Starting phenix.real_space_refine on Sun May 19 16:31:30 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6y9w_10739.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6y9w_10739.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=4.1 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6y9w_10739.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6y9w_10739.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6y9w_10739.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6y9w_10739.pdb" } resolution = 4.1 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= 0.006 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 26 5.16 5 C 2162 2.51 5 N 598 2.21 5 O 649 1.98 5 H 3432 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6867 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2265 Classifications: {'peptide': 146} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 134} Chain: "B" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3432 Classifications: {'peptide': 220} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 202} Chain: "N" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1170 Classifications: {'peptide': 74} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 4, 'TRANS': 69} Time building chain proxies: 1.93, per 1000 atoms: 0.28 Number of scatterers: 6867 At special positions: 0 Unit cell: (108.12, 114.48, 87.98, 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 26 16.00 O 649 8.00 N 598 7.00 C 2162 6.00 H 3432 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 218 " distance=2.04 Simple disulfide: pdb=" SG CYS N 198 " - pdb=" SG CYS N 218 " distance=2.04 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: 2.56 Conformation dependent library (CDL) restraints added in 321.3 milliseconds 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 3432 1.15 - 1.32: 591 1.32 - 1.48: 1345 1.48 - 1.65: 1526 1.65 - 1.82: 48 Bond restraints: 6942 Sorted by residual: bond pdb=" N VAL B 27 " pdb=" H VAL B 27 " ideal model delta sigma weight residual 0.860 1.027 -0.167 2.00e-02 2.50e+03 7.01e+01 bond pdb=" N GLU B 28 " pdb=" H GLU B 28 " ideal model delta sigma weight residual 0.860 1.026 -0.166 2.00e-02 2.50e+03 6.91e+01 bond pdb=" N ALA B 47 " pdb=" H ALA B 47 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.68e+01 bond pdb=" N GLU B 45 " pdb=" H GLU B 45 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.68e+01 bond pdb=" N HIS A 84 " pdb=" H HIS A 84 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.66e+01 ... (remaining 6937 not shown) Histogram of bond angle deviations from ideal: 100.30 - 107.03: 209 107.03 - 113.77: 8402 113.77 - 120.50: 2190 120.50 - 127.23: 1760 127.23 - 133.96: 58 Bond angle restraints: 12619 Sorted by residual: angle pdb=" C ALA A 31 " pdb=" CA ALA A 31 " pdb=" CB ALA A 31 " ideal model delta sigma weight residual 117.23 111.34 5.89 1.36e+00 5.41e-01 1.88e+01 angle pdb=" C ILE B 6 " pdb=" N GLN B 7 " pdb=" CA GLN B 7 " ideal model delta sigma weight residual 121.70 126.75 -5.05 1.80e+00 3.09e-01 7.88e+00 angle pdb=" CA ALA A 31 " pdb=" C ALA A 31 " pdb=" N PHE A 32 " ideal model delta sigma weight residual 119.98 117.99 1.99 8.50e-01 1.38e+00 5.50e+00 angle pdb=" N VAL A 83 " pdb=" CA VAL A 83 " pdb=" C VAL A 83 " ideal model delta sigma weight residual 112.29 110.14 2.15 9.40e-01 1.13e+00 5.22e+00 angle pdb=" C ILE B 37 " pdb=" N PRO B 38 " pdb=" CA PRO B 38 " ideal model delta sigma weight residual 118.97 120.68 -1.71 1.04e+00 9.25e-01 2.72e+00 ... (remaining 12614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.62: 2096 14.62 - 29.25: 218 29.25 - 43.87: 95 43.87 - 58.49: 39 58.49 - 73.11: 6 Dihedral angle restraints: 2454 sinusoidal: 1853 harmonic: 601 Sorted by residual: dihedral pdb=" CB CYS B 198 " pdb=" SG CYS B 198 " pdb=" SG CYS B 218 " pdb=" CB CYS B 218 " ideal model delta sinusoidal sigma weight residual -86.00 -110.81 24.81 1 1.00e+01 1.00e-02 8.86e+00 dihedral pdb=" CB CYS N 198 " pdb=" SG CYS N 198 " pdb=" SG CYS N 218 " pdb=" CB CYS N 218 " ideal model delta sinusoidal sigma weight residual -86.00 -110.80 24.80 1 1.00e+01 1.00e-02 8.85e+00 dihedral pdb=" CB MET N 215 " pdb=" CG MET N 215 " pdb=" SD MET N 215 " pdb=" CE MET N 215 " ideal model delta sinusoidal sigma weight residual -180.00 -131.99 -48.01 3 1.50e+01 4.44e-03 8.58e+00 ... (remaining 2451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 348 0.028 - 0.056: 124 0.056 - 0.084: 36 0.084 - 0.112: 21 0.112 - 0.139: 5 Chirality restraints: 534 Sorted by residual: chirality pdb=" CA ILE B 124 " pdb=" N ILE B 124 " pdb=" C ILE B 124 " pdb=" CB ILE B 124 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 chirality pdb=" CA ILE A 2 " pdb=" N ILE A 2 " pdb=" C ILE A 2 " pdb=" CB ILE A 2 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ILE A 124 " pdb=" N ILE A 124 " pdb=" C ILE A 124 " pdb=" CB ILE A 124 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 531 not shown) Planarity restraints: 1031 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 37 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.65e+00 pdb=" N PRO A 38 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 38 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 38 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 33 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO A 34 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 34 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 34 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 37 " 0.018 5.00e-02 4.00e+02 2.79e-02 1.24e+00 pdb=" N PRO B 38 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 38 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 38 " 0.015 5.00e-02 4.00e+02 ... (remaining 1028 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 506 2.13 - 2.74: 11248 2.74 - 3.36: 19045 3.36 - 3.98: 23772 3.98 - 4.60: 35522 Nonbonded interactions: 90093 Sorted by model distance: nonbonded pdb=" OE1 GLN B 179 " pdb="HD21 ASN B 183 " model vdw 1.507 1.850 nonbonded pdb=" OE1 GLN N 179 " pdb="HD21 ASN N 183 " model vdw 1.509 1.850 nonbonded pdb=" O ASN B 195 " pdb=" H LYS B 199 " model vdw 1.537 1.850 nonbonded pdb=" O ASN N 195 " pdb=" H LYS N 199 " model vdw 1.537 1.850 nonbonded pdb=" O SER A 44 " pdb=" HZ3 LYS A 131 " model vdw 1.593 1.850 ... (remaining 90088 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=0.50 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: 0.070 Extract box with map and model: 0.390 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.190 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:7.410 Internal consistency checks: 0.000 Total: 20.