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/7vvk_32142.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vvk_32142.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=3.3 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vvk_32142.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vvk_32142.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vvk_32142.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vvk_32142.map" } resolution = 3.3 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= 0.010 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 58 5.16 5 C 5720 2.51 5 N 1576 2.21 5 O 1655 1.98 5 H 8871 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 "A TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ASP 113": "OD1" <-> "OD2" Residue "R PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 403": "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: 17880 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3835 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: 5140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5140 Classifications: {'peptide': 340} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "G" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 864 Classifications: {'peptide': 55} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} 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: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 580 Classifications: {'peptide': 34} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 33} Chain: "R" Number of atoms: 5549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 5549 Inner-chain residues flagged as termini: ['pdbres="GLU R 49 "', 'pdbres="GLU R 111 "', 'pdbres="TRP R 118 "', 'pdbres="VAL R 127 "', 'pdbres="VAL R 157 "', 'pdbres="THR R 163 "', 'pdbres="LEU R 174 "', 'pdbres="ARG R 179 "', 'pdbres="SER R 246 "', 'pdbres="TYR R 278 "', 'pdbres="THR R 392 "', 'pdbres="ASP R 398 "'] Classifications: {'peptide': 334} Modifications used: {'COO': 7, 'NH3': 7} Link IDs: {'PTRANS': 6, 'TRANS': 327} Chain breaks: 6 Time building chain proxies: 4.51, per 1000 atoms: 0.25 Number of scatterers: 17880 At special positions: 0 Unit cell: (129.48, 101.814, 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 58 16.00 O 1655 8.00 N 1576 7.00 C 5720 6.00 H 8871 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 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=2.05 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: 6.62 Conformation dependent library (CDL) restraints added in 951.8 milliseconds 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Time building geometry restraints manager: 7.52 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: 8848 1.16 - 1.34: 2954 1.34 - 1.52: 3213 1.52 - 1.70: 2978 1.70 - 1.88: 83 Bond restraints: 18076 Sorted by residual: bond pdb=" N TRP R 118 " pdb=" H TRP R 118 " ideal model delta sigma weight residual 0.860 1.030 -0.170 2.00e-02 2.50e+03 7.27e+01 bond pdb=" N GLU P 19 " pdb=" H GLU P 19 " ideal model delta sigma weight residual 0.860 1.029 -0.169 2.00e-02 2.50e+03 7.17e+01 bond pdb=" NE1 TRP R 112 " pdb=" HE1 TRP R 112 " ideal model delta sigma weight residual 0.860 1.029 -0.169 2.00e-02 2.50e+03 7.14e+01 bond pdb=" N LYS P 13 " pdb=" H LYS P 13 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" N TRP R 474 " pdb=" H TRP R 474 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.77e+01 ... (remaining 18071 not shown) Histogram of bond angle deviations from ideal: 97.28 - 104.66: 89 104.66 - 112.04: 19948 112.04 - 119.42: 4652 119.42 - 126.80: 7644 126.80 - 134.18: 143 Bond angle restraints: 32476 Sorted by residual: angle pdb=" C GLN R 47 " pdb=" N CYS R 48 " pdb=" CA CYS R 48 " ideal model delta sigma weight residual 122.38 113.85 8.53 1.81e+00 3.05e-01 2.22e+01 angle pdb=" C GLU A 360 " pdb=" N ASN A 361 " pdb=" CA ASN A 361 " ideal model delta sigma weight residual 121.54 127.26 -5.72 1.91e+00 2.74e-01 8.98e+00 angle pdb=" CA GLU P 19 " pdb=" C GLU P 19 " pdb=" O GLU P 19 " ideal model delta sigma weight residual 120.90 118.12 2.78 1.03e+00 9.43e-01 7.29e+00 angle pdb=" CA LYS R 34 " pdb=" CB LYS R 34 " pdb=" CG LYS R 34 " ideal model delta sigma weight