Starting phenix.real_space_refine on Thu Mar 14 14:38:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sai_40270/03_2024/8sai_40270_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sai_40270/03_2024/8sai_40270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sai_40270/03_2024/8sai_40270.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sai_40270/03_2024/8sai_40270.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sai_40270/03_2024/8sai_40270_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sai_40270/03_2024/8sai_40270_neut_updated.pdb" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.009 sd= 0.082 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 P 1 5.49 5 S 68 5.16 5 C 5774 2.51 5 N 1534 2.21 5 O 1685 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 303": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "D GLU 14": "OE1" <-> "OE2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D ARG 24": "NH1" <-> "NH2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D ARG 205": "NH1" <-> "NH2" Residue "D ARG 208": "NH1" <-> "NH2" Residue "D GLU 245": "OE1" <-> "OE2" Residue "D GLU 297": "OE1" <-> "OE2" Residue "E ARG 8": "NH1" <-> "NH2" Residue "E ARG 46": "NH1" <-> "NH2" Residue "E ARG 96": "NH1" <-> "NH2" Residue "E ARG 137": "NH1" <-> "NH2" Residue "E GLU 138": "OE1" <-> "OE2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E ARG 219": "NH1" <-> "NH2" Residue "E GLU 226": "OE1" <-> "OE2" Residue "E ARG 256": "NH1" <-> "NH2" Residue "S ARG 160": "NH1" <-> "NH2" Residue "S ARG 218": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9062 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2373 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 4, 'TRANS': 286} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "D" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1824 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 224} Chain breaks: 1 Chain: "E" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Classifications: {'peptide': 1} Time building chain proxies: 5.19, per 1000 atoms: 0.57 Number of scatterers: 9062 At special positions: 0 Unit cell: (92, 121.44, 132.48, 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 68 16.00 P 1 15.00 O 1685 8.00 N 1534 7.00 C 5774 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 204 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 1.7 seconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 13 sheets defined 32.8% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 54 through 74 removed outlier: 3.685A pdb=" N VAL A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 115 removed outlier: 3.655A pdb=" N CYS A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Proline residue: A 108 - end of helix Processing helix chain 'A' and resid 124 through 158 removed outlier: 3.797A pdb=" N ILE A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE A 156 " --> pdb=" O ARG A 152 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN A 157 " --> pdb=" O TYR A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 196 removed outlier: 3.548A pdb=" N LYS A 195 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 249 removed outlier: 3.886A pdb=" N ILE A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL A 225 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TRP A 228 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU A 232 " --> pdb=" O TRP A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 262 No H-bonds generated for 'chain 'A' and resid 259 through 262' Processing helix chain 'A' and resid 268 through 278 Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 286 through 294 removed outlier: 3.635A pdb=" N SER A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 330 Proline residue: A 324 - end of helix removed outlier: 4.469A pdb=" N TYR A 327 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N PHE A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 329 " --> pdb=" O VAL A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 30 through 47 removed outlier: 4.829A pdb=" N LYS C 46 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N GLU C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 27 removed outlier: 4.202A pdb=" N ALA D 11 " --> pdb=" O ALA D 7 