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/6wik_21684.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6wik_21684.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=3.4 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6wik_21684.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6wik_21684.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6wik_21684.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6wik_21684.map" } resolution = 3.4 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= 0.004 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 39 5.16 5 C 4253 2.51 5 N 1077 2.21 5 O 1247 1.98 5 H 6614 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 232": "OD1" <-> "OD2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 308": "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: 13230 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 3225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3225 Inner-chain residues flagged as termini: ['pdbres="ALA C 131 "', 'pdbres="ALA C 132 "', 'pdbres="GLY C 148 "'] Classifications: {'peptide': 213} Modifications used: {'COO': 1, 'NH3': 4} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203} Chain: "D" Number of atoms: 3286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3286 Inner-chain residues flagged as termini: ['pdbres="THR D 142 "', 'pdbres="ALA D 143 "'] Classifications: {'peptide': 219} Modifications used: {'COO': 1, 'NH3': 3} Link IDs: {'PTRANS': 14, 'TRANS': 204} Chain: "A" Number of atoms: 6719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 6719 Inner-chain residues flagged as termini: ['pdbres="ALA A 237 "', 'pdbres="ALA A 289 "', 'pdbres="GLY A 395 "', 'pdbres="ILE A 453 "'] Classifications: {'peptide': 427} Modifications used: {'COO': 3, 'NH3': 3} Link IDs: {'PTRANS': 8, 'TRANS': 418} Chain breaks: 2 Time building chain proxies: 2.79, per 1000 atoms: 0.21 Number of scatterers: 13230 At special positions: 0 Unit cell: (129.47, 117.7, 85.6, 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 39 16.00 O 1247 8.00 N 1077 7.00 C 4253 6.00 H 6614 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " distance=2.03 Simple disulfide: pdb=" SG CYS D 165 " - pdb=" SG CYS D 220 " 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: 4.21 Conformation dependent library (CDL) restraints added in 770.3 milliseconds 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. Time building geometry restraints manager: 4.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.97 - 1.24: 7507 1.24 - 1.51: 3191 1.51 - 1.78: 2617 1.78 - 2.05: 63 2.05 - 2.32: 2 Bond restraints: 13380 Sorted by residual: bond pdb=" CD1 TYR C 160 " pdb=" CE1 TYR C 160 " ideal model delta sigma weight residual 1.382 2.321 -0.939 3.00e-02 1.11e+03 9.80e+02 bond pdb=" CD2 TYR C 160 " pdb=" CE2 TYR C 160 " ideal model delta sigma weight residual 1.382 2.221 -0.839 3.00e-02 1.11e+03 7.81e+02 bond pdb=" CE1 TYR C 160 " pdb=" CZ TYR C 160 " ideal model delta sigma weight residual 1.378 1.964 -0.586 2.40e-02 1.74e+03 5.97e+02 bond pdb=" CE2 TYR C 160 " pdb=" CZ TYR C 160 " ideal model delta sigma weight residual 1.378 1.865 -0.487 2.40e-02 1.74e+03 4.12e+02 bond pdb=" N ALA C 131 " pdb=" CA ALA C 131 " ideal model delta sigma weight residual 1.459 1.710 -0.251 1.27e-02 6.20e+03 3.89e+02 ... (remaining 13375 not shown) Histogram of bond angle deviations from ideal: 55.91 - 74.88: 1 74.88 - 93.84: 7 93.84 - 112.81: 15788 112.81 - 131.77: 8339 131.77 - 150.73: 23 Bond angle restraints: 24158 Sorted by residual: angle pdb=" C GLU C 130 " pdb=" N ALA C 131 " pdb=" CA ALA C 131 " ideal model delta sigma weight residual 123.11 150.73 -27.62 1.42e+00 4.96e-01 3.78e+02 angle pdb=" CB ALA C 131 " pdb=" CA ALA C 131 " pdb=" HA ALA C 131 " ideal model delta sigma weight residual 109.00 55.91 53.09 3.00e+00 1.11e-01 3.13e+02 angle pdb=" CG2 THR D 142 " pdb=" CB THR D 142 " pdb=" HB THR D 142 " ideal model delta sigma weight residual 108.00 75.17 32.83 3.00e+00 1.11e-01 1.20e+02 angle pdb=" H2 ALA C 131 " pdb=" N ALA C 131 " pdb=" H3 ALA C 131 " ideal model delta sigma weight residual 109.47 79.24 30.23 3.00e+00 1.11e-01 1.02e+02 angle pdb=" H1 ALA C 131 " pdb=" N ALA C 131 " pdb=" H2 ALA