residual 114.10 119.48 -5.38 2.00e+00 2.50e-01 7.24e+00 angle pdb=" N LEU R 116 " pdb=" CA LEU R 116 " pdb=" C LEU R 116 " ideal model delta sigma weight residual 109.07 113.03 -3.96 1.52e+00 4.33e-01 6.79e+00 ... (remaining 32471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 5688 17.62 - 35.23: 475 35.23 - 52.84: 173 52.84 - 70.46: 40 70.46 - 88.07: 8 Dihedral angle restraints: 6384 sinusoidal: 4516 harmonic: 1868 Sorted by residual: dihedral pdb=" CB CYS R 281 " pdb=" SG CYS R 281 " pdb=" SG CYS R 351 " pdb=" CB CYS R 351 " ideal model delta sinusoidal sigma weight residual 93.00 130.88 -37.88 1 1.00e+01 1.00e-02 2.02e+01 dihedral pdb=" CB CYS R 48 " pdb=" SG CYS R 48 " pdb=" SG CYS R 117 " pdb=" CB CYS R 117 " ideal model delta sinusoidal sigma weight residual 93.00 60.68 32.32 1 1.00e+01 1.00e-02 1.49e+01 dihedral pdb=" CA CYS R 131 " pdb=" C CYS R 131 " pdb=" N PRO R 132 " pdb=" CA PRO R 132 " ideal model delta harmonic sigma weight residual 180.00 -160.95 -19.05 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 6381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1003 0.040 - 0.079: 270 0.079 - 0.119: 71 0.119 - 0.158: 21 0.158 - 0.197: 2 Chirality restraints: 1367 Sorted by residual: chirality pdb=" CB VAL P 31 " pdb=" CA VAL P 31 " pdb=" CG1 VAL P 31 " pdb=" CG2 VAL P 31 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.75e-01 chirality pdb=" CA ILE A 245 " pdb=" N ILE A 245 " pdb=" C ILE A 245 " pdb=" CB ILE A 245 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CA ILE N 51 " pdb=" N ILE N 51 " pdb=" C ILE N 51 " pdb=" CB ILE N 51 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 1364 not shown) Planarity restraints: 2672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP P 23 " 0.016 2.00e-02 2.50e+03 7.07e-03 2.00e+00 pdb=" CG TRP P 23 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP P 23 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP P 23 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP P 23 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP P 23 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP P 23 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 23 " 0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 23 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP P 23 " -0.008 2.00e-02 2.50e+03 pdb=" HD1 TRP P 23 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TRP P 23 " -0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP P 23 " 0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP P 23 " 0.006 2.00e-02 2.50e+03 pdb=" HZ3 TRP P 23 " -0.003 2.00e-02 2.50e+03 pdb=" HH2 TRP P 23 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 365 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO R 366 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO R 366 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 366 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU P 24 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.67e+00 pdb=" C LEU P 24 " -0.022 2.00e-02 2.50e+03 pdb=" O LEU P 24 " 0.008 2.00e-02 2.50e+03 pdb=" N ARG P 25 " 0.008 2.00e-02 2.50e+03 ... (remaining 2669 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 1555 2.13 - 2.75: 31088 2.75 - 3.37: 51310 3.37 - 3.98: 70522 3.98 - 4.60: 103055 Nonbonded interactions: 257530 Sorted by model distance: nonbonded pdb=" OE1 GLN N 123 " pdb=" HG1 THR N 125 " model vdw 1.516 1.850 nonbonded pdb=" HH TYR A 308 " pdb=" OD2 ASP A 333 " model vdw 1.523 1.850 nonbonded pdb=" HE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 1.545 1.850 nonbonded pdb="HE22 GLN R 364 " pdb=" OH TYR R 429 " model vdw 1.560 1.850 nonbonded pdb=" H PHE B 235 " pdb=" O ALA B 240 " model vdw 1.564 1.850 ... (remaining 257525 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=0.48 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: 0.050 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 28.560 Find NCS groups from input model: 0.230 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:24.770 Internal consistency checks: 0.000 Total: 54.