Starting phenix.real_space_refine on Wed Feb 14 01:58:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ejx_31164/02_2024/7ejx_31164_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ejx_31164/02_2024/7ejx_31164.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ejx_31164/02_2024/7ejx_31164_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ejx_31164/02_2024/7ejx_31164_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ejx_31164/02_2024/7ejx_31164_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ejx_31164/02_2024/7ejx_31164.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ejx_31164/02_2024/7ejx_31164.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ejx_31164/02_2024/7ejx_31164_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ejx_31164/02_2024/7ejx_31164_neut_updated.pdb" } resolution = 2.4 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= -0.000 sd= 0.020 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: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5321 2.51 5 N 1429 2.21 5 O 1527 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 155": "NH1" <-> "NH2" Residue "R ARG 217": "NH1" <-> "NH2" Residue "R ARG 220": "NH1" <-> "NH2" Residue "R ARG 280": "NH1" <-> "NH2" Residue "R ARG 339": "NH1" <-> "NH2" Residue "R GLU 342": "OE1" <-> "OE2" Residue "A GLU 8": "OE1" <-> "OE2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8334 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1728 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved chain links: 1 Chain breaks: 2 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 5 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1710 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 212} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2577 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 431 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1768 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "R" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Unusual residues: {'CLR': 3, 'J5F': 1} Classifications: {'undetermined': 4, 'water': 2} Link IDs: {None: 5} Time building chain proxies: 5.11, per 1000 atoms: 0.61 Number of scatterers: 8334 At special positions: 0 Unit cell: (89.64, 118.69, 125.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1527 8.00 N 1429 7.00 C 5321 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 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: 3.30 Conformation dependent library (CDL) restraints added in 1.8 seconds 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1982 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 12 sheets defined 34.5% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'R' and resid 38 through 58 removed outlier: 3.586A pdb=" N ALA R 42 " --> pdb=" O TYR R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 62 No H-bonds generated for 'chain 'R' and resid 60 through 62' Processing helix chain 'R' and resid 65 through 84 removed outlier: 3.930A pdb=" N PHE R 69 " --> pdb=" O THR R 65 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE R 70 " --> pdb=" O SER R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 114 through 143 Processing helix chain 'R' and resid 146 through 152 Processing helix chain 'R' and resid 155 through 174 Processing helix chain 'R' and resid 192 through 227 removed outlier: 3.802A pdb=" N VAL R 223 " --> pdb=" O VAL R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 308 removed outlier: 3.650A pdb=" N CYS R 290 " --> pdb=" O VAL R 286 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 315 through 337 removed outlier: 3.838A pdb=" N SER R 329 " --> pdb=" O CYS R 325 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA R 330 " --> pdb=" O CYS R 326 " (cutoff:3.500A) Proline residue: R 333 - end of helix Processing helix chain 'R' and resid 341 through 350 Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.609A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.922A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 5 through 24 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 30 through 47 removed outlier: 5.133A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 322 removed outlier: 