Starting phenix.real_space_refine on Mon Mar 11 07:37:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk5_34846/03_2024/8hk5_34846_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk5_34846/03_2024/8hk5_34846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk5_34846/03_2024/8hk5_34846.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk5_34846/03_2024/8hk5_34846.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk5_34846/03_2024/8hk5_34846_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk5_34846/03_2024/8hk5_34846_updated.pdb" } resolution = 3.0 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= 0.002 sd= 0.032 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 4861 2.51 5 N 1303 2.21 5 O 1383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 34": "NH1" <-> "NH2" Residue "A ARG 68": "NH1" <-> "NH2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "A PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 310": "NH1" <-> "NH2" Residue "B GLU 7": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "C GLU 239": "OE1" <-> "OE2" Residue "C GLU 289": "OE1" <-> "OE2" Residue "D ARG 46": "NH1" <-> "NH2" Residue "D ARG 52": "NH1" <-> "NH2" Residue "D ARG 68": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 134": "NH1" <-> "NH2" Residue "D GLU 138": "OE1" <-> "OE2" Residue "D ARG 214": "NH1" <-> "NH2" Residue "D GLU 215": "OE1" <-> "OE2" Residue "D GLU 260": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7604 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2321 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 14, 'TRANS': 278} Chain: "B" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 573 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 1809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1809 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Chain: "D" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2509 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 322} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 356 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 43} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'PLM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.62, per 1000 atoms: 0.61 Number of scatterers: 7604 At special positions: 0 Unit cell: (84.048, 99.704, 147.496, 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 1383 8.00 N 1303 7.00 C 4861 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 47 " distance=1.99 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 54 " distance=2.02 Simple disulfide: pdb=" SG CYS B 34 " - pdb=" SG CYS B 55 " distance=2.05 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: 2.98 Conformation dependent library (CDL) restraints added in 1.4 seconds 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 9 sheets defined 42.7% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 35 through 65 Processing helix chain 'A' and resid 71 through 87 removed outlier: 3.651A pdb=" N PHE A 75 " --> pdb=" O ASN A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 97 Processing helix chain 'A' and resid 108 through 139 Proline residue: A 113 - end of helix Processing helix chain 'A' and resid 141 through 147 Processing helix chain 'A' and resid 150 through 174 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 196 through 210 Processing helix chain 'A' and resid 212 through 230 Processing helix chain 'A' and resid 238 through 265 Proline residue: A 257 - end of helix Processing helix chain 'A' and resid 273 through 303 removed outlier: 4.531A pdb=" N SER A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASN A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N CYS A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N CYS A 294 " --> pdb=" O TYR A 290 " (cutoff:3.500A) Proline residue: A 297 - end of helix Processing helix chain 'A' and resid 307 through 313 Processing helix chain 'B' and resid 2 through 12 removed outlier: 3.605A pdb=" N ILE B 9 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 26 Processing helix chain 'B' and resid 34 through 40 removed outlier: 4.399A pdb=" N ARG B 40 " --> pdb=" O GLN B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 62 Processing helix chain 'C' and resid 6 through 32 removed outlier: 4.135A pdb=" N ALA C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 52 Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 212 through 215 Processing helix chain 'C' and resid 227 through 231 removed outlier: 3.661A pdb=" N TYR C 230 " --> pdb=" O LEU C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 254 Processing helix chain 'C' and resid 271 through 279 removed outlier: 3.644A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 296 through 309 Processing helix chain 'C' and resid 331 through 350 Processing helix chain 'D' and resid 14 through 25 Processing helix chain 'D' and resid 30 through 35 removed outlier: 3.886A pdb=" N ASN D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 24 Processing helix chain 'G' and resid 30 through 43 Processing sheet with id= A, first strand: chain 'A' and resid 175 through 180 Processing sheet with id= B, first strand: chain 'C' and resid 319 through 323 removed outlier: 6.711A pdb=" N ILE C 264 " --> pdb=" O TYR C 320 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N HIS C 322 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU C 266 " --> pdb=" O HIS C 322 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 