Starting phenix.real_space_refine on Sun May 19 16:32:01 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6y9w_10739.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6y9w_10739.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=4.1 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6y9w_10739.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6y9w_10739.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6y9w_10739.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/6y9w_10739.pdb" } resolution = 4.1 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= 0.003 sd= 0.006 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 26 5.16 5 C 2162 2.51 5 N 598 2.21 5 O 649 1.98 5 H 3432 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: 6867 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2265 Classifications: {'peptide': 146} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 134} Chain: "B" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3432 Classifications: {'peptide': 220} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 202} Chain: "N" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1170 Classifications: {'peptide': 74} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 4, 'TRANS': 69} Time building chain proxies: 2.07, per 1000 atoms: 0.30 Number of scatterers: 6867 At special positions: 0 Unit cell: (108.12, 114.48, 87.98, 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 26 16.00 O 649 8.00 N 598 7.00 C 2162 6.00 H 3432 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 218 " distance=2.04 Simple disulfide: pdb=" SG CYS N 198 " - pdb=" SG CYS N 218 " 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: 2.67 Conformation dependent library (CDL) restraints added in 455.6 milliseconds Finding SS restraints... Secondary structure from input PDB file: 23 helices and 1 sheets defined 57.5% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 17 through 30 Processing helix chain 'A' and resid 35 through 43 Processing helix chain 'A' and resid 49 through 57 Processing helix chain 'A' and resid 63 through 83 Processing helix chain 'A' and resid 101 through 104 No H-bonds generated for 'chain 'A' and resid 101 through 104' Processing helix chain 'A' and resid 111 through 119 Processing helix chain 'A' and resid 126 through 144 Processing helix chain 'B' and resid 17 through 26 Processing helix chain 'B' and resid 34 through 43 removed outlier: 3.763A pdb=" N ILE B 37 " --> pdb=" O PRO B 34 " (cutoff:3.500A) Proline residue: B 38 - end of helix Processing helix chain 'B' and resid 49 through 57 Processing helix chain 'B' and resid 63 through 83 Processing helix chain 'B' and resid 111 through 119 Processing helix chain 'B' and resid 126 through 144 Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 161 through 174 Processing helix chain 'B' and resid 179 through 189 removed outlier: 3.704A pdb=" N TRP B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 205 removed outlier: 3.551A pdb=" N LEU B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 217 Processing helix chain 'N' and resid 150 through 152 No H-bonds generated for 'chain 'N' and resid 150 through 152' Processing helix chain 'N' and resid 161 through 174 Processing helix chain 'N' and resid 179 through 189 removed outlier: 3.715A pdb=" N TRP N 184 " --> pdb=" O GLU N 180 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU N 187 " --> pdb=" O ASN N 183 " (cutoff:3.500A) Processing helix chain 'N' and resid 196 through 205 removed outlier: 3.552A pdb=" N LEU N 205 " --> pdb=" O ILE N 201 " (cutoff:3.500A) Processing helix chain 'N' and resid 211 through 217 Processing sheet with id= A, first strand: chain 'A' and resid 2 through 4 156 hydrogen bonds defined for protein. 459 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: 2.19 Time building geometry restraints manager: 2.98 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: 3432 1.15 - 1.32: 591 1.32 - 1.48: 1345 1.48 - 1.65: 1526 1.65 - 1.82: 48 Bond restraints: 6942 Sorted by residual: bond pdb=" N VAL B 27 " pdb=" H VAL B 27 " ideal model delta sigma weight residual 0.860 1.027 -0.167 2.00e-02 2.50e+03 7.01e+01 bond pdb=" N GLU B 28 " pdb=" H GLU B 28 " ideal model delta sigma weight residual 0.860 1.026 -0.166 2.00e-02 2.50e+03 6.91e+01 bond pdb=" N ALA B 47 " pdb=" H ALA B 47 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.68e+01 bond pdb=" N GLU B 45 " pdb=" H GLU B 45 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.68e+01 bond pdb=" N HIS A 84 " pdb=" H HIS A 84 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.66e+01 ... (remaining 6937 not shown) Histogram of bond angle deviations from ideal: 100.30 - 107.03: 209 107.03 - 113.77: 8402 113.77 - 120.50: 2190 120.50 - 127.23: 1760 127.23 - 133.96: 58 Bond angle restraints: 12619 Sorted by