Starting phenix.real_space_refine on Sun May 19 16:31:06 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8jo4_36455.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8jo4_36455.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global c_beta_restraints=False ramachandran_plot_restraints.enabled=False secondary_structure.enabled=False resolution=3.04 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8jo4_36455.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8jo4_36455.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8jo4_36455.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8jo4_36455.pdb" } resolution = 3.04 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 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= 0.021 sd= 0.333 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 27 5.16 5 C 3596 2.51 5 N 941 2.21 5 O 1093 1.98 5 H 5654 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 11311 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 5717 Classifications: {'peptide': 350} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 338} Chain: "B" Number of atoms: 5594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 5594 Inner-chain residues flagged as termini: ['pdbres="PRO B 40 "', 'pdbres="ASP B 53 "'] Classifications: {'peptide': 359} Modifications used: {'COO': 2, 'NH3': 2} Link IDs: {'PTRANS': 19, 'TRANS': 339} Chain breaks: 1 Time building chain proxies: 2.26, per 1000 atoms: 0.20 Number of scatterers: 11311 At special positions: 0 Unit cell: (65.1, 82.77, 115.32, 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 27 16.00 O 1093 8.00 N 941 7.00 C 3596 6.00 H 5654 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: 3.03 Conformation dependent library (CDL) restraints added in 398.2 milliseconds Time building geometry restraints manager: 3.39 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: 5647 1.14 - 1.31: 974 1.31 - 1.48: 2221 1.48 - 1.64: 2533 1.64 - 1.81: 47 Bond restraints: 11422 Sorted by residual: bond pdb=" N GLY B 345 " pdb=" H GLY B 345 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.78e+01 bond pdb=" N VAL A 250 " pdb=" H VAL A 250 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.71e+01 bond pdb=" N VAL A 251 " pdb=" H VAL A 251 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" N ILE B 343 " pdb=" H ILE B 343 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.68e+01 bond pdb=" N ASP A 15 " pdb=" H ASP A 15 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.68e+01 ... (remaining 11417 not shown) Histogram of bond angle deviations from ideal: 98.62 - 105.70: 113 105.70 - 112.78: 13541 112.78 - 119.85: 2950 119.85 - 126.93: 4031 126.93 - 134.01: 57 Bond angle restraints: 20692 Sorted by residual: angle pdb=" N VAL B 341 " pdb=" CA VAL B 341 " pdb=" C VAL B 341 " ideal model delta sigma weight residual 110.23 107.92 2.31 1.04e+00 9.25e-01 4.92e+00 angle pdb=" CA VAL B 165 " pdb=" C VAL B 165 " pdb=" O VAL B 165 " ideal model delta sigma weight residual 120.88 119.58 1.30 6.80e-01 2.16e+00 3.65e+00 angle pdb=" CA TRP B 358 " pdb=" CB TRP B 358 " pdb=" CG TRP B 358 " ideal model delta sigma weight residual 113.60 116.67 -3.07 1.90e+00 2.77e-01 2.61e+00 angle pdb=" CA VAL B 165 " pdb=" C VAL B 165 " pdb=" N PRO B 166 " ideal model delta sigma weight residual 118.12 119.42 -1.30 8.10e-01 1.52e+00 2.56e+00 angle pdb=" N VAL A 239 " pdb=" CA VAL A 239 " pdb=" C VAL A 239 " ideal model delta sigma weight residual 111.58 109.94 1.64 1.06e+00 8.90e-01 2.39e+00 ... (remaining 20687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 3663 17.93 - 35.86: 236 35.86 - 53.80: 99 53.80 - 71.73: 23 71.73 - 89.66: 4 Dihedral angle restraints: 4025 sinusoidal: 2943 harmonic: 1082 Sorted by residual: dihedral pdb=" CA VAL A 239 " pdb=" C VAL A 239 " pdb=" N ALA A 240 " pdb=" CA ALA A 240 " ideal model delta harmonic sigma weight residual 180.00 162.48 17.52 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" N ASP A 321 " pdb=" CA ASP A 321 " pdb=" CB ASP A 321 " pdb=" CG ASP A 321 " ideal model delta sinusoidal sigma weight residual -180.00 -120.45 -59.55 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N GLN A 82 " pdb=" CA GLN A 82 " pdb=" CB GLN A 82 " pdb=" CG GLN A 82 " ideal model delta sinusoidal sigma weight residual -180.00 -121.03 -58.97 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 4022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 555 0.029 - 0.057: 215 0.057 - 0.086: 55 0.086 - 0.114: 38 0.114 - 0.143: 14 Chirality restraints: 877 Sorted by residual: chirality pdb=" CA ILE B 167 " pdb=" N ILE B 167 " pdb=" C ILE B 167 " pdb=" CB ILE B 167 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA ILE B 359 " pdb=" N ILE B 359 " pdb=" C ILE B 359 " pdb=" CB ILE B 359 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA VAL A 236 " pdb=" N VAL A 236 " pdb=" C VAL A 236 " pdb=" CB VAL A 236 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 874 not shown) Planarity restraints: 1680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 165 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.66e+00 pdb=" N PRO B 166 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 166 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 166 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 211 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO A 212 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 16 " 0.016 5.00e-02 4.00e+02 2.39e-02 9.16e-01 pdb=" N PRO A 17 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 17 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 17 " 0.013 5.00e-02 4.00e+02 ... (remaining 1677 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 1008 2.12 - 2.74: 19745 2.74 - 3.36: 34781 3.36 - 3.98: 47116 3.98 - 4.60: 69840 Nonbonded interactions: 172490 Sorted by model distance: nonbonded pdb=" HG SER A 175 " pdb=" OD2 ASP A 298 " model vdw 1.495 1.850 nonbonded pdb=" O ILE B 319 " pdb=" H ALA B 323 " model vdw 1.497 1.850 nonbonded pdb=" OE1 GLU A 343 " pdb=" HG1 THR B 353 " model vdw 1.513 1.850 nonbonded pdb="HH22 ARG B 118 " pdb=" O CYS B 376 " model vdw 1.524 1.850 nonbonded pdb=" O THR B 8 " pdb=" HD1 HIS B 103 " model vdw 1.534 1.850 ... (remaining 172485 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: 0.060 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.690 Find NCS groups from input model: 0.080 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:9.310 Internal consistency checks: 0.000 Total: 21.