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA D 12 " --> pdb=" O GLU D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 52 Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing helix chain 'D' and resid 212 through 215 Processing helix chain 'D' and resid 242 through 254 Processing helix chain 'D' and resid 271 through 278 Processing helix chain 'D' and resid 283 through 285 No H-bonds generated for 'chain 'D' and resid 283 through 285' Processing helix chain 'D' and resid 296 through 310 removed outlier: 3.857A pdb=" N LEU D 310 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 351 Processing helix chain 'E' and resid 2 through 24 Processing helix chain 'E' and resid 30 through 36 removed outlier: 4.704A pdb=" N ASN E 36 " --> pdb=" O GLN E 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'D' and resid 319 through 323 removed outlier: 7.042A pdb=" N ILE D 264 " --> pdb=" O TYR D 320 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N HIS D 322 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU D 266 " --> pdb=" O HIS D 322 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA D 220 " --> pdb=" O LYS D 35 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS D 224 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 58 through 63 removed outlier: 7.005A pdb=" N ALA E 73 " --> pdb=" O TYR E 59 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N MET E 61 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL E 71 " --> pdb=" O MET E 61 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N TRP E 63 " --> pdb=" O LEU E 69 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU E 69 " --> pdb=" O TRP E 63 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER E 74 " --> pdb=" O LYS E 78 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N HIS E 91 " --> pdb=" O ILE E 81 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASP E 83 " --> pdb=" O LYS E 89 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LYS E 89 " --> pdb=" O ASP E 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 102 through 105 removed outlier: 3.606A pdb=" N ARG E 137 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASN E 125 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N VAL E 135 " --> pdb=" O ASN E 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 178 through 181 removed outlier: 3.569A pdb=" N THR E 178 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR E 165 " --> pdb=" O SER E 161 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER E 161 " --> pdb=" O THR E 165 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE E 157 " --> pdb=" O TRP E 169 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 220 through 223 removed outlier: 3.717A pdb=" N GLN E 220 " --> pdb=" O LEU E 210 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER E 207 " --> pdb=" O ALA E 203 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER E 189 " --> pdb=" O GLY E 202 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 229 through 234 removed outlier: 6.783A pdb=" N GLY E 244 " --> pdb=" O ASN E 230 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE E 232 " --> pdb=" O ALA E 242 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA E 242 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE E 234 " --> pdb=" O ALA E 240 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ALA E 240 " --> pdb=" O PHE E 234 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N THR E 249 " --> pdb=" O SER E 245 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET E 262 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASP E 254 " --> pdb=" O GLU E 260 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU E 260 " --> pdb=" O ASP E 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 273 through 277 removed outlier: 6.457A pdb=" N GLY E 288 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL E 276 " --> pdb=" O LEU E 286 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU E 286 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N CYS E 294 " --> pdb=" O LEU E 308 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY E 306 " --> pdb=" O VAL E 296 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ASP E 298 " --> pdb=" O ARG E 304 