6.673A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.741A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.983A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.299A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.791A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.584A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.339A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.616A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 4 through 7 Processing sheet with id= J, first strand: chain 'S' and resid 115 through 117 removed outlier: 5.812A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.462A pdb=" N LYS S 232 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 143 through 148 389 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: 2.56 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1323 1.31 - 1.43: 2309 1.43 - 1.56: 4792 1.56 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 8504 Sorted by residual: bond pdb=" N LEU R 176 " pdb=" CA LEU R 176 " ideal model delta sigma weight residual 1.455 1.499 -0.044 9.60e-03 1.09e+04 2.10e+01 bond pdb=" N PRO B 236 " pdb=" CD PRO B 236 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.83e+01 bond pdb=" C PHE B 235 " pdb=" N PRO B 236 " ideal model delta sigma weight residual 1.334 1.390 -0.056 1.51e-02 4.39e+03 1.36e+01 bond pdb=" C SER R 304 " pdb=" O SER R 304 " ideal model delta sigma weight residual 1.237 1.195 0.041 1.17e-02 7.31e+03 1.25e+01 bond pdb=" CA SER R 304 " pdb=" CB SER R 304 " ideal model delta sigma weight residual 1.528 1.475 0.053 1.56e-02 4.11e+03 1.17e+01 ... (remaining 8499 not shown) Histogram of bond angle deviations from ideal: 59.67 - 75.36: 3 75.36 - 91.05: 0 91.05 - 106.75: 213 106.75 - 122.44: 10076 122.44 - 138.13: 1251 Bond angle restraints: 11543 Sorted by residual: angle pdb=" N SER R 307 " pdb=" CA SER R 307 " pdb=" C SER R 307 " ideal model delta sigma weight residual 112.54 103.34 9.20 1.22e+00 6.72e-01 5.68e+01 angle pdb=" N THR A 324 " pdb=" CA THR A 324 " pdb=" C THR A 324 " ideal model delta sigma weight residual 108.56 121.45 -12.89 1.74e+00 3.30e-01 5.49e+01 angle pdb=" CA LEU R 176 " pdb=" C LEU R 176 " pdb=" N PRO R 177 " ideal model delta sigma weight residual 117.95 122.35 -4.40 7.70e-01 1.69e+00 3.26e+01 angle pdb=" N ARG A 205 " pdb=" CA ARG A 205 " pdb=" C ARG A 205 " ideal model delta sigma weight residual 108.63 117.24 -8.61 1.60e+00 3.91e-01 2.89e+01 angle pdb=" N PRO R 178 " pdb=" CA PRO R 178 " pdb=" C PRO R 178 " ideal model delta sigma weight residual 113.40 120.37 -6.97 1.34e+00 5.57e-01 2.71e+01 ... (remaining 11538 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.01: 4821 25.01 - 50.02: 301 50.02 - 75.03: 42 75.03 - 100.04: 7 100.04 - 125.05: 1 Dihedral angle restraints: 5172 sinusoidal: 2094 harmonic: 3078 Sorted by residual: dihedral pdb=" C11 J5F R 401 " pdb=" C4 J5F R 401 " pdb=" C5 J5F R 401 " pdb=" N6 J5F R 401 " ideal model delta sinusoidal sigma weight residual 111.43 -123.52 -125.05 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 160.17 19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" C LEU B 198 " pdb=" N LEU B 198 " pdb=" CA LEU B 198 " pdb=" CB LEU B 198 " ideal model delta harmonic sigma weight residual -122.60 -113.91 -8.69 0 2.50e+00 1.60e-01 1.21e+01 ... (remaining 5169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1205 0.071 - 0.142: 105 0.142 - 0.213: 16 0.213 - 0.285: 4 0.285 - 0.356: 2 Chirality restraints: 1332 Sorted by residual: chirality pdb=" CA THR A 324 " pdb=" N THR A 324 " pdb=" C THR A 324 " pdb=" CB THR A 324 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CA LEU R 281 " pdb=" N LEU R 281 " pdb=" C LEU R 281 " pdb=" CB LEU R 281 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA LEU B 198 " pdb=" N LEU B 198 " pdb=" C LEU B 198 " pdb=" CB LEU B 198 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 1329 not shown) Planarity restraints: 1438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 281 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.80e+00 pdb=" C LEU R 281 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU R 281 " 0.016 2.00e-02 2.50e+03 pdb=" N SER R 282 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C13 J5F R 401 " 0.020 2.00e-02 2.50e+03 1.53e-02 3.51e+00 pdb=" C2 J5F R 401 " -0.007 2.00e-02 2.50e+03 pdb=" C20 