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/8g94_29861.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8g94_29861.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=3.15 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8g94_29861.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8g94_29861.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8g94_29861.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8g94_29861.map" } resolution = 3.15 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= 0.007 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 67 5.16 5 C 5939 2.51 5 N 1575 2.21 5 O 1727 1.98 5 H 9374 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 18682 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 4812 Inner-chain residues flagged as termini: ['pdbres="ILE A 37 "', 'pdbres="LYS A 46 "', 'pdbres="LYS A 239 "', 'pdbres="LYS A 250 "'] Classifications: {'peptide': 288} Modifications used: {'COO': 3, 'NH3': 3} Link IDs: {'PTRANS': 6, 'TRANS': 281} Chain breaks: 2 Chain: "B" Number of atoms: 3574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3574 Inner-chain residues flagged as termini: ['pdbres="ILE B 55 "', 'pdbres="THR B 182 "', 'pdbres="ALA B 235 "', 'pdbres="MET B 240 "'] Classifications: {'peptide': 221} Modifications used: {'COO': 3, 'NH3': 3} Link IDs: {'PTRANS': 2, 'TRANS': 218} Chain breaks: 2 Chain: "C" Number of atoms: 5095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 5095 Classifications: {'peptide': 337} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "D" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 902 Classifications: {'peptide': 58} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 3500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3500 Inner-chain residues flagged as termini: ['pdbres="SER E 120 "', 'pdbres="SER E 124 "'] Classifications: {'peptide': 231} Modifications used: {'COO': 2, 'NH3': 2} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "F" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 392 Classifications: {'peptide': 25} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'TRANS': 24} Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 407 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 26} Time building chain proxies: 5.02, per 1000 atoms: 0.27 Number of scatterers: 18682 At special positions: 0 Unit cell: (90.47, 119.52, 129.48, 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 67 16.00 O 1727 8.00 N 1575 7.00 C 5939 6.00 H 9374 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 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: 8.68 Conformation dependent library (CDL) restraints added in 1.3 seconds Finding SS restraints... Secondary structure from input PDB file: 27 helices and 12 sheets defined 35.2% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 22 through 32 Processing helix chain 'A' and resid 47 through 72 removed outlier: 3.747A pdb=" N ILE A 70 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TRP A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 104 Processing helix chain 'A' and resid 107 through 111 removed outlier: 3.816A pdb=" N TYR A 110 " --> pdb=" O ALA A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 147 Processing helix chain 'A' and resid 157 through 176 Processing helix chain 'A' and resid 200 through 234 Processing helix chain 'A' and resid 252 through 280 removed outlier: 3.549A pdb=" N LYS A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 257 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 293 through 313 removed outlier: 3.795A pdb=" N SER A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Proline residue: A 308 - end of helix Processing helix chain 'A' and resid 316 through 321 removed outlier: 3.628A pdb=" N ALA A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 31 removed outlier: 3.696A pdb=" N ALA B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 Processing helix chain 'B' and resid 208 through 215 removed outlier: 5.322A pdb=" N HIS B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N CYS B 214 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N PHE B 215 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 242 through 254 Processing helix chain 'B' and resid 271 through 280 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 296 through 309 Processing helix chain 'B' and resid 330 through 350 Processing helix chain 'C' and resid 5 through 24 Processing helix chain 'D' and resid 6 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'F' and resid 41 through 63 Processing helix chain 'G' and resid 42 through 63 Processing sheet with id= A, first strand: chain 'B' and resid 263 through 269 removed outlier: 3.736A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU B 37 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N HIS B 195 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LEU B 36 " --> pdb=" O HIS B 195 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LYS B 197 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU B 38 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE B 199 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 194 " --> pdb=" O PHE B 191 