residual: angle pdb=" C ALA A 31 " pdb=" CA ALA A 31 " pdb=" CB ALA A 31 " ideal model delta sigma weight residual 117.23 111.34 5.89 1.36e+00 5.41e-01 1.88e+01 angle pdb=" C ILE B 6 " pdb=" N GLN B 7 " pdb=" CA GLN B 7 " ideal model delta sigma weight residual 121.70 126.75 -5.05 1.80e+00 3.09e-01 7.88e+00 angle pdb=" CA ALA A 31 " pdb=" C ALA A 31 " pdb=" N PHE A 32 " ideal model delta sigma weight residual 119.98 117.99 1.99 8.50e-01 1.38e+00 5.50e+00 angle pdb=" N VAL A 83 " pdb=" CA VAL A 83 " pdb=" C VAL A 83 " ideal model delta sigma weight residual 112.29 110.14 2.15 9.40e-01 1.13e+00 5.22e+00 angle pdb=" C ILE B 37 " pdb=" N PRO B 38 " pdb=" CA PRO B 38 " ideal model delta sigma weight residual 118.97 120.68 -1.71 1.04e+00 9.25e-01 2.72e+00 ... (remaining 12614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.62: 2096 14.62 - 29.25: 218 29.25 - 43.87: 95 43.87 - 58.49: 39 58.49 - 73.11: 6 Dihedral angle restraints: 2454 sinusoidal: 1853 harmonic: 601 Sorted by residual: dihedral pdb=" CB CYS B 198 " pdb=" SG CYS B 198 " pdb=" SG CYS B 218 " pdb=" CB CYS B 218 " ideal model delta sinusoidal sigma weight residual -86.00 -110.81 24.81 1 1.00e+01 1.00e-02 8.86e+00 dihedral pdb=" CB CYS N 198 " pdb=" SG CYS N 198 " pdb=" SG CYS N 218 " pdb=" CB CYS N 218 " ideal model delta sinusoidal sigma weight residual -86.00 -110.80 24.80 1 1.00e+01 1.00e-02 8.85e+00 dihedral pdb=" CB MET N 215 " pdb=" CG MET N 215 " pdb=" SD MET N 215 " pdb=" CE MET N 215 " ideal model delta sinusoidal sigma weight residual -180.00 -131.99 -48.01 3 1.50e+01 4.44e-03 8.58e+00 ... (remaining 2451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 348 0.028 - 0.056: 124 0.056 - 0.084: 36 0.084 - 0.112: 21 0.112 - 0.139: 5 Chirality restraints: 534 Sorted by residual: chirality pdb=" CA ILE B 124 " pdb=" N ILE B 124 " pdb=" C ILE B 124 " pdb=" CB ILE B 124 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-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 -0.13 2.00e-01 2.50e+01 4.48e-01 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 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 531 not shown) Planarity restraints: 1031 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 37 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.65e+00 pdb=" N PRO A 38 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 38 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 38 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 33 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO A 34 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 34 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 34 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 37 " 0.018 5.00e-02 4.00e+02 2.79e-02 1.24e+00 pdb=" N PRO B 38 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 38 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 38 " 0.015 5.00e-02 4.00e+02 ... (remaining 1028 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 360 2.13 - 2.74: 11238 2.74 - 3.36: 18889 3.36 - 3.98: 23456 3.98 - 4.60: 35370 Nonbonded interactions: 89313 Sorted by model distance: nonbonded pdb=" OE1 GLN B 179 " pdb="HD21 ASN B 183 " model vdw 1.507 1.850 nonbonded pdb=" OE1 GLN N 179 " pdb="HD21 ASN N 183 " model vdw 1.509 1.850 nonbonded pdb=" O ASN B 195 " pdb=" H LYS B 199 " model vdw 1.537 1.850 nonbonded pdb=" O ASN N 195 " pdb=" H LYS N 199 " model vdw 1.537 1.850 nonbonded pdb=" O SER A 44 " pdb=" HZ3 LYS A 131 " model vdw 1.593 1.850 ... (remaining 89308 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: 0.070 Extract box with map and model: 0.400 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.340 Find NCS groups from input model: 0.070 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:9.140 Internal consistency checks: 0.000 Total: 23.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 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 0.024 3510 Z= 0.147 Angle : 0.448 5.894 4772 Z= 0.241 Chirality : 0.037 0.139 534 Planarity : 0.004 0.048 625 Dihedral : 11.751 73.114 1334 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.80 % Allowed : 2.67 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.25 % 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: -0.69 (0.38), residues: 434 helix: -0.08 (0.30), residues: 280 sheet: -3.20 (0.75), residues: 9 loop : -0.77 (0.48), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 18 TYR 0.006 0.001 TYR B 130 PHE 0.004 0.001 PHE A 32 TRP 0.006 0.001 TRP N 184 HIS 0.002 0.001 HIS A 84 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3510 Z= 0.231 Angle : 0.485 4.954 4772 Z= 0.249 Chirality : 0.043 0.154 534 Planarity : 0.004 0.030 625 Dihedral : 10.335 58.358 1334 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.69 % Favored : 96.08 % Rotamer: Outliers : 0.80 % Allowed : 3.21 