J5F R 401 " 0.002 2.00e-02 2.50e+03 pdb=" C3 J5F R 401 " 0.015 2.00e-02 2.50e+03 pdb=" N12 J5F R 401 " -0.027 2.00e-02 2.50e+03 pdb=" O1 J5F R 401 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 280 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" C ARG R 280 " -0.028 2.00e-02 2.50e+03 pdb=" O ARG R 280 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU R 281 " 0.010 2.00e-02 2.50e+03 ... (remaining 1435 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 84 2.59 - 3.17: 7071 3.17 - 3.75: 12867 3.75 - 4.32: 19016 4.32 - 4.90: 31498 Nonbonded interactions: 70536 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.016 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.044 2.440 nonbonded pdb=" OD2 ASP B 83 " pdb=" OG1 THR B 86 " model vdw 2.073 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.121 2.440 nonbonded pdb=" OG SER S 149 " pdb=" O LYS S 151 " model vdw 2.141 2.440 ... (remaining 70531 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: 1.920 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: 0.010 Extract box with map and model: 7.140 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.950 Find NCS groups from input model: 0.270 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: 0.010 Load rotamer database and sin/cos tables:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 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 : 0.004 0.060 8504 Z= 0.250 Angle : 0.711 13.127 11543 Z= 0.420 Chirality : 0.047 0.356 1332 Planarity : 0.002 0.024 1438 Dihedral : 15.676 125.054 3184 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.25 % Allowed : 17.52 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % 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: 1.71 (0.27), residues: 1045 helix: 3.06 (0.27), residues: 354 sheet: 0.94 (0.32), residues: 265 loop : -0.43 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 322 HIS 0.005 0.001 HIS A 188 PHE 0.009 0.001 PHE B 234 TYR 0.009 0.001 TYR S 103 ARG 0.004 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 137 time to evaluate : 0.944 Fit side-chains TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: A 6 SER cc_start: 0.8274 (t) cc_final: 0.7999 (p) REVERT: A 17 LYS cc_start: 0.7391 (mmtt) cc_final: 0.7011 (mtpt) REVERT: A 24 ARG cc_start: 0.7748 (ttp-110) cc_final: 0.7538 (ttp80) REVERT: A 208 ARG cc_start: 0.7965 (ttm170) cc_final: 0.7333 (ttp-110) REVERT: A 269 ASN cc_start: 0.8514 (m110) cc_final: 0.8307 (m110) REVERT: B 44 GLN cc_start: 0.8459 (mm-40) cc_final: 0.7951 (mt0) REVERT: G 47 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7908 (mt-10) REVERT: S 120 SER cc_start: 0.8590 (t) cc_final: 0.8118 (p) REVERT: S 174 GLN cc_start: 0.8282 (tt0) cc_final: 0.8040 (tt0) outliers start: 11 outliers final: 5 residues processed: 146 average time/residue: 1.2952 time to fit residues: 200.5656 Evaluate side-chains 120 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 115 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 220 ARG Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS B 175 GLN B 237 ASN B 340 ASN G 59 ASN S 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8504 Z= 0.206 Angle : 0.560 15.195 11543 Z= 0.282 Chirality : 0.042 0.273 1332 Planarity : 0.003 0.027 1438 Dihedral : 7.334 126.925 1371 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.98 % Allowed : 19.00 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % 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: 1.80 (0.27), residues: 1045 helix: 3.32 (0.27), residues: 352 sheet: 0.68 (0.31), residues: 267 loop : -0.31 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.011 0.001 PHE B 151 TYR 0.010 0.001 TYR S 178 ARG 0.004 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 120 time to evaluate : 0.977 Fit side-chains TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 49 ASN cc_start: 0.8182 (m-40) cc_final: 0.7799 (m110) REVERT: R 196 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7784 (pp) REVERT: A 6 SER cc_start: 0.8286 (t) cc_final: 0.8024 (p) REVERT: A 17 LYS cc_start: 0.7685 (mmtt) cc_final: 0.7287 (mtpt) REVERT: A 24 ARG cc_start: 0.7789 (ttp-110) cc_final: 0.7575 (ttp80) REVERT: A 208 ARG cc_start: 0.7943 (ttm170) cc_final: 0.7349 (ttp-110) REVERT: B 44 GLN