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/8cl2_16710.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8cl2_16710.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=3.45 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8cl2_16710.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8cl2_16710.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8cl2_16710.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8cl2_16710.pdb" } resolution = 3.45 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= 0.039 sd= 0.187 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1393 atoms to isotropic. 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 23 5.16 5 C 1710 2.51 5 N 469 2.21 5 O 519 1.98 5 H 2719 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: 5440 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1053 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain: "C" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1029 Classifications: {'peptide': 65} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "A" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3358 Inner-chain residues flagged as termini: ['pdbres="HIS A 87 "', 'pdbres="MET A 96 "'] Classifications: {'peptide': 213} Modifications used: {'COO': 2, 'NH2': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Time building chain proxies: 1.26, per 1000 atoms: 0.23 Number of scatterers: 5440 At special positions: 0 Unit cell: (87.42, 74.4, 97.65, 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 23 16.00 O 519 8.00 N 469 7.00 C 1710 6.00 H 2719 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.16 Conformation dependent library (CDL) restraints added in 313.9 milliseconds 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. Time building geometry restraints manager: 2.46 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: 2713 1.15 - 1.31: 478 1.31 - 1.48: 1048 1.48 - 1.65: 1215 1.65 - 1.81: 40 Bond restraints: 5494 Sorted by residual: bond pdb=" ND1 HIS A 87 " pdb=" HD1 HIS A 87 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.81e+01 bond pdb=" N GLU A 98 " pdb=" H GLU A 98 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.72e+01 bond pdb=" N THR A 186 " pdb=" H THR A 186 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" N ALA A 42 " pdb=" H ALA A 42 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" N HIS A 87 " pdb=" H HIS A 87 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.66e+01 ... (remaining 5489 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.27: 116 106.27 - 113.19: 6567 113.19 - 120.12: 1655 120.12 - 127.04: 1592 127.04 - 133.96: 42 Bond angle restraints: 9972 Sorted by residual: angle pdb=" C VAL A 59 " pdb=" N GLY A 60 " pdb=" CA GLY A 60 " ideal model delta sigma weight residual 119.92 122.04 -2.12 9.60e-01 1.09e+00 4.88e+00 angle pdb=" C ARG A 97 " pdb=" N GLU A 98 " pdb=" CA GLU A 98 " ideal model delta sigma weight residual 120.49 117.97 2.52 1.42e+00 4.96e-01 3.15e+00 angle pdb=" N GLY A 61 " pdb=" CA GLY A 61 " pdb=" C GLY A 61 " ideal model delta sigma weight residual 113.18 109.26 3.92 2.37e+00 1.78e-01 2.74e+00 angle pdb=" C PRO A 38 " pdb=" CA PRO A 38 " pdb=" CB PRO A 38 " ideal model delta sigma weight residual 113.20 110.42 2.78 1.69e+00 3.50e-01 2.71e+00 angle pdb=" CA LYS A 30 " pdb=" CB LYS A 30 " pdb=" CG LYS A 30 " ideal model delta sigma weight residual 114.10 111.10 3.00 2.00e+00 2.50e-01 2.25e+00 ... (remaining 9967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.67: 1734 15.67 - 31.33: 130 31.33 - 47.00: 46 47.00 - 62.67: 22 62.67 - 78.34: 1 Dihedral angle restraints: 1933 sinusoidal: 1455 harmonic: 478 Sorted by residual: dihedral pdb=" CA GLU C 175 " pdb=" C GLU C 175 " pdb=" N GLN C 176 " pdb=" CA GLN C 176 " ideal model delta harmonic sigma weight residual 180.00 -159.53 -20.47 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA HIS A 62 " pdb=" C HIS A 62 " pdb=" N GLN A 63 " pdb=" CA GLN A 63 " ideal model delta harmonic sigma weight residual 180.00 -163.04 -16.96 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA GLY A 61 " pdb=" C GLY A 61 " pdb=" N HIS A 62 " pdb=" CA HIS A 62 " ideal model delta harmonic sigma weight residual 180.00 163.82 16.18 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 1930 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 296 0.031 - 0.062: 81 0.062 - 0.093: 31 0.093 - 0.124: 10 0.124 - 0.155: 2 Chirality restraints: 420 Sorted by residual: 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 2.59 -0.15 2.00e-01 2.50e+01 5.99e-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 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE A 153 " pdb=" N ILE A 153 " pdb=" C ILE A 153 " pdb=" CB ILE A 153 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.53e-01 ... (remaining 417 not shown) Planarity restraints: 811 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 186 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.15e+00 pdb=" C THR C 186 " -0.031 2.00e-02 2.50e+03 pdb=" O THR C 186 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU C 187 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 186 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" C THR A 186 " 0.030 2.00e-02 2.50e+03 pdb=" O THR A 186 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU A 187 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 195 " 0.018 5.00e-02 4.00e+02 2.65e-02 1.12e+00 pdb=" N PRO B 196 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 196 