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.25 % 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: -2.77 (0.34), residues: 434 helix: -1.67 (0.26), residues: 278 sheet: -3.03 (1.10), residues: 9 loop : -1.75 (0.47), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 143 TYR 0.006 0.001 TYR B 130 PHE 0.007 0.001 PHE A 32 TRP 0.004 0.001 TRP B 184 HIS 0.003 0.001 HIS B 12 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 13 optimal weight: 30.0000 chunk 32 optimal weight: 20.0000 chunk 8 optimal weight: 40.0000 chunk 18 optimal weight: 20.0000 chunk 6 optimal weight: 30.0000 chunk 39 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 34 optimal weight: 50.0000 chunk 38 optimal weight: 20.0000 chunk 9 optimal weight: 40.0000 chunk 19 optimal weight: 6.9990 overall best weight: 17.3998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 3510 Z= 0.433 Angle : 0.706 4.939 4772 Z= 0.397 Chirality : 0.050 0.187 534 Planarity : 0.006 0.044 625 Dihedral : 12.344 66.617 1334 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 25.93 Ramachandran Plot: Outliers : 5.76 % Allowed : 20.51 % Favored : 73.73 % Rotamer: Outliers : 4.01 % Allowed : 7.22 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.25 % 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: -6.45 (0.26), residues: 434 helix: -3.96 (0.19), residues: 277 sheet: -3.07 (1.25), residues: 9 loop : -4.66 (0.36), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 100 TYR 0.010 0.003 TYR B 164 PHE 0.017 0.002 PHE B 161 TRP 0.007 0.001 TRP B 23 HIS 0.004 0.001 HIS B 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 6 optimal weight: 30.0000 chunk 4 optimal weight: 30.0000 chunk 21 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 39 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 overall best weight: 12.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3510 Z= 0.252 Angle : 0.511 4.529 4772 Z= 0.279 Chirality : 0.045 0.168 534 Planarity : 0.004 0.039 625 Dihedral : 11.318 70.564 1334 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 2.07 % Allowed : 8.76 % Favored : 89.17 % Rotamer: Outliers : 3.21 % Allowed : 4.81 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.25 % 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: -4.86 (0.30), residues: 434 helix: -2.78 (0.23), residues: 274 sheet: -2.88 (1.05), residues: 9 loop : -3.85 (0.39), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 18 TYR 0.008 0.002 TYR B 164 PHE 0.006 0.001 PHE B 161 TRP 0.005 0.001 TRP B 117 HIS 0.003 0.001 HIS B 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 40.0000 chunk 30 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 33 optimal weight: 30.0000 chunk 16 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 5 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 42 optimal weight: 30.0000 chunk 40 optimal weight: 20.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.5993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 3510 Z= 0.484 Angle : 0.737 5.447 4772 Z= 0.423 Chirality : 0.052 0.180 534 Planarity : 0.006 0.043 625 Dihedral : 12.859 85.105 1334 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 34.38 Ramachandran Plot: Outliers : 8.53 % Allowed : 25.58 % Favored : 65.90 % Rotamer: Outliers : 5.88 % Allowed : 9.63 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.25 % 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: -6.77 (0.25), residues: 434 helix: -4.17 (0.18), residues: 276 sheet: None (None), residues: 0 loop : -4.86 (0.34), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 97 TYR 0.009 0.002 TYR B 164 PHE 0.017 0.002 PHE B 161 TRP 0.014 0.002 TRP B 184 HIS 0.005 0.002 HIS B 84 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 0 optimal weight: 40.0000 chunk 39 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 12 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 9 optimal weight: 50.0000 overall best weight: 16.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.6192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3510 Z= 0.355 Angle : 0.602 4.593 4772 Z= 0.336 Chirality : 0.048 0.172 534 Planarity : 0.005 0.045 625 Dihedral : 12.550 85.307 1334 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 4.38 % Allowed : 16.13 % Favored : 79.49 % Rotamer: Outliers : 5.35 % Allowed : 8.56 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.25 % 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: -5.70 (0.28), residues: 434 helix: -3.39 (0.22), residues: 268 sheet: None (None), residues: 0 loop : -4.30 (0.34), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 18 TYR 0.008 0.002 TYR A 130 PHE 0.010 0.001 PHE B 32 TRP 0.008 0.001 TRP B 184 HIS 0.005 0.002 HIS A 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 226.56 seconds wall clock time: 4 minutes 26.34 seconds (266.34 seconds total)