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 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 0.035 5768 Z= 0.099 Angle : 0.434 4.101 7805 Z= 0.237 Chirality : 0.039 0.143 877 Planarity : 0.003 0.041 1004 Dihedral : 11.622 89.662 2177 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.84 % Favored : 97.01 % Rotamer: Outliers : 2.09 % Allowed : 4.82 % Favored : 93.10 % 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: 0.24 (0.31), residues: 703 helix: 0.39 (0.26), residues: 379 sheet: -0.52 (0.59), residues: 64 loop : 0.27 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 337 TYR 0.007 0.001 TYR A 132 PHE 0.009 0.001 PHE A 125 TRP 0.009 0.001 TRP B 358 HIS 0.004 0.001 HIS A 300 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5768 Z= 0.189 Angle : 0.485 4.560 7805 Z= 0.253 Chirality : 0.049 0.182 877 Planarity : 0.003 0.037 1004 Dihedral : 11.526 88.584 2177 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.12 % Favored : 94.31 % Rotamer: Outliers : 2.09 % Allowed : 4.49 % Favored : 93.42 % 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: -3.69 (0.26), residues: 703 helix: -3.21 (0.17), residues: 378 sheet: -1.39 (0.60), residues: 67 loop : -1.07 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 149 TYR 0.007 0.001 TYR A 229 PHE 0.012 0.001 PHE A 31 TRP 0.010 0.002 TRP A 277 HIS 0.003 0.001 HIS A 300 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 64 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 39 optimal weight: 30.0000 chunk 9 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 overall best weight: 9.5996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 5768 Z= 0.302 Angle : 0.584 4.712 7805 Z= 0.316 Chirality : 0.054 0.180 877 Planarity : 0.004 0.041 1004 Dihedral : 12.600 106.064 2177 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 2.13 % Allowed : 13.51 % Favored : 84.35 % Rotamer: Outliers : 2.57 % Allowed : 5.62 % Favored : 91.81 % 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: -5.73 (0.25), residues: 703 helix: -4.68 (0.13), residues: 361 sheet: -2.74 (0.59), residues: 67 loop : -2.45 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 101 TYR 0.009 0.002 TYR A 53 PHE 0.014 0.002 PHE B 33 TRP 0.010 0.002 TRP A 277 HIS 0.003 0.001 HIS B 163 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 12 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 56 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 overall best weight: 9.7998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 5768 Z= 0.278 Angle : 0.547 5.143 7805 Z= 0.294 Chirality : 0.051 0.175 877 Planarity : 0.004 0.035 1004 Dihedral : 12.728 101.839 2177 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 1.71 % Allowed : 12.23 % Favored : 86.06 % Rotamer: Outliers : 2.73 % Allowed : 5.78 % Favored : 91.49 % 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: -5.99 (0.24), residues: 703 helix: -4.81 (0.12), residues: 358 sheet: -3.32 (0.56), residues: 67 loop : -2.59 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 101 TYR 0.008 0.002 TYR A 42 PHE 0.010 0.002 PHE A 31 TRP 0.009 0.002 TRP A 277 HIS 0.003 0.001 HIS B 163 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 11 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 overall best weight: 9.7998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 5768 Z= 0.301 Angle : 0.575 4.681 7805 Z= 0.311 Chirality : 0.053 0.181 877 Planarity : 0.004 0.037 1004 Dihedral : 13.040 105.034 2177 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 1.85 % Allowed : 15.22 % Favored : 82.93 % Rotamer: Outliers : 3.05 % Allowed : 6.26 % Favored : 90.69 % 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: -6.31 (0.23), residues: 703 helix: -4.88 (0.12), residues: 363 sheet: -3.74 (0.57), residues: 62 loop : -2.96 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 101 TYR 0.010 0.002 TYR A 42 PHE 0.014 0.002 PHE B 33 TRP 0.010 0.002 TRP A 277 HIS 0.004 0.001 HIS B 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 18 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 37 optimal weight: 8.9990 overall best weight: 9.1996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 5768 Z= 0.276 Angle : 0.540 4.649 7805 Z= 0.291 Chirality : 0.051 0.176 877 Planarity : 0.004 0.037 1004 Dihedral : 13.011 103.444 2177 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 1.42 % Allowed : 14.65 % Favored : 83.93 % Rotamer: Outliers : 2.57 % Allowed : 6.74 % Favored : 90.69 % 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: -6.31 (0.23), residues: 703 helix: -4.89 (0.11), residues: 363 sheet: -3.77 (0.58), residues: 62 loop : -2.91 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 101 TYR 0.009 0.002 TYR A 42 PHE 0.011 0.002 PHE B 33 TRP 0.010 0.002 TRP A 277 HIS 0.003 0.001 HIS B 163 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 307.61 seconds wall clock time: 6 minutes 8.06 seconds (368.06 seconds total)