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 196 " 0.015 5.00e-02 4.00e+02 ... (remaining 808 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 302 2.06 - 2.70: 7838 2.70 - 3.33: 16576 3.33 - 3.97: 19832 3.97 - 4.60: 29850 Nonbonded interactions: 74398 Sorted by model distance: nonbonded pdb=" O ASN B 195 " pdb=" H LYS B 199 " model vdw 1.431 1.850 nonbonded pdb=" O ASN A 195 " pdb=" H LYS A 199 " model vdw 1.527 1.850 nonbonded pdb=" O ASN C 195 " pdb=" H LYS C 199 " model vdw 1.540 1.850 nonbonded pdb=" HG SER B 178 " pdb=" OE2 GLU A 180 " model vdw 1.593 1.850 nonbonded pdb=" O ILE A 153 " pdb="HD22 ASN A 193 " model vdw 1.606 1.850 ... (remaining 74393 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and resid 157 through 221) selection = (chain 'C' and ((resid 157 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name HA or name HB2 or name HB3 or name HG2 or name HG \ 3 or name HD2 or name HD3)) or resid 158 through 221)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 5 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.49 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will not be refined Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 10.350 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:6.600 Internal consistency checks: 0.000 Total: 17.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 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 0.044 2775 Z= 0.117 Angle : 0.528 3.921 3762 Z= 0.293 Chirality : 0.037 0.155 420 Planarity : 0.004 0.027 491 Dihedral : 10.485 78.336 1060 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.63 (0.41), residues: 337 helix: -0.52 (0.30), residues: 229 sheet: -1.96 (0.86), residues: 9 loop : 0.53 (0.59), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 100 TYR 0.008 0.001 TYR B 169 PHE 0.002 0.001 PHE B 161 TRP 0.006 0.001 TRP A 184 HIS 0.002 0.001 HIS A 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2775 Z= 0.156 Angle : 0.500 4.407 3762 Z= 0.252 Chirality : 0.045 0.170 420 Planarity : 0.003 0.031 491 Dihedral : 9.315 79.829 1060 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.70 (0.43), residues: 337 helix: 0.49 (0.32), residues: 234 sheet: -1.30 (0.97), residues: 9 loop : 1.04 (0.63), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 173 TYR 0.004 0.001 TYR A 169 PHE 0.008 0.001 PHE A 40 TRP 0.003 0.001 TRP A 133 HIS 0.001 0.001 HIS A 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 32 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 6 optimal weight: 0.1980 chunk 16 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 4 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 overall best weight: 6.6388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2775 Z= 0.167 Angle : 0.467 4.299 3762 Z= 0.235 Chirality : 0.044 0.156 420 Planarity : 0.003 0.024 491 Dihedral : 9.354 84.224 1060 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.67 % Allowed : 0.34 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.98 (0.44), residues: 337 helix: 0.68 (0.33), residues: 224 sheet: -1.06 (1.15), residues: 9 loop : 1.16 (0.60), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 173 TYR 0.003 0.001 TYR A 164 PHE 0.005 0.001 PHE A 32 TRP 0.005 0.001 TRP B 184 HIS 0.001 0.000 HIS A 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 7.9990 chunk 20 optimal weight: 30.0000 chunk 13 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2775 Z= 0.180 Angle : 0.481 4.685 3762 Z= 0.244 Chirality : 0.044 0.164 420 Planarity : 0.003 0.025 491 Dihedral : 9.485 85.631 1060 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.67 % Allowed : 1.01 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.64 (0.44), residues: 337 helix: 0.40 (0.34), residues: 220 sheet: -0.81 (1.34), residues: 9 loop : 1.00 (0.59), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 173 TYR 0.004 0.001 TYR A 169 PHE 0.008 0.001 PHE A 40 TRP 0.004 0.001 TRP A 184 HIS 0.001 0.001 HIS A 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 21 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 20.0000 chunk 28 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 32 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2775 Z= 0.162 Angle : 0.449 4.398 3762 Z= 0.224 Chirality : 0.042 0.158 420 Planarity : 0.003 0.024 491 Dihedral : 9.432 87.132 1060 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.34 % Allowed : 2.02 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.78 (0.45), residues: 337 helix: 0.51 (0.35), residues: 219 sheet: -0.90 (1.37), residues: 9 loop : 1.05 (0.60), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 173 TYR 0.003 0.001 TYR A 169 PHE 0.006 0.001 PHE A 40 TRP 0.004 0.001 TRP B 184 HIS 0.001 0.000 HIS A 12 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 6 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2775 Z= 0.118 Angle : 0.413 4.203 3762 Z= 0.202 Chirality : 0.041 0.158 420 Planarity : 0.003 0.024 491 Dihedral : 9.066 88.809 1060 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.34 % Allowed : 1.68 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.10 (0.45), residues: 337 helix: 0.79 (0.35), residues: 218 sheet: -0.88 (1.40), residues: 9 loop : 1.13 (0.60), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 173 TYR 0.004 0.001 TYR A 169 PHE 0.005 0.001 PHE A 32 TRP 0.002 0.001 TRP A 133 HIS 0.001 0.000 HIS A 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 502.55 seconds wall clock time: 8 minutes 58.32 seconds (538.32 seconds total)