Starting phenix.real_space_refine on Sun May 19 16:32:00 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7pcq_13325.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7pcq_13325.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global c_beta_restraints=False ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True resolution=3.62 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7pcq_13325.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7pcq_13325.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7pcq_13325.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7pcq_13325.pdb" } resolution = 3.62 refinement { run = *minimization_global rigid_body local_grid_search morphing \ simulated_annealing adp occupancy nqh_flips } pdb_interpretation { c_beta_restraints = False ramachandran_plot_restraints { enabled = 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= 0.024 sd= 0.035 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 6 5.16 5 C 1409 2.51 5 N 382 2.21 5 O 395 1.98 5 H 2189 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: 4381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2145 Classifications: {'peptide': 141} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "B" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2236 Classifications: {'peptide': 146} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Time building chain proxies: 1.47, per 1000 atoms: 0.34 Number of scatterers: 4381 At special positions: 0 Unit cell: (58.68, 61.94, 68.46, 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 6 16.00 O 395 8.00 N 382 7.00 C 1409 6.00 H 2189 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: 1.83 Conformation dependent library (CDL) restraints added in 414.0 milliseconds Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 76.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 4 through 35 removed outlier: 5.916A pdb=" N ALA A 19 " --> pdb=" O GLY A 15 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N HIS A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA A 21 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N GLY A 22 " --> pdb=" O GLY A 18 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLU A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 43 Processing helix chain 'A' and resid 53 through 71 Processing helix chain 'A' and resid 73 through 79 removed outlier: 3.936A pdb=" N MET A 76 " --> pdb=" O VAL A 73 " (cutoff:3.500A) Proline residue: A 77 - end of helix No H-bonds generated for 'chain 'A' and resid 73 through 79' Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 95 through 112 Processing helix chain 'A' and resid 119 through 137 Processing helix chain 'B' and resid 5 through 17 removed outlier: 3.758A pdb=" N LYS B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 34 removed outlier: 3.956A pdb=" N GLY B 24 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLY B 25 " --> pdb=" O ASP B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 Processing helix chain 'B' and resid 51 through 56 Processing helix chain 'B' and resid 58 through 76 Processing helix chain 'B' and resid 86 through 94 Processing helix chain 'B' and resid 100 through 121 removed outlier: 3.525A pdb=" N ARG B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LYS B 120 " --> pdb=" O HIS B 116 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N GLU B 121 " --> pdb=" O HIS B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 141 146 hydrogen bonds defined for protein. 420 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.54 Time building geometry restraints manager: 1.95 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: 2186 1.14 - 1.31: 360 1.31 - 1.48: 910 1.48 - 1.65: 974 1.65 - 1.81: 9 Bond restraints: 4439 Sorted by residual: bond pdb=" N SER A 52 " pdb=" H SER A 52 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" N ALA B 62 " pdb=" H ALA B 62 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" N SER A 84 " pdb=" H SER A 84 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" N VAL A 93 " pdb=" H VAL A 93 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" N TYR B 35 " pdb=" H TYR B 35 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.55e+01 ... (remaining 4434 not shown) Histogram of bond angle deviations from ideal: 100.96 - 107.55: 246 107.55 - 114.14: 5234 114.14 - 120.73: 1488 120.73 - 127.32: 1044 127.32 - 133.91: 38 Bond angle restraints: 8050 Sorted by residual: angle pdb=" N GLY A 18 " pdb=" CA GLY A 18 " pdb=" C GLY A 18 " ideal model delta sigma weight residual 110.77 115.07 -4.30 1.93e+00 2.68e-01 4.97e+00 angle pdb=" N PRO B 124 " pdb=" CA PRO B 124 " pdb=" C PRO B 124 " ideal model delta sigma weight residual 110.70 112.49 -1.79 1.22e+00 6.72e-01 2.15e+00 angle pdb=" CA PRO B 124 " pdb=" C PRO B 124 " pdb=" N PRO B 125 " ideal model delta sigma weight residual 117.93 119.33 -1.40 1.20e+00 6.94e-01 1.37e+00 angle pdb=" C THR A 118 " pdb=" N PRO A 119 " pdb=" CD PRO A 119 " ideal model delta sigma weight residual 125.00 129.46 -4.46 4.10e+00 5.95e-02 1.18e+00 angle pdb=" C PRO B 124 " pdb=" N PRO B 125 " pdb=" CD PRO B 125 " ideal model delta sigma weight residual 125.00 129.38 -4.38 4.10e+00 5.95e-02 1.14e+00 ... (remaining 8045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.73: 1398 15.73 - 31.47: 95 31.47 - 47.20: 40 47.20 - 62.94: 31 62.94 - 78.67: 1 Dihedral angle restraints: 1565 sinusoidal: 1097 harmonic: 468 Sorted by residual: dihedral pdb=" CA ARG A 92 " pdb=" CB ARG A 92 " pdb=" CG ARG A 92 " pdb=" CD ARG A 92 " ideal model delta sinusoidal sigma weight residual -60.00 -116.32 56.32 3 1.50e+01 4.44e-03 9.39e+00 dihedral pdb=" CA ARG B 40 " pdb=" CB ARG B 40 " pdb=" CG ARG B 40 " pdb=" CD ARG B 40 " ideal model delta sinusoidal sigma weight residual -180.00 -126.84 -53.16 3 1.50e+01 4.44e-03 9.18e+00 dihedral pdb=" N PHE A 46 " pdb=" CA PHE A 46 " pdb=" CB PHE A 46 " pdb=" CG PHE A 46 " ideal model delta sinusoidal sigma weight residual -60.00 -102.13 42.13 3 1.50e+01 4.44e-03 7.55e+00 ... (remaining 1562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 222 0.022 - 0.044: 77 0.044 - 0.066: 19 0.066 - 0.088: 26 0.088 - 0.109: 6 Chirality restraints: 350 Sorted by residual: chirality pdb=" CA PRO B 36 " pdb=" N PRO B 36 " pdb=" C PRO B 36 " pdb=" CB PRO B 36 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.00e-01 chirality pdb=" CA VAL B 98 " pdb=" N VAL B 98 " pdb=" C VAL B 98 " pdb=" CB VAL B 98 " both_signs ideal model delta sigma weight residual False 2.44 2.54 -0.10 2.00e-01 2.50e+01 2.56e-01 chirality pdb=" CA PRO A 77 " pdb=" N PRO A 77 " pdb=" C PRO A 77 " pdb=" CB PRO A 77 " both_signs ideal model delta sigma weight residual False 2.72 2.63 0.09 2.00e-01 2.50e+01 2.10e-01 ... (remaining 347 not shown) Planarity restraints: 662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 123 " 0.018 5.00e-02 4.00e+02 2.79e-02 1.24e+00 pdb=" N PRO B 124 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 124 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 124 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 35 " 0.015 5.00e-02 4.00e+02 2.24e-02 8.02e-01 pdb=" N PRO B 36 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO B 36 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 36 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 3 " -0.014 5.00e-02 4.00e+02 2.13e-02 7.27e-01 pdb=" N PRO A 4 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO A 4 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 4 " -0.012 5.00e-02 4.00e+02 ... (remaining 659 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 432 2.24 - 2.83: 9240 2.83 - 3.42: 12399 3.42 - 4.01: 15834 4.01 - 4.60: 24530 Nonbonded interactions: 62435 Sorted by model distance: nonbonded pdb=" O THR A 118 " pdb=" H HIS A 122 " model vdw 1.647 1.850 nonbonded pdb=" HE1 TRP A 14 " pdb=" OG1 THR A 67 " model vdw 1.651 1.850 nonbonded pdb=" O THR B 4 " pdb=" H LYS B 8 " model vdw 1.670 1.850 nonbonded pdb=" OE1 GLU A 27 " pdb=" HE2 HIS A 112 " model vdw 1.779 1.850 nonbonded pdb=" H THR A 137 " pdb=" HG1 THR A 137 " model vdw 1.787 2.100 ... (remaining 62430 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: 0.040 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: 0.050 Extract box with map and model: 0.310 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.110 Find NCS groups from input model: 0.050 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:5.930 Internal consistency checks: 0.000 Total: 15.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 0.042 2250 Z= 0.152 Angle : 0.442 4.460 3061 Z= 0.241 Chirality : 0.032 0.109 350 Planarity : 0.003 0.028 391 Dihedral : 10.870 78.670 784 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 0.