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/7lkh_23408.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7lkh_23408.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=3.5 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7lkh_23408.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7lkh_23408.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7lkh_23408.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7lkh_23408.map" } resolution = 3.5 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= 0.002 sd= 0.021 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 8 5.16 5 C 2645 2.51 5 N 715 2.21 5 O 788 1.98 5 H 4080 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 87": "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: 8236 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4686 Inner-chain residues flagged as termini: ['pdbres="VAL A 72 "', 'pdbres="ARG A 81 "', 'pdbres="GLU A 278 "', 'pdbres="THR A 637 "'] Classifications: {'peptide': 286} Modifications used: {'COO': 3, 'NH3': 3} Link IDs: {'PTRANS': 22, 'TRANS': 263} Chain breaks: 2 Chain: "H" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1865 Classifications: {'peptide': 121} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "L" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1685 Classifications: {'peptide': 109} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Time building chain proxies: 2.20, per 1000 atoms: 0.27 Number of scatterers: 8236 At special positions: 0 Unit cell: (71.28, 100.44, 84.24, 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 8 16.00 O 788 8.00 N 715 7.00 C 2645 6.00 H 4080 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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: 2.82 Conformation dependent library (CDL) restraints added in 551.5 milliseconds 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.14: 4079 1.14 - 1.31: 676 1.31 - 1.48: 1790 1.48 - 1.64: 1787 1.64 - 1.81: 9 Bond restraints: 8341 Sorted by residual: bond pdb=" N SER A 661 " pdb=" H SER A 661 " ideal model delta sigma weight residual 0.860 1.026 -0.166 2.00e-02 2.50e+03 6.90e+01 bond pdb=" N LEU H 45 " pdb=" H LEU H 45 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.76e+01 bond pdb=" N ASN A 224 " pdb=" H ASN A 224 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.73e+01 bond pdb=" N GLN H 39 " pdb=" H GLN H 39 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.67e+01 bond pdb=" N TYR L 50 " pdb=" H TYR L 50 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.65e+01 ... (remaining 8336 not shown) Histogram of bond angle deviations from ideal: 101.10 - 107.70: 670 107.70 - 114.29: 9525 114.29 - 120.88: 2770 120.88 - 127.48: 2017 127.48 - 134.07: 57 Bond angle restraints: 15039 Sorted by residual: angle pdb=" N SER L 52 " pdb=" CA SER L 52 " pdb=" CB SER L 52 " ideal model delta sigma weight residual 114.17 110.90 3.27 1.14e+00 7.69e-01 8.25e+00 angle pdb=" CA SER A 117 " pdb=" C SER A 117 " pdb=" N PRO A 118 " ideal model delta sigma weight residual 120.81 118.47 2.34 8.60e-01 1.35e+00 7.42e+00 angle pdb=" C ASP A 83 " pdb=" N TRP A 84 " pdb=" CA TRP A 84 " ideal model delta sigma weight residual 121.54 126.56 -5.02 1.91e+00 2.74e-01 6.91e+00 angle pdb=" N SER A 117 " pdb=" CA SER A 117 " pdb=" C SER A 117 " ideal model delta sigma weight residual 112.35 109.62 2.73 1.34e+00 5.57e-01 4.14e+00 angle pdb=" N PRO A 155 " pdb=" CA PRO A 155 " pdb=" C PRO A 155 " ideal model delta sigma weight residual 113.47 110.58 2.89 1.43e+00 4.89e-01 4.09e+00 ... (remaining 15034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 2665 16.26 - 32.52: 217 32.52 - 48.77: 68 48.77 - 65.03: 28 65.03 - 81.29: 8 Dihedral angle restraints: 2986 sinusoidal: 2137 harmonic: 849 Sorted by residual: dihedral pdb=" CA ARG H 98 " pdb=" C ARG H 98 " pdb=" N TYR H 99 " pdb=" CA TYR H 99 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA THR L 93 " pdb=" C THR L 93 " pdb=" N LEU L 94 " pdb=" CA LEU L 94 " ideal model delta harmonic sigma weight residual -180.00 -162.12 -17.88 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA PRO A 155 " pdb=" C PRO A 155 " pdb=" N GLY A 156 " pdb=" CA GLY A 156 " ideal model delta harmonic sigma weight residual 180.00 162.42 17.58 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 2983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 381 0.029 - 0.057: 175 0.057 - 0.086: 32 0.086 - 0.114: 38 0.114 - 0.143: 12 Chirality restraints: 638 Sorted by residual: chirality pdb=" CA ILE A 271 " pdb=" N ILE A 271 " pdb=" C ILE A 271 " pdb=" CB ILE A 271 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA ILE A 96 " pdb=" N ILE A 96 " pdb=" C ILE A 96 " pdb=" CB ILE A 96 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.93e-01 chirality pdb=" CA VAL H 93 " pdb=" N VAL H 93 " pdb=" C VAL H 93 " pdb=" CB VAL H 93 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 635 not shown) Planarity restraints: 1228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 154 " -0.034 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO A 155 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 155 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 155 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 65 " -0.025 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO