R 315 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE R 315 " 0.008 2.00e-02 2.50e+03 pdb=" HD1 PHE R 315 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE R 315 " -0.005 2.00e-02 2.50e+03 pdb=" HE1 PHE R 315 " -0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE R 315 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE R 315 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS R 48 " 0.011 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" N GLU R 49 " -0.032 2.00e-02 2.50e+03 pdb=" CA GLU R 49 " 0.008 2.00e-02 2.50e+03 pdb=" H GLU R 49 " 0.013 2.00e-02 2.50e+03 ... (remaining 2579 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 1184 2.08 - 2.71: 26832 2.71 - 3.34: 50263 3.34 - 3.97: 67135 3.97 - 4.60: 98526 Nonbonded interactions: 243940 Sorted by model distance: nonbonded pdb=" O GLN B 75 " pdb=" HG SER B 98 " model vdw 1.452 1.850 nonbonded pdb=" HG1 THR B 29 " pdb=" OE1 GLN B 32 " model vdw 1.459 1.850 nonbonded pdb=" O SER N 30 " pdb="HE22 GLN N 53 " model vdw 1.459 1.850 nonbonded pdb=" O VAL R 326 " pdb=" H GLY R 330 " model vdw 1.497 1.850 nonbonded pdb=" O VAL R 384 " pdb=" HG1 THR R 387 " model vdw 1.533 1.850 ... (remaining 243935 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: 0.020 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: 0.170 Extract box with map and model: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 26.330 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:23.960 Internal consistency checks: 0.000 Total: 51.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 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 : 0.004 0.078 8915 Z= 0.233 Angle : 0.641 8.231 12061 Z= 0.362 Chirality : 0.041 0.161 1328 Planarity : 0.005 0.088 1539 Dihedral : 13.845 86.012 3220 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.26 % Favored : 93.55 % Rotamer: Outliers : 1.28 % Allowed : 7.58 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.89 (0.22), residues: 1054 helix: -1.78 (0.21), residues: 410 sheet: -1.87 (0.35), residues: 192 loop : -1.90 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 343 TYR 0.017 0.001 TYR R 421 PHE 0.028 0.002 PHE R 315 TRP 0.027 0.002 TRP R 352 HIS 0.005 0.001 HIS R 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8915 Z= 0.271 Angle : 0.567 5.899 12061 Z= 0.309 Chirality : 0.052 0.251 1328 Planarity : 0.004 0.036 1539 Dihedral : 13.097 85.843 3220 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.89 % Favored : 96.02 % Rotamer: Outliers : 1.07 % Allowed : 7.58 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.06 (0.24), residues: 1054 helix: -0.69 (0.24), residues: 402 sheet: -1.99 (0.33), residues: 210 loop : -1.52 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 68 TYR 0.014 0.002 TYR N 95 PHE 0.022 0.002 PHE R 315 TRP 0.019 0.002 TRP R 352 HIS 0.004 0.001 HIS A 347 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 chunk 102 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8915 Z= 0.352 Angle : 0.628 6.931 12061 Z= 0.342 Chirality : 0.056 0.359 1328 Planarity : 0.005 0.034 1539 Dihedral : 13.718 88.093 3220 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.35 % Allowed : 9.71 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.41 (0.24), residues: 1054 helix: -1.15 (0.24), residues: 401 sheet: -2.14 (0.33), residues: 222 loop : -1.51 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 181 TYR 0.017 0.002 TYR N 95 PHE 0.018 0.002 PHE R 454 TRP 0.013 0.002 TRP R 352 HIS 0.005 0.001 HIS A 347 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 68 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8915 Z= 0.164 Angle : 0.456 4.763 12061 Z= 0.245 Chirality : 0.049 0.255 1328 Planarity : 0.003 0.030 1539 Dihedral : 13.023 85.277 3220 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.92 % Allowed : 8.32 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1054 helix: -0.65 (0.26), residues: 400 sheet: -1.96 (0.33), residues: 214 loop : -1.19 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 256 TYR 0.010 0.001 TYR N 95 PHE 0.014 0.001 PHE R 315 TRP 0.010 0.001 TRP A 271 HIS 0.004 0.001 HIS A 347 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 60 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 81 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8915 Z= 0.215 Angle : 0.490 5.540 12061 Z= 0.265 Chirality : 0.050 0.283 1328 Planarity : 0.004 0.031 1539 Dihedral : 13.020 87.903 3220 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.03 % Allowed : 8.32 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.91 (0.25), residues: 1054 helix: -0.75 (0.25), residues: 397 sheet: -2.03 (0.33), residues: 207 loop : -1.17 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 256 TYR 0.013 0.001 TYR N 95 PHE 0.015 0.001 PHE R 454 TRP 0.011 0.002 TRP R 352 HIS 0.004 0.001 HIS A 347 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 56 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8915 Z= 0.301 Angle : 0.604 6.941 12061 Z= 0.329 Chirality : 0.055 0.338 1328 Planarity : 0.005 0.038 1539 Dihedral : 13.895 88.387 3220 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 3.74 % Allowed : 9.61 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.60 (0.24), residues: 1054 helix: -1.34 (0.25), residues: 399 sheet: -2.29 (0.33), residues: 210 loop : -1.58 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 256 TYR 0.017 0.002 TYR N 95 PHE 0.018 0.002 PHE R 454 TRP 0.014 0.002 TRP A 271 HIS 0.005 0.001 HIS A 347 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 738.77 seconds wall clock time: 13 minutes 19.87 seconds (799.87 seconds total)