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % 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: 2.20 (0.46), residues: 283 helix: 1.71 (0.32), residues: 220 sheet: None (None), residues: 0 loop : 0.79 (0.76), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 30 TYR 0.003 0.001 TYR B 145 PHE 0.006 0.001 PHE A 46 TRP 0.004 0.001 TRP A 14 HIS 0.002 0.001 HIS B 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2250 Z= 0.195 Angle : 0.433 4.621 3061 Z= 0.224 Chirality : 0.038 0.135 350 Planarity : 0.003 0.024 391 Dihedral : 9.391 67.928 784 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.35 % Allowed : 1.77 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % 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: 0.84 (0.47), residues: 283 helix: 0.86 (0.33), residues: 223 sheet: None (None), residues: 0 loop : -0.24 (0.80), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 31 TYR 0.003 0.001 TYR B 145 PHE 0.007 0.001 PHE A 98 TRP 0.005 0.001 TRP A 14 HIS 0.002 0.001 HIS B 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 15 optimal weight: 30.0000 chunk 11 optimal weight: 30.0000 chunk 18 optimal weight: 30.0000 chunk 6 optimal weight: 30.0000 chunk 16 optimal weight: 40.0000 chunk 4 optimal weight: 30.0000 chunk 9 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 3 optimal weight: 30.0000 chunk 19 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 overall best weight: 18.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 2250 Z= 0.328 Angle : 0.549 5.010 3061 Z= 0.311 Chirality : 0.040 0.142 350 Planarity : 0.004 0.033 391 Dihedral : 9.452 51.821 784 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.71 % Allowed : 8.13 % Favored : 91.17 % Rotamer: Outliers : 1.30 % Allowed : 4.76 % Favored : 93.94 % 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: -2.98 (0.42), residues: 283 helix: -1.49 (0.30), residues: 223 sheet: None (None), residues: 0 loop : -3.20 (0.66), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 31 TYR 0.004 0.001 TYR A 140 PHE 0.008 0.001 PHE A 98 TRP 0.003 0.001 TRP A 14 HIS 0.004 0.001 HIS B 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 40.0000 chunk 17 optimal weight: 20.0000 chunk 22 optimal weight: 30.0000 chunk 25 optimal weight: 30.0000 chunk 19 optimal weight: 20.0000 chunk 4 optimal weight: 30.0000 chunk 9 optimal weight: 20.0000 chunk 3 optimal weight: 30.0000 chunk 23 optimal weight: 20.0000 chunk 2 optimal weight: 40.0000 chunk 27 optimal weight: 20.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2250 Z= 0.314 Angle : 0.511 4.851 3061 Z= 0.282 Chirality : 0.038 0.135 350 Planarity : 0.003 0.021 391 Dihedral : 9.100 41.602 784 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.71 % Allowed : 6.01 % Favored : 93.29 % Rotamer: Outliers : 1.73 % Allowed : 3.03 % Favored : 95.24 % 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: -2.14 (0.45), residues: 283 helix: -0.84 (0.32), residues: 220 sheet: None (None), residues: 0 loop : -3.07 (0.65), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 31 TYR 0.006 0.001 TYR B 130 PHE 0.007 0.001 PHE A 117 TRP 0.005 0.001 TRP A 14 HIS 0.006 0.001 HIS B 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 21 optimal weight: 30.0000 chunk 10 optimal weight: 30.0000 chunk 15 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 3 optimal weight: 30.0000 chunk 11 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 chunk 19 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2250 Z= 0.350 Angle : 0.538 4.964 3061 Z= 0.309 Chirality : 0.039 0.136 350 Planarity : 0.004 0.030 391 Dihedral : 9.394 42.967 784 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 1.41 % Allowed : 9.19 % Favored : 89.40 % Rotamer: Outliers : 2.60 % Allowed : 3.46 % Favored : 93.94 % 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: -3.55 (0.42), residues: 283 helix: -1.79 (0.30), residues: 221 sheet: None (None), residues: 0 loop : -3.81 (0.65), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 31 TYR 0.005 0.001 TYR B 130 PHE 0.007 0.001 PHE A 98 TRP 0.005 0.001 TRP B 37 HIS 0.005 0.001 HIS B 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 20.0000 chunk 16 optimal weight: 40.0000 chunk 8 optimal weight: 40.0000 chunk 1 optimal weight: 40.0000 chunk 25 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 2 optimal weight: 40.0000 chunk 23 optimal weight: 30.0000 chunk 26 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 overall best weight: 18.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2250 Z= 0.296 Angle : 0.486 4.869 3061 Z= 0.272 Chirality : 0.038 0.130 350 Planarity : 0.003 0.023 391 Dihedral : 9.385 53.995 784 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 1.77 % Allowed : 7.07 % Favored : 91.17 % Rotamer: Outliers : 2.60 % Allowed : 3.03 % Favored : 94.37 % 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: -2.56 (0.46), residues: 283 helix: -1.18 (0.32), residues: 221 sheet: None (None), residues: 0 loop : -3.05 (0.71), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 92 TYR 0.005 0.001 TYR B 130 PHE 0.007 0.001 PHE A 117 TRP 0.004 0.001 TRP A 14 HIS 0.006 0.001 HIS B 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 172.23 seconds wall clock time: 3 minutes 31.17 seconds (211.17 seconds total)