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG E 304 " --> pdb=" O ASP E 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 47 through 52 removed outlier: 6.879A pdb=" N ILE E 338 " --> pdb=" O ARG E 48 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR E 50 " --> pdb=" O LEU E 336 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU E 336 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N PHE E 335 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER E 331 " --> pdb=" O PHE E 335 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS E 317 " --> pdb=" O GLY E 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.614A pdb=" N GLY S 10 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL S 12 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 140 through 142 Processing sheet with id= L, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.973A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'S' and resid 225 through 231 removed outlier: 3.684A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 384 hydrogen bonds defined for protein. 1110 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.63 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1457 1.30 - 1.43: 2440 1.43 - 1.56: 5240 1.56 - 1.69: 3 1.69 - 1.82: 101 Bond restraints: 9241 Sorted by residual: bond pdb=" C TYR A 261 " pdb=" O TYR A 261 " ideal model delta sigma weight residual 1.236 1.166 0.070 1.28e-02 6.10e+03 2.97e+01 bond pdb=" CA ARG A 208 " pdb=" C ARG A 208 " ideal model delta sigma weight residual 1.523 1.456 0.067 1.28e-02 6.10e+03 2.73e+01 bond pdb=" C ARG A 208 " pdb=" O ARG A 208 " ideal model delta sigma weight residual 1.234 1.176 0.058 1.22e-02 6.72e+03 2.29e+01 bond pdb=" C5 S12 A 401 " pdb=" O52 S12 A 401 " ideal model delta sigma weight residual 1.330 1.398 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" NE ARG A 208 " pdb=" CZ ARG A 208 " ideal model delta sigma weight residual 1.326 1.302 0.024 1.10e-02 8.26e+03 4.73e+00 ... (remaining 9236 not shown) Histogram of bond angle deviations from ideal: 99.36 - 106.29: 166 106.29 - 113.22: 5029 113.22 - 120.15: 3204 120.15 - 127.08: 4001 127.08 - 134.01: 82 Bond angle restraints: 12482 Sorted by residual: angle pdb=" CA PRO S 75 " pdb=" N PRO S 75 " pdb=" CD PRO S 75 " ideal model delta sigma weight residual 112.00 104.21 7.79 1.40e+00 5.10e-01 3.09e+01 angle pdb=" C TYR A 261 " pdb=" N ALA A 262 " pdb=" CA ALA A 262 " ideal model delta sigma weight residual 120.29 127.73 -7.44 1.42e+00 4.96e-01 2.74e+01 angle pdb=" CA LYS A 260 " pdb=" C LYS A 260 " pdb=" N TYR A 261 " ideal model delta sigma weight residual 118.43 112.44 5.99 1.33e+00 5.65e-01 2.03e+01 angle pdb=" O LYS A 260 " pdb=" C LYS A 260 " pdb=" N TYR A 261 " ideal model delta sigma weight residual 122.46 128.46 -6.00 1.38e+00 5.25e-01 1.89e+01 angle pdb=" O3 S12 A 401 " pdb=" P S12 A 401 " pdb=" O4 S12 A 401 " ideal model delta sigma weight residual 121.84 109.43 12.41 3.00e+00 1.11e-01 1.71e+01 ... (remaining 12477 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.84: 5285 28.84 - 57.68: 204 57.68 - 86.51: 12 86.51 - 115.35: 0 115.35 - 144.19: 1 Dihedral angle restraints: 5502 sinusoidal: 2174 harmonic: 3328 Sorted by residual: dihedral pdb=" CA ASN A 116 " pdb=" C ASN A 116 " pdb=" N GLN A 117 " pdb=" CA GLN A 117 " ideal model delta harmonic sigma weight residual 180.00 156.11 23.89 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" C4 S12 A 401 " pdb=" C5 S12 A 401 " pdb=" O52 S12 A 401 " pdb=" C6 S12 A 401 " ideal model delta sinusoidal sigma weight residual 176.02 31.83 144.19 1 3.00e+01 1.11e-03 1.93e+01 dihedral pdb=" CA ARG A 208 " pdb=" C ARG A 208 " pdb=" N ASP A 209 " pdb=" CA ASP A 209 " ideal model delta harmonic sigma weight residual -180.00 -160.83 -19.17 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 5499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1098 0.045 - 0.091: 252 0.091 - 0.136: 63 0.136 - 0.182: 0 0.182 - 0.227: 1 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CA ARG A 208 " pdb=" N ARG A 208 " pdb=" C ARG A 208 " pdb=" CB ARG A 208 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ILE E 93 " pdb=" N ILE E 93 " pdb=" C ILE E 93 " pdb=" CB ILE E 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA ILE S 216 " pdb=" N ILE S 216 " pdb=" C ILE S 216 " pdb=" CB ILE S 216 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 1411 not shown) Planarity restraints: 1566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.084 5.00e-02 4.00e+02 1.22e-01 2.38e+01 pdb=" N PRO S 75 " -0.211 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 208 " 0.018 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C ARG A 208 " -0.066 2.00e-02 2.50e+03 pdb=" O ARG A 208 " 0.025 2.00e-02 2.50e+03 pdb=" N ASP A 209 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 323 " -0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO A 324 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 324 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 324 " -0.031 5.00e-02 4.00e+02 ... (remaining 1563 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 552 2.74 - 3.28: 8596 3.28 - 3.82: 13972 3.82 - 4.36: 16267 4.36 - 4.90: 29580 Nonbonded interactions: 68967 Sorted by model distance: nonbonded pdb=" OG SER E 245 " pdb=" OD1 ASP E 247 " model vdw 2.199 2.440 nonbonded pdb=" OG SER E 74 " pdb=" OD1 ASP E 76 " model vdw 2.206 2.440 nonbonded pdb=" NH1 ARG S 202 " pdb=" OE1 GLU S 220 " model vdw 2.206 2.520 nonbonded pdb=" OD1 ASN A 200 " pdb=" OG1 THR A 202 " model vdw 2.228 2.440 nonbonded pdb=" OG1 THR E 274 " pdb=" O VAL E 315 " model vdw 2.280 2.440 ... (remaining 68962 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: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.680 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: 0.000 Extract box with map and model: 3.840 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.900 Find NCS groups from input model: 0.250 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 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 : 0.003 0.089 9241 Z= 0.180 Angle : 0.567 12.408 12482 Z= 0.321 Chirality : 0.039 0.227 1414 Planarity : 0.004 0.122 1566 Dihedral : 13.992 144.191 3352 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.10 % Allowed : 0.40 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.99 (0.26), residues: 1133 helix: 2.30 (0.28), residues: 379 sheet: 1.13 (0.31), residues: 294 loop : -1.14 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 339 HIS 0.003 0.000 HIS S 35 PHE 0.015 0.001 PHE A 279 TYR 0.020 0.001 TYR A 261 ARG 0.006 0.000 ARG D 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 1.034 Fit side-chains REVERT: A 74 ILE cc_start: 0.8371 (mm) cc_final: 0.8064 (mt) REVERT: D 345 LYS cc_start: 0.8220 (ttpp) cc_final: 0.7941 (mttp) REVERT: E 153 ASP cc_start: 0.7447 (p0) cc_final: 0.7197 (p0) REVERT: S 154 SER cc_start: 0.7473 (m) cc_final: 0.7043 (p) outliers start: 1 outliers final: 1 residues processed: 166 average time/residue: 0.2419 time to fit residues: 53.4324 Evaluate side-chains 130 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 0.0170 chunk 88 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 0.0370 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN A 206 HIS D 255 ASN ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9241 Z= 0.166 Angle : 0.480 7.316 12482 Z= 0.252 Chirality : 0.040 0.166 1414 Planarity : 0.004 0.071 1566 Dihedral : 6.260 101.343 1263 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.01 % Allowed : 5.84 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.04 (0.26), residues: 1133 helix: 2.39 (0.27), residues: 386 sheet: 1.17 (0.31), residues: 292 loop : -1.21 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 339 HIS 0.005 0.001 HIS S 35 PHE 0.022 0.001 PHE A 205 TYR 0.022 0.001 TYR A 261 ARG 0.003 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 129 time to evaluate : 1.151 Fit side-chains REVERT: A 279 PHE cc_start: 0.5640 (OUTLIER) cc_final: 0.4049 (t80) REVERT: D 248 LYS cc_start: 0.8417 (tttt) cc_final: 0.8000 (mmtt) REVERT: D 275 GLU cc_start: 0.7782 (tp30) cc_final: 0.7549 (tm-30) REVERT: E 153 ASP cc_start: 0.7525 (p0) cc_final: 0.7259 (p0) REVERT: S 154 SER cc_start: 0.7449 (m) cc_final: 0.7034 (p) outliers start: 10 outliers final: 7 residues processed: 135 average time/residue: 0.2504 time to fit residues: 45.1819 Evaluate side-chains 128 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 206 