C 131 " ideal model delta sigma weight residual 109.47 79.59 29.88 3.00e+00 1.11e-01 9.92e+01 ... (remaining 24153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 4118 16.87 - 33.75: 384 33.75 - 50.62: 167 50.62 - 67.49: 70 67.49 - 84.37: 10 Dihedral angle restraints: 4749 sinusoidal: 3376 harmonic: 1373 Sorted by residual: dihedral pdb=" CB CYS D 165 " pdb=" SG CYS D 165 " pdb=" SG CYS D 220 " pdb=" CB CYS D 220 " ideal model delta sinusoidal sigma weight residual -86.00 -134.77 48.77 1 1.00e+01 1.00e-02 3.27e+01 dihedral pdb=" CA TRP D 213 " pdb=" C TRP D 213 " pdb=" N PRO D 214 " pdb=" CA PRO D 214 " ideal model delta harmonic sigma weight residual -180.00 -152.32 -27.68 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA PHE D 171 " pdb=" C PHE D 171 " pdb=" N PRO D 172 " pdb=" CA PRO D 172 " ideal model delta harmonic sigma weight residual 180.00 158.41 21.59 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 4746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.234: 1071 0.234 - 0.468: 2 0.468 - 0.702: 0 0.702 - 0.936: 0 0.936 - 1.170: 1 Chirality restraints: 1074 Sorted by residual: chirality pdb=" CB THR D 142 " pdb=" CA THR D 142 " pdb=" OG1 THR D 142 " pdb=" CG2 THR D 142 " both_signs ideal model delta sigma weight residual False 2.55 1.38 1.17 2.00e-01 2.50e+01 3.42e+01 chirality pdb=" CA ALA C 131 " pdb=" N ALA C 131 " pdb=" C ALA C 131 " pdb=" CB ALA C 131 " both_signs ideal model delta sigma weight residual False 2.54 2.08 0.46 2.00e-01 2.50e+01 5.22e+00 chirality pdb=" CA PRO D 144 " pdb=" N PRO D 144 " pdb=" C PRO D 144 " pdb=" CB PRO D 144 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 1071 not shown) Planarity restraints: 1963 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 171 " 0.118 5.00e-02 4.00e+02 1.82e-01 5.33e+01 pdb=" N PRO D 172 " -0.316 5.00e-02 4.00e+02 pdb=" CA PRO D 172 " 0.105 5.00e-02 4.00e+02 pdb=" CD PRO D 172 " 0.092 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 143 " 0.106 5.00e-02 4.00e+02 1.60e-01 4.08e+01 pdb=" N PRO D 144 " -0.276 5.00e-02 4.00e+02 pdb=" CA PRO D 144 " 0.088 5.00e-02 4.00e+02 pdb=" CD PRO D 144 " 0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 147 " 0.085 5.00e-02 4.00e+02 1.30e-01 2.68e+01 pdb=" N PRO D 148 " -0.224 5.00e-02 4.00e+02 pdb=" CA PRO D 148 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO D 148 " 0.067 5.00e-02 4.00e+02 ... (remaining 1960 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.92: 375 1.92 - 2.59: 13871 2.59 - 3.26: 41024 3.26 - 3.93: 51891 3.93 - 4.60: 77652 Nonbonded interactions: 184813 Sorted by model distance: nonbonded pdb=" HA ALA C 131 " pdb=" HB3 ALA C 131 " model vdw 1.253 1.952 nonbonded pdb=" O THR D 142 " pdb=" H2 ALA D 143 " model vdw 1.342 1.960 nonbonded pdb=" O TRP D 213 " pdb=" H SER D 215 " model vdw 1.352 1.850 nonbonded pdb=" O GLU C 130 " pdb=" H2 ALA C 131 " model vdw 1.398 1.960 nonbonded pdb=" HZ3 LYS D 140 " pdb=" O SER D 197 " model vdw 1.418 1.850 ... (remaining 184808 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=0.46 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: 0.040 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: 0.090 Extract box with map and model: 0.500 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 19.240 Find NCS groups from input model: 0.140 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:17.050 Internal consistency checks: 0.000 Total: 37.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 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 : 0.020 0.939 6766 Z= 0.977 Angle : 0.926 27.623 9214 Z= 0.515 Chirality : 0.059 1.170 1074 Planarity : 0.011 0.182 1145 Dihedral : 13.250 84.365 2375 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 2.71 % Allowed : 8.83 % Favored : 88.46 % Rotamer: Outliers : 2.60 % Allowed : 8.88 % Favored : 88.52 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.25), residues: 849 helix: -1.30 (0.24), residues: 359 sheet: -1.75 (0.34), residues: 190 loop : -3.55 (0.31), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 59 TYR 0.043 0.002 TYR C 160 PHE 0.026 0.002 PHE D 171 TRP 0.022 0.002 TRP D 179 HIS 0.019 0.003 HIS D 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 30.0000 