cc_start: 0.8379 (mm-40) cc_final: 0.8003 (mt0) REVERT: G 17 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7287 (mm-30) REVERT: G 42 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7413 (mt-10) REVERT: S 174 GLN cc_start: 0.8351 (tt0) cc_final: 0.8114 (tt0) outliers start: 35 outliers final: 18 residues processed: 144 average time/residue: 1.2905 time to fit residues: 197.4554 Evaluate side-chains 129 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 220 ARG Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 332 ASN A 244 HIS S 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8504 Z= 0.286 Angle : 0.566 11.318 11543 Z= 0.291 Chirality : 0.043 0.217 1332 Planarity : 0.004 0.029 1438 Dihedral : 6.997 119.569 1367 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.44 % Allowed : 19.57 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % 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: 1.62 (0.27), residues: 1045 helix: 3.16 (0.26), residues: 353 sheet: 0.53 (0.29), residues: 297 loop : -0.43 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.014 0.001 PHE B 151 TYR 0.011 0.001 TYR S 103 ARG 0.007 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 112 time to evaluate : 1.012 Fit side-chains TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 51 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.7223 (ttm) REVERT: R 196 LEU cc_start: 0.8264 (tt) cc_final: 0.7749 (pp) REVERT: A 6 SER cc_start: 0.8421 (t) cc_final: 0.8159 (p) REVERT: A 17 LYS cc_start: 0.7668 (mmtt) cc_final: 0.7333 (mttp) REVERT: A 24 ARG cc_start: 0.7810 (ttp-110) cc_final: 0.7589 (ttp80) REVERT: A 208 ARG cc_start: 0.7947 (ttm170) cc_final: 0.7326 (ttp-110) REVERT: B 44 GLN cc_start: 0.8384 (mm-40) cc_final: 0.8029 (mt0) REVERT: G 17 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7327 (mm-30) REVERT: S 19 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8308 (tttm) REVERT: S 174 GLN cc_start: 0.8350 (tt0) cc_final: 0.8131 (tt0) outliers start: 39 outliers final: 18 residues processed: 143 average time/residue: 1.2843 time to fit residues: 194.8171 Evaluate side-chains 127 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 51 MET Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 220 ARG Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 332 ASN A 244 HIS G 59 ASN S 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8504 Z= 0.197 Angle : 0.511 9.289 11543 Z= 0.264 Chirality : 0.041 0.197 1332 Planarity : 0.003 0.032 1438 Dihedral : 6.896 117.886 1367 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.55 % Allowed : 19.80 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % 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: 1.69 (0.26), residues: 1045 helix: 3.19 (0.26), residues: 358 sheet: 0.57 (0.30), residues: 278 loop : -0.37 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE B 151 TYR 0.010 0.001 TYR S 178 ARG 0.007 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 112 time to evaluate : 1.000 Fit side-chains TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 51 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7216 (ttm) REVERT: R 196 LEU cc_start: 0.8238 (tt) cc_final: 0.7723 (pp) REVERT: A 6 SER cc_start: 0.8318 (t) cc_final: 0.8075 (p) REVERT: A 17 LYS cc_start: 0.7724 (mmtt) cc_final: 0.7428 (mttp) REVERT: A 24 ARG cc_start: 0.7827 (ttp-110) cc_final: 0.7605 (ttp80) REVERT: A 208 ARG cc_start: 0.7947 (ttm170) cc_final: 0.7319 (ttp-110) REVERT: B 44 GLN cc_start: 0.8401 (mm-40) cc_final: 0.8079 (mt0) REVERT: G 17 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7315 (mm-30) REVERT: G 42 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7338 (mt-10) REVERT: S 19 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8322 (tttm) REVERT: S 174 GLN cc_start: 0.8371 (tt0) cc_final: 0.8160 (tt0) outliers start: 40 outliers final: 23 residues processed: 142 average time/residue: 1.2435 time to fit residues: 187.5592 Evaluate side-chains 133 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 106 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 51 MET Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 220 ARG Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 0.0570 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 