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 HIS ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9241 Z= 0.196 Angle : 0.498 8.354 12482 Z= 0.262 Chirality : 0.041 0.170 1414 Planarity : 0.004 0.065 1566 Dihedral : 5.371 82.501 1261 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.61 % Allowed : 8.45 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.95 (0.26), residues: 1133 helix: 2.41 (0.28), residues: 387 sheet: 0.98 (0.30), residues: 298 loop : -1.29 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 339 HIS 0.004 0.001 HIS S 35 PHE 0.019 0.002 PHE A 205 TYR 0.023 0.001 TYR A 77 ARG 0.006 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 1.465 Fit side-chains REVERT: A 74 ILE cc_start: 0.8473 (mm) cc_final: 0.8249 (mm) REVERT: D 248 LYS cc_start: 0.8458 (tttt) cc_final: 0.8057 (mmtt) REVERT: D 347 ASN cc_start: 0.7676 (t0) cc_final: 0.7463 (t0) REVERT: S 154 SER cc_start: 0.7500 (m) cc_final: 0.7091 (t) outliers start: 16 outliers final: 11 residues processed: 137 average time/residue: 0.2251 time to fit residues: 42.4130 Evaluate side-chains 132 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 121 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 137 ASP Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 206 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 0.3980 chunk 69 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9241 Z= 0.154 Angle : 0.460 8.523 12482 Z= 0.243 Chirality : 0.040 0.187 1414 Planarity : 0.003 0.060 1566 Dihedral : 4.981 58.509 1261 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.31 % Allowed : 9.86 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.99 (0.26), residues: 1133 helix: 2.47 (0.27), residues: 392 sheet: 0.93 (0.30), residues: 297 loop : -1.28 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.019 0.001 PHE A 205 TYR 0.017 0.001 TYR A 77 ARG 0.002 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 1.176 Fit side-chains REVERT: A 105 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7656 (m-10) REVERT: D 248 LYS cc_start: 0.8450 (tttt) cc_final: 0.8089 (mmtt) REVERT: D 275 GLU cc_start: 0.7787 (tp30) cc_final: 0.7567 (tm-30) REVERT: D 347 ASN cc_start: 0.7750 (t0) cc_final: 0.7445 (t0) REVERT: S 154 SER cc_start: 0.7522 (m) cc_final: 0.7099 (t) outliers start: 13 outliers final: 10 residues processed: 130 average time/residue: 0.2404 time to fit residues: 42.3308 Evaluate side-chains 133 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 259 GLN Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 158 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.0010 chunk 1 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 75 optimal weight: 0.0770 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 27 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 overall best weight: 0.4546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9241 Z= 0.124 Angle : 0.444 8.622 12482 Z= 0.234 Chirality : 0.039 0.194 1414 Planarity : 0.003 0.056 1566 Dihedral : 4.698 46.413 1261 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.51 % Allowed : 10.56 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.01 (0.26), residues: 1133 helix: 2.49 (0.27), residues: 396 sheet: 0.94 (0.30), residues: 292 loop : -1.28 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.020 0.001 PHE A 205 TYR 0.015 0.001 TYR A 77 ARG 0.002 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 0.937 Fit side-chains REVERT: A 74 ILE cc_start: 0.8443 (mm) cc_final: 0.8177 (mt) REVERT: A 105 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.7600 (m-10) REVERT: A 279 PHE cc_start: 0.6393 (OUTLIER) cc_final: 0.4384 (t80) REVERT: D 248 LYS cc_start: 0.8450 (tttt) cc_final: 0.8086 (mmtt) REVERT: D 347 ASN cc_start: 0.7719 (t0) cc_final: 0.7387 (t0) REVERT: S 154 SER cc_start: 0.7497 (m) cc_final: 0.7077 (t) outliers start: 15 outliers final: 11 residues processed: 130 average time/residue: 0.2251 time to fit residues: 39.7494 Evaluate side-chains 135 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 158 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9241 Z= 0.170 Angle : 0.462 8.524 12482 Z= 0.245 Chirality : 0.040 0.199 1414 Planarity : 0.003 0.044 1566 Dihedral : 4.689 50.009 1261 