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.919A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.920A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.854A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.998A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA C 203 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.859A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 294 through 298 removed outlier: 3.720A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.686A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.883A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 128 through 130 Processing sheet with id= L, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.939A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ARG E 168 " --> pdb=" O PRO E 173 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1269 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: 5.89 Time building geometry restraints manager: 8.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.97 - 1.14: 9338 1.14 - 1.31: 1534 1.31 - 1.48: 3851 1.48 - 1.65: 4042 1.65 - 1.82: 96 Bond restraints: 18861 Sorted by residual: bond pdb=" N ILE F 55 " pdb=" H ILE F 55 " ideal model delta sigma weight residual 0.860 1.032 -0.172 2.00e-02 2.50e+03 7.42e+01 bond pdb=" N SER G 56 " pdb=" H SER G 56 " ideal model delta sigma weight residual 0.860 1.028 -0.168 2.00e-02 2.50e+03 7.09e+01 bond pdb=" N ASN C 119 " pdb=" H ASN C 119 " ideal model delta sigma weight residual 0.860 1.026 -0.166 2.00e-02 2.50e+03 6.91e+01 bond pdb=" N PHE C 335 " pdb=" H PHE C 335 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.81e+01 bond pdb=" N SER E 7 " pdb=" H SER E 7 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.77e+01 ... (remaining 18856 not shown) Histogram of bond angle deviations from ideal: 99.97 - 106.78: 279 106.78 - 113.59: 22369 113.59 - 120.41: 6110 120.41 - 127.22: 5172 127.22 - 134.03: 86 Bond angle restraints: 34016 Sorted by residual: angle pdb=" N ALA E 92 " pdb=" CA ALA E 92 " pdb=" C ALA E 92 " ideal model delta sigma weight residual 107.73 112.54 -4.81 1.61e+00 3.86e-01 8.94e+00 angle pdb=" N ASP C 291 " pdb=" CA ASP C 291 " pdb=" C ASP C 291 " ideal model delta sigma weight residual 112.93 109.95 2.98 1.12e+00 7.97e-01 7.09e+00 angle pdb=" C LEU A 290 " pdb=" N PHE A 291 " pdb=" CA PHE A 291 " ideal model delta sigma weight residual 121.54 126.12 -4.58 1.91e+00 2.74e-01 5.75e+00 angle pdb=" N SER C 277 " pdb=" CA SER C 277 " pdb=" C SER C 277 " ideal model delta sigma weight residual 108.32 111.93 -3.61 1.64e+00 3.72e-01 4.84e+00 angle pdb=" CB LYS G 58 " pdb=" CG LYS G 58 " pdb=" CD LYS G 58 " ideal model delta sigma weight residual 111.30 106.33 4.97 2.30e+00 1.89e-01 4.67e+00 ... (remaining 34011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 5935 16.96 - 33.92: 458 33.92 - 50.88: 175 50.88 - 67.84: 42 67.84 - 84.80: 11 Dihedral angle restraints: 6621 sinusoidal: 4750 harmonic: 1871 Sorted by residual: dihedral pdb=" CA GLN C 75 " pdb=" C GLN C 75 " pdb=" N ASP C 76 " pdb=" CA ASP C 76 " ideal model delta harmonic sigma weight residual 180.00 160.03 19.97 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ARG E 179 " pdb=" C ARG E 179 " pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta harmonic sigma weight residual 180.00 161.62 18.38 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 6618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 911 0.029 - 0.058: 400 0.058 - 0.087: 102 0.087 - 0.115: 59 0.115 - 0.144: 14 Chirality restraints: 1486 Sorted by residual: chirality pdb=" CA ILE B 265 " pdb=" N ILE B 265 " pdb=" C ILE B 265 " pdb=" CB ILE B 265 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA VAL C 327 " pdb=" N VAL C 327 " pdb=" C VAL C 327 " pdb=" CB VAL C 327 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA ILE C 58 " pdb=" N ILE C 58 " pdb=" C ILE C 58 " pdb=" CB ILE C 58 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 1483 not shown) Planarity restraints: 2756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 270 " -0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO A 271 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 58 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.74e+00 pdb=" C LYS G 58 " 0.023 2.00e-02 2.50e+03 pdb=" O LYS G 58 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP G 59 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 281 " -0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO B 282 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO B 282 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 282 " -0.015 5.00e-02 4.00e+02 ... (remaining 2753 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.08: 932 2.08 - 2.71: 29215 2.71 - 3.34: 54061 3.34 - 3.97: 73108 3.97 - 4.60: 108297 Nonbonded interactions: 265613 Sorted by model distance: nonbonded pdb=" OE2 GLU B 8 " pdb=" HH TYR E 163 " model vdw 1.456 1.850 nonbonded pdb=" O LEU A 174 " pdb=" HH TYR A 202 " model vdw 1.463 1.850 nonbonded pdb=" O LYS B 277 " pdb=" H SER B 281 " model vdw 1.479 1.850 nonbonded pdb=" HG1 THR C 274 " pdb=" O VAL C 315 " model vdw 1.482 1.850 nonbonded pdb=" HZ1 LYS B 210 " pdb=" OD1 ASN C 230 " model vdw 1.498 1.850 ... (remaining 265608 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=0.49 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: 0.080 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: 0.190 Extract box with map and model: 0.430 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 35.320 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:25.900 Internal consistency checks: 0.000 Total: 62.