244 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8504 Z= 0.166 Angle : 0.490 7.876 11543 Z= 0.255 Chirality : 0.040 0.220 1332 Planarity : 0.003 0.036 1438 Dihedral : 6.913 116.623 1367 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.66 % Allowed : 19.57 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % 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: 1.70 (0.26), residues: 1045 helix: 3.23 (0.26), residues: 358 sheet: 0.47 (0.30), residues: 280 loop : -0.32 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS R 131 PHE 0.011 0.001 PHE B 151 TYR 0.010 0.001 TYR S 178 ARG 0.009 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 110 time to evaluate : 0.946 Fit side-chains TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 196 LEU cc_start: 0.8215 (tt) cc_final: 0.7707 (pp) REVERT: A 6 SER cc_start: 0.8223 (t) cc_final: 0.7993 (p) REVERT: A 17 LYS cc_start: 0.7698 (mmtt) cc_final: 0.7430 (mttp) REVERT: A 24 ARG cc_start: 0.7822 (ttp-110) cc_final: 0.7602 (ttp80) REVERT: A 208 ARG cc_start: 0.7915 (ttm170) cc_final: 0.7309 (ttp-110) REVERT: B 44 GLN cc_start: 0.8434 (mm-40) cc_final: 0.8099 (mt0) REVERT: G 42 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7380 (mp0) outliers start: 41 outliers final: 24 residues processed: 142 average time/residue: 1.1589 time to fit residues: 175.5451 Evaluate side-chains 135 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 220 ARG Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 59 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 52 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS A 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8504 Z= 0.189 Angle : 0.504 7.717 11543 Z= 0.263 Chirality : 0.041 0.186 1332 Planarity : 0.003 0.035 1438 Dihedral : 6.931 116.276 1367 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.44 % Allowed : 20.71 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % 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: 1.69 (0.26), residues: 1045 helix: 3.18 (0.26), residues: 360 sheet: 0.46 (0.30), residues: 275 loop : -0.28 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE B 151 TYR 0.010 0.001 TYR S 178 ARG 0.009 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 109 time to evaluate : 0.953 Fit side-chains TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 41 LEU cc_start: 0.7744 (tt) cc_final: 0.7454 (tm) REVERT: R 152 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7774 (tt) REVERT: R 196 LEU cc_start: 0.8207 (tt) cc_final: 0.7706 (pp) REVERT: R 341 GLU cc_start: 0.7824 (tp30) cc_final: 0.7402 (mm-30) REVERT: A 6 SER cc_start: 0.8278 (t) cc_final: 0.8053 (p) REVERT: A 17 LYS cc_start: 0.7688 (mmtt) cc_final: 0.7436 (mttp) REVERT: A 24 ARG cc_start: 0.7821 (ttp-110) cc_final: 0.7605 (ttp80) REVERT: A 208 ARG cc_start: 0.7914 (ttm170) cc_final: 0.7299 (ttp-110) REVERT: B 44 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8088 (mt0) REVERT: G 42 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7417 (mp0) outliers start: 39 outliers final: 24 residues processed: 137 average time/residue: 1.2231 time to fit residues: 178.2043 Evaluate side-chains 134 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 108 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 152 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 220 ARG Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8504 Z= 0.213 Angle : 0.516 7.866 11543 Z= 0.269 Chirality : 0.041 0.163 1332 Planarity : 0.003 0.034 1438 Dihedral : 6.890 116.138 1367 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.98 % Allowed : 20.93 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % 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: 1.67 (0.27), residues: 1045 helix: 3.10 (0.26), residues: 362 sheet: 0.45 (0.30), residues: 290 loop : -0.26 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE B 151 TYR 0.010 0.001 TYR S 178 ARG 0.008 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 108 time to evaluate : 0.963 Fit side-chains TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 51 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.7308 (ttm) REVERT: R 152 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7796 (tt) REVERT: R 196 LEU cc_start: 0.8166 (tt) cc_final: 