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.01 % Allowed : 10.76 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.96 (0.26), residues: 1133 helix: 2.54 (0.27), residues: 393 sheet: 0.89 (0.30), residues: 286 loop : -1.32 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 339 HIS 0.004 0.001 HIS S 35 PHE 0.019 0.001 PHE A 205 TYR 0.014 0.001 TYR A 77 ARG 0.003 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 0.818 Fit side-chains REVERT: A 74 ILE cc_start: 0.8460 (mm) cc_final: 0.8160 (mt) REVERT: A 105 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.7671 (m-10) REVERT: A 330 MET cc_start: 0.8121 (mmm) cc_final: 0.7771 (mmm) REVERT: D 248 LYS cc_start: 0.8462 (tttt) cc_final: 0.8116 (mmtt) REVERT: D 347 ASN cc_start: 0.7767 (t0) cc_final: 0.7354 (t0) REVERT: S 154 SER cc_start: 0.7491 (m) cc_final: 0.7075 (t) outliers start: 20 outliers final: 17 residues processed: 140 average time/residue: 0.2331 time to fit residues: 44.1125 Evaluate side-chains 142 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 259 GLN Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 206 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 0.0370 chunk 79 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 108 optimal weight: 0.0570 chunk 68 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9241 Z= 0.128 Angle : 0.448 9.471 12482 Z= 0.234 Chirality : 0.040 0.210 1414 Planarity : 0.003 0.044 1566 Dihedral : 4.656 54.088 1261 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.81 % Allowed : 11.67 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.04 (0.26), residues: 1133 helix: 2.60 (0.27), residues: 393 sheet: 0.97 (0.30), residues: 287 loop : -1.32 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP S 47 HIS 0.002 0.001 HIS S 35 PHE 0.019 0.001 PHE A 205 TYR 0.026 0.001 TYR A 77 ARG 0.003 0.000 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 1.100 Fit side-chains REVERT: A 74 ILE cc_start: 0.8445 (mm) cc_final: 0.8163 (mt) REVERT: A 105 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.7663 (m-10) REVERT: A 330 MET cc_start: 0.8096 (mmm) cc_final: 0.7873 (mmm) REVERT: D 248 LYS cc_start: 0.8452 (tttt) cc_final: 0.8103 (mmtt) REVERT: D 347 ASN cc_start: 0.7753 (t0) cc_final: 0.7294 (t0) REVERT: E 262 MET cc_start: 0.7942 (tpp) cc_final: 0.7719 (tpp) REVERT: S 154 SER cc_start: 0.7481 (m) cc_final: 0.7053 (t) outliers start: 18 outliers final: 16 residues processed: 132 average time/residue: 0.2208 time to fit residues: 39.9720 Evaluate side-chains 135 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 259 GLN Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 158 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 69 optimal weight: 0.0980 chunk 74 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 95 optimal weight: 0.0470 overall best weight: 1.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9241 Z= 0.242 Angle : 0.522 9.122 12482 Z= 0.273 Chirality : 0.041 0.215 1414 Planarity : 0.003 0.045 1566 Dihedral : 4.976 58.647 1261 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.11 % Allowed : 11.87 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.82 (0.25), residues: 1133 helix: 2.52 (0.28), residues: 386 sheet: 0.85 (0.30), residues: 281 loop : -1.45 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 82 HIS 0.005 0.001 HIS S 35 PHE 0.020 0.002 PHE A 205 TYR 0.024 0.002 TYR A 77 ARG 0.002 0.000 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 1.063 Fit side-chains REVERT: A 74 ILE cc_start: 0.8520 (mm) cc_final: 0.8233 (mt) REVERT: A 105 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7743 (m-10) REVERT: A 330 MET cc_start: 0.8161 (mmm) cc_final: 0.7938 (mmm) REVERT: D 248 LYS cc_start: 0.8447 (tttt) cc_final: 0.8109 (mmtt) REVERT: D 275 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7565 (tm-30) REVERT: D 318 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7167 (tt0) REVERT: D 347 ASN cc_start: 0.7792 (t0) cc_final: 0.7288 (t0) REVERT: S 154 SER cc_start: 0.7504 (m) cc_final: 0.7076 (t) outliers start: 21 outliers final: 17 residues processed: 141 average time/residue: 0.2427 time to fit residues: 45.7162 Evaluate side-chains 140 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 206 