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 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 0.024 3510 Z= 0.115 Angle : 0.448 5.894 4772 Z= 0.241 Chirality : 0.037 0.139 534 Planarity : 0.004 0.048 625 Dihedral : 11.751 73.114 1334 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.80 % Allowed : 2.67 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.38), residues: 434 helix: -0.08 (0.30), residues: 280 sheet: -3.20 (0.75), residues: 9 loop : -0.77 (0.48), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 18 TYR 0.006 0.001 TYR B 130 PHE 0.004 0.001 PHE A 32 TRP 0.006 0.001 TRP N 184 HIS 0.002 0.001 HIS A 84 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3510 Z= 0.168 Angle : 0.485 4.495 4772 Z= 0.255 Chirality : 0.044 0.160 534 Planarity : 0.004 0.033 625 Dihedral : 10.492 53.680 1334 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.80 % Allowed : 2.94 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.25 % 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: 0.86 (0.39), residues: 434 helix: 1.01 (0.31), residues: 276 sheet: -2.28 (1.16), residues: 9 loop : 0.14 (0.51), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 18 TYR 0.006 0.001 TYR A 130 PHE 0.006 0.001 PHE A 40 TRP 0.009 0.001 TRP N 184 HIS 0.003 0.001 HIS B 12 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 13 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 8 optimal weight: 0.9980 chunk 18 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 34 optimal weight: 30.0000 chunk 38 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 overall best weight: 5.5588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3510 Z= 0.135 Angle : 0.432 4.882 4772 Z= 0.211 Chirality : 0.042 0.173 534 Planarity : 0.004 0.036 625 Dihedral : 9.503 59.522 1334 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.80 % Allowed : 3.48 % Favored : 95.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.25 % 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: 1.94 (0.40), residues: 434 helix: 1.80 (0.31), residues: 275 sheet: -1.87 (1.22), residues: 9 loop : 0.69 (0.53), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 143 TYR 0.006 0.001 TYR B 130 PHE 0.007 0.001 PHE B 40 TRP 0.005 0.001 TRP A 80 HIS 0.001 0.000 HIS B 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 6 optimal weight: 30.0000 chunk 4 optimal weight: 30.0000 chunk 21 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 35 optimal weight: 30.0000 chunk 22 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3510 Z= 0.132 Angle : 0.433 4.679 4772 Z= 0.220 Chirality : 0.041 0.162 534 Planarity : 0.004 0.032 625 Dihedral : 9.252 59.102 1334 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.80 % Allowed : 3.48 % Favored : 95.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.25 % 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: 1.86 (0.40), residues: 434 helix: 1.71 (0.30), residues: 272 sheet: -1.83 (1.17), residues: 9 loop : 0.75 (0.52), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 18 TYR 0.006 0.001 TYR B 130 PHE 0.004 0.001 PHE A 32 TRP 0.006 0.001 TRP N 184 HIS 0.002 0.001 HIS B 12 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 5 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 42 optimal weight: 9.9990 chunk 40 optimal weight: 30.0000 overall best weight: 11.5994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3510 Z= 0.216 Angle : 0.543 4.686 4772 Z= 0.292 Chirality : 0.044 0.164 534 Planarity : 0.005 0.035 625 Dihedral : 10.395 54.594 1334 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.41 % Allowed : 5.61 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.25 % 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 (0.38), residues: 434 helix: 0.59 (0.30), residues: 261 sheet: -2.66 (0.97), residues: 9 loop : 0.59 (0.47), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 154 TYR 0.007 0.002 TYR B 164 PHE 0.006 0.001 PHE B 161 TRP 0.007 0.001 TRP B 184 HIS 0.003 0.001 HIS B 84 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 868 Ramachandran restraints generated. 434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 0 optimal weight: 30.0000 chunk 39 optimal weight: 7.9990 chunk 31 optimal weight: 30.0000 chunk 21 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 9 optimal weight: 40.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3510 Z= 0.133 Angle : 0.434 4.731 4772 Z= 0.218 Chirality : 0.042 0.163 534 Planarity : 0.004 0.035 625 Dihedral : 9.809 62.863 1334 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.14 % Allowed : 5.35 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.25 % 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: 0.88 (0.38), residues: 434 helix: 0.91 (0.30), residues: 262 sheet: -2.47 (0.99), residues: 9 loop : 0.45 (0.47), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 18 TYR 0.006 0.001 TYR A 130 PHE 0.004 0.001 PHE B 161 TRP 0.003 0.001 TRP N 184 HIS 0.002 0.001 HIS A 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 482.98 seconds wall clock time: 8 minutes 38.23 seconds (518.23 seconds total)