Starting phenix.real_space_refine on Sun May 19 16:30:35 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+local_grid_search+nqh_flips resolution=3.15 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { 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" 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" } resolution = 3.15 refinement { run = *minimization_global rigid_body *local_grid_search morphing \ simulated_annealing adp occupancy *nqh_flips } 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: 0.01s 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: 2.82, per 1000 atoms: 0.15 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: 4.19 Conformation dependent library (CDL) restraints added in 603.6 milliseconds 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 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: 0.46 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: 3.30 Time building geometry restraints manager: 4.75 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: 8163 16.96 - 33.92: 458 33.92 - 50.88: 175 50.88 - 67.84: 42 67.84 - 84.80: 11 Dihedral angle restraints: 8849 sinusoidal: 4750 harmonic: 4099 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 8846 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: 0.060 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: 0.100 Extract box with map and model: 0.270 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 21.030 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:15.450 Internal consistency checks: 0.000 Total: 37.870 ------------------------------------------------------------------------------- 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 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Evaluate side-chains 245 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 240 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.7774 (mtm) cc_final: 0.7524 (mtp) REVERT: B 9 ASP cc_start: 0.8422 (m-30) cc_final: 0.8098 (m-30) REVERT: C 10 GLU cc_start: 0.8544 (tt0) cc_final: 0.8308 (tt0) REVERT: C 67 SER cc_start: 0.9129 (m) cc_final: 0.8864 (t) REVERT: D 14 LYS cc_start: 0.9158 (tppp) cc_final: 0.8956 (tttp) REVERT: D 18 GLN cc_start: 0.8655 (tp40) cc_final: 0.8197 (tp-100) outliers start: 5 outliers final: 3 residues processed: 243 average time/residue: 0.4710 time to fit residues: 152.9447 Evaluate side-chains 192 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 189 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain G residue 60 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- 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: 8.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS B 311 ASN E 82 GLN G 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9487 Z= 0.313 Angle : 0.521 5.517 12842 Z= 0.280 Chirality : 0.039 0.170 1486 Planarity : 0.003 0.039 1608 Dihedral : 5.822 66.169 1298 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.96 % Allowed : 8.02 % Favored : 90.02 % 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: -1.03 (0.23), residues: 1163 helix: 0.90 (0.25), residues: 426 sheet: -1.60 (0.28), residues: 278 loop : -1.52 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 24 TYR 0.010 0.001 TYR E 178 PHE 0.014 0.001 PHE A 158 TRP 0.010 0.001 TRP C 339 HIS 0.004 0.001 HIS A 201 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 194 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 PHE cc_start: 0.8032 (m-80) cc_final: 0.7690 (m-10) REVERT: B 9 ASP cc_start: 0.8439 (m-30) cc_final: 0.8080 (m-30) REVERT: C 10 GLU cc_start: 0.8534 (tt0) cc_final: 0.8114 (tt0) REVERT: C 67 SER cc_start: 0.9201 (m) cc_final: 0.8937 (t) REVERT: D 18 GLN cc_start: 0.8669 (tp40) cc_final: 0.8336 (tp-100) REVERT: D 20 LYS cc_start: 0.8990 (mttm) cc_final: 0.8687 (mttm) outliers start: 20 outliers final: 13 residues processed: 201 average time/residue: 0.3035 time to fit residues: 83.6685 Evaluate side-chains 197 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 184 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 52 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 106 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN C 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9487 Z= 0.246 Angle : 0.493 5.266 12842 Z= 0.263 Chirality : 0.038 0.145 1486 Planarity : 0.003 0.041 1608 Dihedral : 4.952 59.930 1291 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.66 % Allowed : 9.30 % Favored : 89.04 % 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: -0.55 (0.24), residues: 1163 helix: 1.41 (0.25), residues: 423 sheet: -1.34 (0.29), residues: 273 loop : -1.36 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 197 TYR 0.009 0.001 TYR E 178 PHE 0.009 0.001 PHE A 322 TRP 0.010 0.001 TRP C 339 HIS 0.002 0.001 HIS B 213 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 190 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 PHE cc_start: 0.8129 (m-80) cc_final: 0.7827 (m-10) REVERT: B 9 ASP cc_start: 0.8389 (m-30) cc_final: 0.8024 (m-30) REVERT: B 29 LYS cc_start: 0.8872 (ttmt) cc_final: 0.8549 (tttm) REVERT: C 10 GLU cc_start: 0.8533 (tt0) cc_final: 0.8094 (tt0) REVERT: C 67 SER cc_start: 0.9195 (m) cc_final: 0.8924 (t) REVERT: D 14 LYS cc_start: 0.9047 (tttp) cc_final: 0.8815 (ttpp) REVERT: D 20 LYS cc_start: 0.8996 (mttm) cc_final: 0.8703 (mttm) REVERT: E 171 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7976 (mt0) outliers start: 17 outliers final: 13 residues processed: 195 average time/residue: 0.2303 time to fit residues: 62.8616 Evaluate side-chains 194 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 180 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain G residue 51 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN B 52 GLN B 269 ASN C 220 GLN D 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9487 Z= 0.291 Angle : 0.499 5.194 12842 Z= 0.269 Chirality : 0.039 0.147 1486 Planarity : 0.003 0.036 1608 Dihedral : 4.784 50.693 1291 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.86 % Allowed : 9.78 % Favored : 88.36 % 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: -0.32 (0.24), residues: 1163 helix: 1.65 (0.25), residues: 423 sheet: -1.33 (0.29), residues: 275 loop : -1.20 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 197 TYR 0.010 0.001 TYR E 95 PHE 0.010 0.001 PHE B 189 TRP 0.011 0.001 TRP C 339 HIS 0.003 0.001 HIS B 213 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 186 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 ASP cc_start: 0.8368 (m-30) cc_final: 0.8009 (m-30) REVERT: B 29 LYS cc_start: 0.8865 (ttmt) cc_final: 0.8538 (tttm) REVERT: C 10 GLU cc_start: 0.8531 (tt0) cc_final: 0.8115 (tt0) REVERT: C 67 SER cc_start: 0.9191 (m) cc_final: 0.8899 (t) REVERT: C 163 ASP cc_start: 0.7828 (m-30) cc_final: 0.7595 (m-30) REVERT: D 14 LYS cc_start: 0.9078 (tttp) cc_final: 0.8840 (ttpp) REVERT: D 20 LYS cc_start: 0.8987 (mttm) cc_final: 0.8710 (mttm) outliers start: 19 outliers final: 17 residues processed: 192 average time/residue: 0.2284 time to fit residues: 60.2221 Evaluate side-chains 197 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 180 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain G residue 51 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- 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: 9.9990 chunk 42 optimal weight: 10.0000 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: 8.9990 chunk 40 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 182 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9487 Z= 0.389 Angle : 0.534 5.218 12842 Z= 0.290 Chirality : 0.040 0.232 1486 Planarity : 0.003 0.037 1608 Dihedral : 4.804 39.077 1291 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.05 % Allowed : 10.27 % Favored : 87.67 % 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: -0.32 (0.24), residues: 1163 helix: 1.53 (0.25), residues: 428 sheet: -1.27 (0.29), residues: 273 loop : -1.14 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 197 TYR 0.010 0.001 TYR E 178 PHE 0.011 0.001 PHE B 189 TRP 0.011 0.001 TRP C 339 HIS 0.003 0.001 HIS B 213 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 182 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 ASP cc_start: 0.8352 (m-30) cc_final: 0.7983 (m-30) REVERT: B 29 LYS cc_start: 0.8876 (ttmt) cc_final: 0.8556 (tttm) REVERT: C 10 GLU cc_start: 0.8523 (tt0) cc_final: 0.8112 (tt0) REVERT: C 67 SER cc_start: 0.9219 (m) cc_final: 0.8917 (t) REVERT: C 163 ASP cc_start: 0.7843 (m-30) cc_final: 0.7590 (m-30) REVERT: C 217 MET cc_start: 0.7866 (ptp) cc_final: 0.7640 (ptp) REVERT: D 14 LYS cc_start: 0.9086 (tttp) cc_final: 0.8857 (ttpp) REVERT: D 20 LYS cc_start: 0.9000 (mttm) cc_final: 0.8726 (mttm) outliers start: 21 outliers final: 21 residues processed: 190 average time/residue: 0.1987 time to fit residues: 52.3164 Evaluate side-chains 199 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 178 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain G residue 51 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 81 optimal weight: 7.9990 chunk 26 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 110 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 1 optimal weight: 0.0000 overall best weight: 3.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9487 Z= 0.196 Angle : 0.495 6.344 12842 Z= 0.263 Chirality : 0.039 0.218 1486 Planarity : 0.003 0.039 1608 Dihedral : 4.513 32.272 1291 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.27 % Allowed : 11.25 % Favored : 87.48 % 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: -0.01 (0.25), residues: 1163 helix: 1.91 (0.25), residues: 418 sheet: -1.18 (0.29), residues: 274 loop : -0.98 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 8 TYR 0.010 0.001 TYR A 225 PHE 0.010 0.001 PHE B 189 TRP 0.011 0.001 TRP C 339 HIS 0.002 0.001 HIS A 199 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1075.73 seconds wall clock time: 19 minutes 18.04 seconds (1158.04 seconds total)