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 31 optimal weight: 0.0030 chunk 91 optimal weight: 2.9990 chunk 95 optimal weight: 0.0980 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9241 Z= 0.125 Angle : 0.460 9.407 12482 Z= 0.242 Chirality : 0.040 0.217 1414 Planarity : 0.003 0.043 1566 Dihedral : 4.841 59.725 1261 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.71 % Allowed : 12.78 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.01 (0.26), residues: 1133 helix: 2.66 (0.27), residues: 389 sheet: 0.93 (0.31), residues: 281 loop : -1.34 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.022 0.001 PHE A 318 TYR 0.022 0.001 TYR A 77 ARG 0.004 0.000 ARG D 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8498 (mm) cc_final: 0.8200 (mt) REVERT: A 105 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7631 (m-10) REVERT: A 189 MET cc_start: 0.7016 (tpp) cc_final: 0.6592 (tpt) REVERT: A 245 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6527 (mp) REVERT: A 330 MET cc_start: 0.8135 (mmm) cc_final: 0.7825 (mmm) REVERT: D 248 LYS cc_start: 0.8450 (tttt) cc_final: 0.8112 (mmtt) REVERT: D 275 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7581 (tm-30) REVERT: D 318 GLU cc_start: 0.7748 (pm20) cc_final: 0.7181 (tt0) REVERT: D 347 ASN cc_start: 0.7738 (t0) cc_final: 0.7215 (t0) REVERT: S 154 SER cc_start: 0.7526 (m) cc_final: 0.7112 (t) outliers start: 17 outliers final: 13 residues processed: 133 average time/residue: 0.2392 time to fit residues: 43.3293 Evaluate side-chains 134 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 139 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.5980 chunk 74 optimal weight: 0.0980 chunk 112 optimal weight: 0.1980 chunk 103 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 95 optimal weight: 0.0980 chunk 27 optimal weight: 4.9990 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9241 Z= 0.120 Angle : 0.451 8.268 12482 Z= 0.237 Chirality : 0.040 0.230 1414 Planarity : 0.003 0.044 1566 Dihedral : 4.702 59.739 1261 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.81 % Allowed : 13.18 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.06 (0.26), residues: 1133 helix: 2.79 (0.27), residues: 384 sheet: 0.84 (0.31), residues: 281 loop : -1.25 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 82 HIS 0.002 0.001 HIS S 35 PHE 0.022 0.001 PHE A 205 TYR 0.022 0.001 TYR A 77 ARG 0.004 0.000 ARG D 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8510 (mm) cc_final: 0.8213 (mt) REVERT: A 105 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.7633 (m-10) REVERT: A 189 MET cc_start: 0.7027 (tpp) cc_final: 0.6630 (tpt) REVERT: A 245 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6347 (mp) REVERT: A 330 MET cc_start: 0.8103 (mmm) cc_final: 0.7746 (mmm) REVERT: D 248 LYS cc_start: 0.8451 (tttt) cc_final: 0.8093 (mmtt) REVERT: D 275 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7612 (tm-30) REVERT: D 318 GLU cc_start: 0.7748 (pm20) cc_final: 0.7091 (tt0) REVERT: D 347 ASN cc_start: 0.7736 (t0) cc_final: 0.7236 (t0) REVERT: S 154 SER cc_start: 0.7464 (m) cc_final: 0.7128 (p) outliers start: 18 outliers final: 14 residues processed: 134 average time/residue: 0.2286 time to fit residues: 41.6748 Evaluate side-chains 135 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 158 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.117445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.091680 restraints weight = 16393.391| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.13 r_work: 0.3100 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9241 Z= 0.197 Angle : 0.509 8.690 12482 Z= 0.266 Chirality : 0.041 0.216 1414 Planarity : 0.003 0.045 1566 Dihedral : 4.827 57.375 1261 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.71 % Allowed : 13.28 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.94 (0.25), residues: 1133 helix: 2.62 (0.27), residues: 391 sheet: 0.87 (0.30), residues: 288 loop : -1.43 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 82 HIS 0.004 0.001 HIS S 35 PHE 0.025 0.001 PHE A 205 TYR 0.024 0.001 TYR A 77 ARG 0.005 0.000 ARG D 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2130.69 seconds wall clock time: 39 minutes 9.39 seconds (2349.39 seconds total)