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.977 6766 Z= 0.985 Angle : 0.763 25.897 9214 Z= 0.428 Chirality : 0.080 1.563 1074 Planarity : 0.008 0.147 1145 Dihedral : 12.497 83.893 2375 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.94 % Allowed : 7.77 % Favored : 91.28 % Rotamer: Outliers : 2.32 % Allowed : 6.83 % Favored : 90.85 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % 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: -2.46 (0.27), residues: 849 helix: -0.71 (0.25), residues: 362 sheet: -1.16 (0.35), residues: 194 loop : -3.03 (0.33), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 88 TYR 0.039 0.002 TYR C 160 PHE 0.015 0.002 PHE D 126 TRP 0.011 0.001 TRP D 213 HIS 0.007 0.002 HIS D 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 8.9990 chunk 64 optimal weight: 0.0870 chunk 17 optimal weight: 30.0000 chunk 36 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 79 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 overall best weight: 6.0166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.968 6766 Z= 0.964 Angle : 0.685 25.530 9214 Z= 0.390 Chirality : 0.080 1.594 1074 Planarity : 0.007 0.140 1145 Dihedral : 11.728 89.129 2375 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.82 % Allowed : 8.48 % Favored : 90.69 % Rotamer: Outliers : 1.91 % Allowed : 6.69 % Favored : 91.39 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % 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: -1.59 (0.29), residues: 849 helix: 0.05 (0.26), residues: 363 sheet: -0.93 (0.36), residues: 202 loop : -2.49 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 467 TYR 0.040 0.002 TYR C 160 PHE 0.009 0.001 PHE A 392 TRP 0.014 0.001 TRP D 213 HIS 0.006 0.001 HIS D 224 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 12 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 60 optimal weight: 0.6980 chunk 71 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 overall best weight: 4.4986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.918 6766 Z= 0.957 Angle : 0.646 24.707 9214 Z= 0.369 Chirality : 0.080 1.576 1074 Planarity : 0.007 0.134 1145 Dihedral : 11.256 88.000 2375 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.59 % Allowed : 4.48 % Favored : 94.94 % Rotamer: Outliers : 1.78 % Allowed : 6.42 % Favored : 91.80 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % 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: -1.11 (0.29), residues: 849 helix: 0.53 (0.26), residues: 363 sheet: -0.75 (0.36), residues: 206 loop : -2.35 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 167 TYR 0.038 0.001 TYR C 160 PHE 0.010 0.001 PHE C 159 TRP 0.010 0.001 TRP D 179 HIS 0.004 0.001 HIS D 224 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.942 6766 Z= 0.978 Angle : 0.677 24.777 9214 Z= 0.390 Chirality : 0.080 1.564 1074 Planarity : 0.006 0.136 1145 Dihedral : 11.280 81.868 2375 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.71 % Allowed : 8.01 % Favored : 91.28 % Rotamer: Outliers : 1.91 % Allowed : 6.97 % Favored : 91.12 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -1.44 (0.28), residues: 849 helix: 0.10 (0.26), residues: 363 sheet: -0.76 (0.36), residues: 206 loop : -2.42 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 467 TYR 0.040 0.002 TYR C 160 PHE 0.010 0.001 PHE D 126 TRP 0.012 0.001 TRP D 213 HIS 0.004 0.001 HIS C 218 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 42 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.935 6766 Z= 0.952 Angle : 0.620 24.555 9214 Z= 0.354 Chirality : 0.079 1.575 1074 Planarity : 0.006 0.133 1145 Dihedral : 10.894 78.677 2375 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.65 % Favored : 93.76 % Rotamer: Outliers : 1.91 % Allowed : 6.28 % Favored : 91.80 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.83 (0.29), residues: 849 helix: 0.81 (0.26), residues: 363 sheet: -0.63 (0.36), residues: 204 loop : -2.25 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 467 TYR 0.038 0.001 TYR C 160 PHE 0.008 0.001 PHE A 392 TRP 0.012 0.001 TRP D 179 HIS 0.004 0.001 HIS A 536 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 614.77 seconds wall clock time: 11 minutes 3.44 seconds (663.44 seconds total)