0.7666 (pp) REVERT: R 341 GLU cc_start: 0.7768 (tp30) cc_final: 0.7342 (mm-30) REVERT: A 6 SER cc_start: 0.8323 (t) cc_final: 0.8103 (p) REVERT: A 17 LYS cc_start: 0.7674 (mmtt) cc_final: 0.7396 (mtpt) REVERT: A 24 ARG cc_start: 0.7827 (ttp-110) cc_final: 0.7613 (ttp80) REVERT: A 208 ARG cc_start: 0.7911 (ttm170) cc_final: 0.7338 (ttp-110) REVERT: B 44 GLN cc_start: 0.8393 (mm-40) cc_final: 0.8062 (mt0) REVERT: G 42 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7435 (mp0) REVERT: S 19 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8346 (tttm) outliers start: 35 outliers final: 26 residues processed: 135 average time/residue: 1.2362 time to fit residues: 177.5752 Evaluate side-chains 137 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 107 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 51 MET Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 152 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 220 ARG Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 78 optimal weight: 0.0870 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 87 optimal weight: 0.0070 chunk 93 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 332 ASN A 244 HIS B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8504 Z= 0.158 Angle : 0.488 8.036 11543 Z= 0.254 Chirality : 0.040 0.161 1332 Planarity : 0.003 0.031 1438 Dihedral : 6.701 115.581 1367 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.10 % Allowed : 20.82 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % 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: 1.75 (0.26), residues: 1045 helix: 3.21 (0.26), residues: 362 sheet: 0.42 (0.30), residues: 280 loop : -0.18 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 131 PHE 0.011 0.001 PHE B 151 TYR 0.010 0.001 TYR S 178 ARG 0.008 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 108 time to evaluate : 0.987 Fit side-chains TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 41 LEU cc_start: 0.7735 (tt) cc_final: 0.7464 (tm) REVERT: R 51 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.7297 (ttm) REVERT: R 152 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7767 (tt) REVERT: R 196 LEU cc_start: 0.8168 (tt) cc_final: 0.7692 (pp) REVERT: R 332 ASN cc_start: 0.7748 (OUTLIER) cc_final: 0.7534 (m110) REVERT: R 341 GLU cc_start: 0.7790 (tp30) cc_final: 0.7404 (mm-30) REVERT: A 6 SER cc_start: 0.8191 (t) cc_final: 0.7978 (p) REVERT: A 17 LYS cc_start: 0.7669 (mmtt) cc_final: 0.7396 (mtpt) REVERT: A 24 ARG cc_start: 0.7829 (ttp-110) cc_final: 0.7611 (ttp80) REVERT: A 208 ARG cc_start: 0.7904 (ttm170) cc_final: 0.7344 (ttp-110) REVERT: B 44 GLN cc_start: 0.8368 (mm-40) cc_final: 0.8126 (mt0) REVERT: G 42 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: S 19 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8347 (tttm) outliers start: 36 outliers final: 24 residues processed: 136 average time/residue: 1.2435 time to fit residues: 179.6749 Evaluate side-chains 138 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 109 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 51 MET Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 152 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 220 ARG Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 332 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 0.0970 chunk 56 optimal weight: 2.9990 chunk 40 optimal weight: 0.0770 chunk 73 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 93 optimal weight: 0.2980 chunk 61 optimal weight: 0.6980 chunk 98 optimal weight: 0.0040 chunk 60 optimal weight: 0.6980 overall best weight: 0.2348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8504 Z= 0.123 Angle : 0.477 8.914 11543 Z= 0.247 Chirality : 0.039 0.160 1332 Planarity : 0.003 0.042 1438 Dihedral : 6.403 112.751 1365 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.41 % Allowed : 21.96 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % 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: 1.82 (0.27), residues: 1045 helix: 3.30 (0.26), residues: 362 sheet: 0.37 (0.29), residues: 279 loop : -0.11 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS R 131 PHE 0.009 0.001 PHE B 151 TYR 0.009 0.001 TYR S 178 ARG 0.010 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 115 time