A 66 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 117 " 0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO A 118 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 118 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 118 " 0.018 5.00e-02 4.00e+02 ... (remaining 1225 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.11: 488 2.11 - 2.73: 13139 2.73 - 3.35: 22374 3.35 - 3.98: 30903 3.98 - 4.60: 45361 Nonbonded interactions: 112265 Sorted by model distance: nonbonded pdb="HD22 ASN L 34 " pdb=" O TYR L 49 " model vdw 1.483 1.850 nonbonded pdb=" O SER A 117 " pdb=" HG SER A 120 " model vdw 1.538 1.850 nonbonded pdb=" O GLY A 87 " pdb=" HH TYR A 674 " model vdw 1.572 1.850 nonbonded pdb=" OD2 ASP A 188 " pdb=" HG1 THR A 194 " model vdw 1.590 1.850 nonbonded pdb=" OE1 GLN H 5 " pdb=" H GLN H 5 " model vdw 1.620 1.850 ... (remaining 112260 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: 0.020 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: 0.080 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.020 Find NCS groups from input model: 0.160 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:8.960 Internal consistency checks: 0.000 Total: 23.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 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 0.055 4261 Z= 0.152 Angle : 0.554 5.275 5799 Z= 0.303 Chirality : 0.042 0.143 638 Planarity : 0.004 0.052 746 Dihedral : 12.270 81.289 1562 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.13 % Favored : 93.48 % Rotamer: Outliers : 0.43 % Allowed : 1.74 % Favored : 97.83 % 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: -1.47 (0.36), residues: 506 helix: -0.64 (0.55), residues: 73 sheet: -0.68 (0.38), residues: 161 loop : -1.20 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 652 TYR 0.015 0.001 TYR H 99 PHE 0.010 0.001 PHE A 97 TRP 0.007 0.001 TRP A 84 HIS 0.003 0.001 HIS H 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4261 Z= 0.249 Angle : 0.546 5.795 5799 Z= 0.277 Chirality : 0.064 0.263 638 Planarity : 0.005 0.056 746 Dihedral : 11.817 79.128 1562 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.65 % Allowed : 1.96 % Favored : 97.39 % 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: -0.94 (0.38), residues: 506 helix: -0.27 (0.56), residues: 79 sheet: -0.36 (0.39), residues: 167 loop : -0.84 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 53 TYR 0.017 0.002 TYR H 99 PHE 0.010 0.001 PHE L 98 TRP 0.010 0.001 TRP A 84 HIS 0.002 0.001 HIS A 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 37 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4261 Z= 0.242 Angle : 0.538 5.169 5799 Z= 0.271 Chirality : 0.063 0.227 638 Planarity : 0.005 0.060 746 Dihedral : 11.887 80.161 1562 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.09 % Allowed : 3.70 % Favored : 95.22 % 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: -0.99 (0.38), residues: 506 helix: -0.67 (0.52), residues: 78 sheet: -0.39 (0.40), residues: 165 loop : -0.73 (0.42), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 696 TYR 0.016 0.002 TYR H 99 PHE 0.010 0.002 PHE A 97 TRP 0.006 0.001 TRP A 84 HIS 0.003 0.001 HIS A 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 38 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 46 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 4261 Z= 0.318 Angle : 0.602 5.304 5799 Z= 0.309 Chirality : 0.066 0.257 638 Planarity : 0.005 0.062 746 Dihedral : 12.284 79.587 1562 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.74 % Allowed : 4.35 % Favored : 93.91 % 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: -1.45 (0.38), residues: 506 helix: -1.26 (0.55), residues: 77 sheet: -0.79 (0.39), residues: 171 loop : -0.86 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 53 TYR 0.018 0.002 TYR L 49 PHE 0.010 0.002 PHE L 98 TRP 0.009 0.002 TRP A 84 HIS 0.003 0.001 HIS A 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4261 Z= 0.191 Angle : 0.500 4.395 5799 Z= 0.249 Chirality : 0.061 0.219 638 Planarity : 0.004 0.054 746 Dihedral : 11.751 75.976 1562 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.30 % Allowed : 4.13 % Favored : 94.57 % 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: -1.34 (0.38), residues: 506 helix: -1.21 (0.56), residues: 77 sheet: -0.68 (0.40), residues: 165 loop : -0.81 (0.42), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 696 TYR 0.014 0.001 TYR H 99 PHE 0.007 0.001 PHE A 123 TRP 0.007 0.001 TRP A 84 HIS 0.002 0.001 HIS A 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 42 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4261 Z= 0.133 Angle : 0.450 4.639 5799 Z= 0.219 Chirality : 0.059 0.226 638 Planarity : 0.004 0.045 746 Dihedral : 10.963 73.576 1562 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.09 % Allowed : 3.91 % Favored : 95.00 % 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: -1.05 (0.39), residues: 506 helix: -0.95 (0.58), residues: 77 sheet: -0.52 (0.40), residues: 171 loop : -0.60 (0.43), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 246 TYR 0.014 0.001 TYR H 99 PHE 0.006 0.001 PHE A 97 TRP 0.006 0.001 TRP A 84 HIS 0.002 0.000 HIS A 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 600.69 seconds wall clock time: 10 minutes 40.53 seconds (640.53 seconds total)