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 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 0.072 9205 Z= 0.204 Angle : 0.576 8.528 12457 Z= 0.323 Chirality : 0.041 0.197 1367 Planarity : 0.004 0.032 1591 Dihedral : 12.814 88.074 3326 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.66 % Favored : 94.89 % Rotamer: Outliers : 1.03 % Allowed : 4.12 % Favored : 94.85 % 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: -1.70 (0.23), residues: 1095 helix: -1.21 (0.22), residues: 434 sheet: -0.66 (0.35), residues: 216 loop : -1.06 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 146 TYR 0.010 0.001 TYR A 329 PHE 0.018 0.001 PHE R 335 TRP 0.015 0.001 TRP P 23 HIS 0.007 0.001 HIS P 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 9205 Z= 0.315 Angle : 0.612 5.191 12457 Z= 0.335 Chirality : 0.059 0.217 1367 Planarity : 0.005 0.049 1591 Dihedral : 12.595 86.461 3326 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.03 % Allowed : 4.74 % Favored : 94.23 % 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: -1.42 (0.24), residues: 1095 helix: -0.86 (0.23), residues: 430 sheet: -0.96 (0.35), residues: 204 loop : -0.79 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 146 TYR 0.012 0.002 TYR R 245 PHE 0.018 0.002 PHE R 327 TRP 0.022 0.002 TRP R 298 HIS 0.006 0.002 HIS A 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 9205 Z= 0.305 Angle : 0.578 5.234 12457 Z= 0.314 Chirality : 0.057 0.213 1367 Planarity : 0.005 0.059 1591 Dihedral : 13.041 84.143 3326 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.06 % Allowed : 6.49 % Favored : 91.44 % 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: -1.88 (0.24), residues: 1095 helix: -1.26 (0.23), residues: 416 sheet: -1.16 (0.35), residues: 203 loop : -1.08 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 404 TYR 0.012 0.002 TYR N 80 PHE 0.020 0.002 PHE R 327 TRP 0.015 0.002 TRP R 298 HIS 0.004 0.001 HIS A 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 10.0000 chunk 32 optimal weight: 0.0770 chunk 68 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 12 optimal weight: 0.0370 chunk 93 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.4220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9205 Z= 0.109 Angle : 0.403 4.079 12457 Z= 0.214 Chirality : 0.049 0.176 1367 Planarity : 0.003 0.039 1591 Dihedral : 11.886 89.305 3326 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.65 % Allowed : 4.54 % Favored : 93.81 % 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: -0.95 (0.25), residues: 1095 helix: -0.25 (0.25), residues: 415 sheet: -1.22 (0.34), residues: 221 loop : -0.45 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 67 TYR 0.010 0.001 TYR R 191 PHE 0.009 0.001 PHE R 335 TRP 0.007 0.001 TRP R 329 HIS 0.002 0.001 HIS B 266 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9205 Z= 0.250 Angle : 0.533 5.657 12457 Z= 0.289 Chirality : 0.055 0.200 1367 Planarity : 0.005 0.050 1591 Dihedral : 12.627 84.363 3326 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.06 % Allowed : 6.19 % Favored : 91.75 % 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: -1.57 (0.25), residues: 1095 helix: -0.83 (0.25), residues: 410 sheet: -1.27 (0.35), residues: 209 loop : -0.93 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 379 TYR 0.012 0.002 TYR R 191 PHE 0.017 0.002 PHE R 327 TRP 0.017 0.002 TRP R 298 HIS 0.003 0.001 HIS B 266 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 26 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 33 optimal weight: 0.3980 chunk 7 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 overall best weight: 5.2788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9205 Z= 0.221 Angle : 0.516 4.501 12457 Z= 0.279 Chirality : 0.054 0.185 1367 Planarity : 0.005 0.042 1591 Dihedral : 13.120 86.231 3326 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.78 % Allowed : 7.63 % Favored : 89.59 % 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: 1095 helix: -1.08 (0.25), residues: 410 sheet: -1.33 (0.35), residues: 216 loop : -1.11 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 404 TYR 0.014 0.002 TYR R 191 PHE 0.017 0.002 PHE R 327 TRP 0.012 0.002 TRP R 298 HIS 0.004 0.001 HIS A 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 797.56 seconds wall clock time: 14 minutes 19.41 seconds (859.41 seconds total)