to evaluate : 0.957 Fit side-chains TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 152 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7735 (tt) REVERT: R 196 LEU cc_start: 0.8179 (tt) cc_final: 0.7696 (pp) REVERT: R 220 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7564 (mtm-85) REVERT: R 341 GLU cc_start: 0.7759 (tp30) cc_final: 0.7419 (mm-30) REVERT: A 6 SER cc_start: 0.8085 (t) cc_final: 0.7885 (p) REVERT: A 17 LYS cc_start: 0.7661 (mmtt) cc_final: 0.7393 (mtpt) REVERT: A 24 ARG cc_start: 0.7809 (ttp-110) cc_final: 0.7602 (ttp80) REVERT: A 208 ARG cc_start: 0.7879 (ttm170) cc_final: 0.7316 (ttp-110) REVERT: B 44 GLN cc_start: 0.8366 (mm-40) cc_final: 0.8119 (mt0) REVERT: G 42 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: S 19 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8346 (tttm) outliers start: 30 outliers final: 16 residues processed: 136 average time/residue: 1.2899 time to fit residues: 185.9249 Evaluate side-chains 129 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 152 LEU Chi-restraints excluded: chain R residue 220 ARG Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 211 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.0020 chunk 68 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 8 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS B 237 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8504 Z= 0.208 Angle : 0.527 9.510 11543 Z= 0.271 Chirality : 0.041 0.162 1332 Planarity : 0.004 0.040 1438 Dihedral : 6.580 115.738 1365 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.62 % Allowed : 22.87 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % 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: 1.78 (0.26), residues: 1045 helix: 3.22 (0.26), residues: 362 sheet: 0.48 (0.30), residues: 274 loop : -0.19 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE B 151 TYR 0.010 0.001 TYR S 103 ARG 0.009 0.000 ARG B 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 0.995 Fit side-chains TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 41 LEU cc_start: 0.7726 (tt) cc_final: 0.7423 (tm) REVERT: R 152 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7770 (tt) REVERT: R 196 LEU cc_start: 0.8174 (tt) cc_final: 0.7691 (pp) REVERT: R 220 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7561 (mtm-85) REVERT: R 341 GLU cc_start: 0.7774 (tp30) cc_final: 0.7427 (mm-30) REVERT: A 6 SER cc_start: 0.8281 (t) cc_final: 0.8079 (p) REVERT: A 17 LYS cc_start: 0.7651 (mmtt) cc_final: 0.7389 (mtpt) REVERT: A 24 ARG cc_start: 0.7837 (ttp-110) cc_final: 0.7629 (ttp80) REVERT: A 208 ARG cc_start: 0.7913 (ttm170) cc_final: 0.7344 (ttp-110) REVERT: B 44 GLN cc_start: 0.8354 (mm-40) cc_final: 0.8116 (mt0) REVERT: G 42 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: S 19 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8351 (tttm) outliers start: 23 outliers final: 18 residues processed: 130 average time/residue: 1.3360 time to fit residues: 183.7609 Evaluate side-chains 131 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 152 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 220 ARG Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 211 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.7980 chunk 12 optimal weight: 0.0970 chunk 22 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.128933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.085213 restraints weight = 10247.337| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.27 r_work: 0.2866 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8504 Z= 0.171 Angle : 0.508 9.474 11543 Z= 0.261 Chirality : 0.040 0.161 1332 Planarity : 0.003 0.037 1438 Dihedral : 6.492 115.187 1365 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.39 % Allowed : 23.32 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % 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: 1.78 (0.26), residues: 1045 helix: 3.27 (0.26), residues: 361 sheet: 0.37 (0.29), residues: 280 loop : -0.14 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS R 131 PHE 0.011 0.001 PHE B 151 TYR 0.010 0.001 TYR S 178 ARG 0.009 0.000 ARG B 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3904.57 seconds wall clock time: 70 minutes 13.45 seconds (4213.45 seconds total)