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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 0.055 9487 Z= 0.157 Angle : 0.526 6.148 12842 Z= 0.286 Chirality : 0.039 0.144 1486 Planarity : 0.003 0.034 1608 Dihedral : 12.278 84.300 3417 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.16 % Favored : 94.75 % Rotamer: Outliers : 0.49 % Allowed : 2.45 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.85 (0.22), residues: 1163 helix: -0.10 (0.23), residues: 421 sheet: -1.69 (0.29), residues: 271 loop : -1.88 (0.25), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 159 TYR 0.010 0.001 TYR E 95 PHE 0.011 0.001 PHE B 189 TRP 0.010 0.001 TRP C 339 HIS 0.002 0.001 HIS C 142 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 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 100 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 9487 Z= 0.317 Angle : 0.502 6.221 12842 Z= 0.271 Chirality : 0.052 0.186 1486 Planarity : 0.003 0.036 1608 Dihedral : 11.414 81.381 3417 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 1.03 % Allowed : 7.14 % Favored : 91.83 % Rotamer: Outliers : 0.59 % Allowed : 2.45 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -2.45 (0.22), residues: 1163 helix: -0.24 (0.23), residues: 427 sheet: -2.23 (0.26), residues: 284 loop : -2.46 (0.24), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 159 TYR 0.011 0.001 TYR E 178 PHE 0.010 0.001 PHE B 189 TRP 0.008 0.001 TRP C 339 HIS 0.002 0.001 HIS C 142 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 106 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 114 optimal weight: 40.0000 chunk 27 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 17 optimal weight: 30.0000 chunk 36 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 overall best weight: 8.7996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 9487 Z= 0.457 Angle : 0.540 5.071 12842 Z= 0.293 Chirality : 0.054 0.209 1486 Planarity : 0.003 0.029 1608 Dihedral : 11.408 74.163 3417 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 1.63 % Allowed : 9.20 % Favored : 89.17 % Rotamer: Outliers : 0.68 % Allowed : 4.21 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -2.94 (0.21), residues: 1163 helix: -0.62 (0.22), residues: 432 sheet: -2.41 (0.26), residues: 280 loop : -2.86 (0.24), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 159 TYR 0.010 0.001 TYR E 178 PHE 0.011 0.001 PHE A 161 TRP 0.010 0.001 TRP C 339 HIS 0.002 0.001 HIS C 142 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 overall best weight: 8.1992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 9487 Z= 0.378 Angle : 0.494 4.983 12842 Z= 0.268 Chirality : 0.052 0.190 1486 Planarity : 0.003 0.031 1608 Dihedral : 11.163 70.788 3417 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 1.72 % Allowed : 9.46 % Favored : 88.82 % Rotamer: Outliers : 1.17 % Allowed : 4.31 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -2.96 (0.21), residues: 1163 helix: -0.46 (0.23), residues: 423 sheet: -2.46 (0.26), residues: 288 loop : -3.01 (0.23), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 159 TYR 0.011 0.001 TYR E 178 PHE 0.010 0.001 PHE B 189 TRP 0.009 0.001 TRP C 82 HIS 0.003 0.001 HIS C 142 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 9 optimal weight: 20.0000 chunk 108 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 overall best weight: 8.7994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 9487 Z= 0.443 Angle : 0.526 4.860 12842 Z= 0.288 Chirality : 0.054 0.201 1486 Planarity : 0.003 0.031 1608 Dihedral : 11.261 69.819 3417 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 2.06 % Allowed : 10.40 % Favored : 87.53 % Rotamer: Outliers : 1.47 % Allowed : 4.89 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -3.12 (0.21), residues: 1163 helix: -0.62 (0.22), residues: 425 sheet: -2.47 (0.27), residues: 290 loop : -3.13 (0.24), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 159 TYR 0.011 0.001 TYR E 178 PHE 0.011 0.001 PHE C 235 TRP 0.009 0.001 TRP C 339 HIS 0.002 0.001 HIS C 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 81 optimal weight: 7.9990 chunk 26 optimal weight: 30.0000 chunk 70 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 chunk 1 optimal weight: 50.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 9487 Z= 0.383 Angle : 0.492 4.774 12842 Z= 0.268 Chirality : 0.052 0.193 1486 Planarity : 0.003 0.030 1608 Dihedral : 11.042 71.447 3417 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 1.81 % Allowed : 9.46 % Favored : 88.74 % Rotamer: Outliers : 1.57 % Allowed : 5.48 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -3.02 (0.21), residues: 1163 helix: -0.56 (0.22), residues: 429 sheet: -2.49 (0.27), residues: 288 loop : -3.02 (0.24), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 159 TYR 0.011 0.001 TYR E 178 PHE 0.009 0.001 PHE B 189 TRP 0.009 0.001 TRP C 339 HIS 0.003 0.001 HIS B 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 376.27 seconds wall clock time: 7 minutes 25.41 seconds (445.41 seconds total)