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/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=True 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 { 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: 0.01s 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: 3.25, per 1000 atoms: 0.29 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: 5.65 Conformation dependent library (CDL) restraints added in 758.0 milliseconds Finding SS restraints... Secondary structure from input PDB file: 35 helices and 5 sheets defined 52.0% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 Processing helix chain 'A' and resid 21 through 36 Processing helix chain 'A' and resid 42 through 54 Processing helix chain 'A' and resid 58 through 71 Processing helix chain 'A' and resid 73 through 76 No H-bonds generated for 'chain 'A' and resid 73 through 76' Processing helix chain 'A' and resid 78 through 90 removed outlier: 3.669A pdb=" N SER A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 150 through 163 removed outlier: 4.711A pdb=" N VAL A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N MET A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LEU A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 229 through 232 No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 244 through 258 removed outlier: 4.065A pdb=" N ASP A 258 " --> pdb=" O LYS A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 283 Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 299 through 307 Processing helix chain 'A' and resid 321 through 351 Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 81 through 93 Processing helix chain 'B' and resid 100 through 102 No H-bonds generated for 'chain 'B' and resid 100 through 102' Processing helix chain 'B' and resid 115 through 127 Processing helix chain 'B' and resid 139 through 147 removed outlier: 3.681A pdb=" N SER B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 197 Processing helix chain 'B' and resid 205 through 217 Processing helix chain 'B' and resid 225 through 234 Processing helix chain 'B' and resid 254 through 263 removed outlier: 3.552A pdb=" N ARG B 258 " --> pdb=" O GLU B 255 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N CYS B 259 " --> pdb=" O ARG B 256 " (cutoff:3.500A) Proline residue: B 260 - end of helix Processing helix chain 'B' and resid 266 through 269 Processing helix chain 'B' and resid 276 through 285 Processing helix chain 'B' and resid 289 through 297 removed outlier: 3.677A pdb=" N ARG B 292 " --> pdb=" O ILE B 289 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LYS B 293 " --> pdb=" O ASP B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 311 through 322 Processing helix chain 'B' and resid 337 through 349 removed outlier: 5.444A pdb=" N VAL B 341 " --> pdb=" O LYS B 338 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA B 349 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 356 removed outlier: 3.823A pdb=" N GLN B 356 " --> pdb=" O THR B 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 353 through 356' Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 369 through 375 removed outlier: 3.871A pdb=" N LYS B 375 " --> pdb=" O VAL B 372 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 190 through 193 Processing sheet with id= B, first strand: chain 'B' and resid 134 through 138 removed outlier: 6.851A pdb=" N THR B 105 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ALA B 137 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU B 107 " --> pdb=" O ALA B 137 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU B 10 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N THR B 108 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N CYS B 12 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 37 through 39 Processing sheet with id= D, first strand: chain 'B' and resid 299 through 302 removed outlier: 6.338A pdb=" N ILE B 153 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N SER B 302 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU B 155 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 240 through 243 251 hydrogen bonds defined for protein. 642 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: 4.22 Time building geometry restraints manager: 5.29 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: 782 2.12 - 2.74: 19720 2.74 - 3.36: 34527 3.36 - 3.98: 46578 3.98 - 4.60: 69628 Nonbonded interactions: 171235 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 171230 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: 0.110 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 22.100 Find NCS groups from input model: 0.140 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:15.510 Internal consistency checks: 0.000 Total: 38.140 ------------------------------------------------------------------------------- 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= 0.135 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: 0.7526 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5768 Z= 0.314 Angle : 0.509 5.242 7805 Z= 0.270 Chirality : 0.051 0.177 877 Planarity : 0.004 0.042 1004 Dihedral : 11.560 89.565 2177 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.55 % Favored : 94.88 % Rotamer: Outliers : 1.61 % Allowed : 5.14 % Favored : 93.26 % 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: -1.90 (0.28), residues: 703 helix: -1.17 (0.23), residues: 377 sheet: -1.50 (0.55), residues: 66 loop : -1.04 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 256 TYR 0.008 0.001 TYR A 330 PHE 0.010 0.002 PHE A 31 TRP 0.010 0.002 TRP A 277 HIS 0.004 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: 0.7620 moved from start: 0.1782 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= 0.459 Angle : 0.594 5.262 7805 Z= 0.322 Chirality : 0.055 0.221 877 Planarity : 0.004 0.040 1004 Dihedral : 12.419 102.503 2177 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 1.42 % Allowed : 9.25 % Favored : 89.33 % Rotamer: Outliers : 2.73 % Allowed : 4.82 % Favored : 92.46 % 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: -3.57 (0.27), residues: 703 helix: -2.18 (0.22), residues: 371 sheet: -2.28 (0.58), residues: 67 loop : -2.41 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 101 TYR 0.009 0.002 TYR A 42 PHE 0.012 0.002 PHE B 33 TRP 0.012 0.003 TRP A 277 HIS 0.006 0.001 HIS A 300 *********************** 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: 0.7631 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 5768 Z= 0.437 Angle : 0.579 4.980 7805 Z= 0.312 Chirality : 0.054 0.191 877 Planarity : 0.004 0.035 1004 Dihedral : 12.864 97.737 2177 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 1.56 % Allowed : 10.10 % Favored : 88.34 % Rotamer: Outliers : 2.73 % Allowed : 6.58 % 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: -3.97 (0.27), residues: 703 helix: -2.40 (0.22), residues: 365 sheet: -2.76 (0.56), residues: 67 loop : -2.69 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 101 TYR 0.010 0.002 TYR A 42 PHE 0.013 0.002 PHE B 33 TRP 0.010 0.002 TRP A 277 HIS 0.005 0.001 HIS B 175 *********************** 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: 10.0000 chunk 30 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2411 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= 0.477 Angle : 0.603 4.925 7805 Z= 0.327 Chirality : 0.056 0.214 877 Planarity : 0.004 0.039 1004 Dihedral : 13.089 101.095 2177 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 2.28 % Allowed : 11.81 % Favored : 85.92 % Rotamer: Outliers : 3.21 % Allowed : 5.94 % Favored : 90.85 % 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: -4.21 (0.26), residues: 703 helix: -2.50 (0.21), residues: 364 sheet: -2.94 (0.58), residues: 66 loop : -2.95 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 101 TYR 0.010 0.002 TYR A 42 PHE 0.013 0.002 PHE B 33 TRP 0.010 0.002 TRP A 277 HIS 0.005 0.001 HIS A 300 *********************** 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: 5.9990 chunk 40 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 overall best weight: 8.3994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 5768 Z= 0.411 Angle : 0.559 4.680 7805 Z= 0.300 Chirality : 0.053 0.192 877 Planarity : 0.004 0.035 1004 Dihedral : 12.972 95.982 2177 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 1.42 % Allowed : 11.52 % Favored : 87.06 % Rotamer: Outliers : 3.21 % Allowed : 5.94 % Favored : 90.85 % 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: -4.06 (0.27), residues: 703 helix: -2.37 (0.22), residues: 366 sheet: -2.99 (0.56), residues: 66 loop : -2.87 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 101 TYR 0.009 0.002 TYR A 42 PHE 0.011 0.002 PHE B 33 TRP 0.009 0.002 TRP A 277 HIS 0.004 0.001 HIS A 300 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 302.56 seconds wall clock time: 5 minutes 53.12 seconds (353.12 seconds total)