58 through 63 removed outlier: 6.975A pdb=" N ALA D 73 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N MET D 61 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL D 71 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N TRP D 63 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU D 69 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 74 " --> pdb=" O LYS D 78 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N HIS D 91 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASP D 83 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS D 89 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 100 through 105 removed outlier: 7.193A pdb=" N GLY D 115 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N CYS D 103 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA D 113 " --> pdb=" O CYS D 103 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N TYR D 105 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N TYR D 111 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG D 137 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 146 through 151 removed outlier: 6.853A pdb=" N SER D 160 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N CYS D 149 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL D 158 " --> pdb=" O CYS D 149 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N PHE D 151 " --> pdb=" O GLN D 156 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLN D 156 " --> pdb=" O PHE D 151 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR D 165 " --> pdb=" O SER D 161 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASP D 170 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN D 176 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.795A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER D 207 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN D 220 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ASP D 212 " --> pdb=" O CYS D 218 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N CYS D 218 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 229 through 234 removed outlier: 6.421A pdb=" N GLY D 244 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE D 232 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA D 242 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N PHE D 234 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALA D 240 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 273 through 278 removed outlier: 6.420A pdb=" N GLY D 288 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL D 276 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU D 286 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N PHE D 278 " --> pdb=" O LEU D 284 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU D 284 " --> pdb=" O PHE D 278 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP D 298 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ARG D 304 " --> pdb=" O ASP D 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 47 through 51 removed outlier: 6.691A pdb=" N ILE D 338 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR D 50 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU D 336 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS D 317 " --> pdb=" O GLY D 330 " (cutoff:3.500A) 364 hydrogen bonds defined for protein. 1062 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: 2.21 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1239 1.31 - 1.44: 2067 1.44 - 1.57: 4372 1.57 - 1.70: 0 1.70 - 1.83: 76 Bond restraints: 7754 Sorted by residual: bond pdb=" CA TYR B 23 " pdb=" C TYR B 23 " ideal model delta sigma weight residual 1.524 1.462 0.061 1.29e-02 6.01e+03 2.24e+01 bond pdb=" C CYS B 34 " pdb=" O CYS B 34 " ideal model delta sigma weight residual 1.237 1.187 0.050 1.16e-02 7.43e+03 1.86e+01 bond pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 1.459 1.407 0.052 1.23e-02 6.61e+03 1.78e+01 bond pdb=" N ASP D 291 " pdb=" CA ASP D 291 " ideal model delta sigma weight residual 1.462 1.417 0.045 1.15e-02 7.56e+03 1.53e+01 bond pdb=" N ARG B 37 " pdb=" CA ARG B 37 " ideal model delta sigma weight residual 1.459 1.414 0.046 1.20e-02 6.94e+03 1.44e+01 ... (remaining 7749 not shown) Histogram of bond angle deviations from ideal: 100.78 - 107.42: 213 107.42 - 114.06: 4489 114.06 - 120.70: 3241 120.70 - 127.34: 2468 127.34 - 133.98: 84 Bond angle restraints: 10495 Sorted by residual: angle pdb=" N GLU A 180 " pdb=" CA GLU A 180 " pdb=" C GLU A 180 " ideal model delta sigma weight residual 109.24 101.90 7.34 1.63e+00 3.76e-01 2.03e+01 angle pdb=" N TYR B 23 " pdb=" CA TYR B 23 " pdb=" C TYR B 23 " ideal model delta sigma weight residual 111.36 106.58 4.78 1.09e+00 8.42e-01 1.92e+01 angle pdb=" O GLU B 32 " pdb=" C GLU B 32 " pdb=" N THR B 33 " ideal model delta sigma weight residual 123.19 118.62 4.57 1.30e+00 5.92e-01 1.24e+01 angle pdb=" CA GLU B 32 " pdb=" C GLU B 32 " pdb=" N THR B 33 " ideal model delta sigma weight residual 115.63 120.52 -4.89 1.51e+00 4.39e-01 1.05e+01 angle pdb=" CA CYS B 55 " pdb=" CB CYS B 55 " pdb=" SG CYS B 55 " ideal model delta sigma weight residual 114.40 121.77 -7.37 2.30e+00 1.89e-01 1.03e+01 ... (remaining 10490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 4293 16.04 - 32.08: 278 32.08 - 48.12: 51 48.12 - 64.17: 13 64.17 - 80.21: 7 Dihedral angle restraints: 4642 sinusoidal: 1826 harmonic: 2816 Sorted by residual: dihedral pdb=" CA PHE A 182 " pdb=" C PHE A 182 " pdb=" N PRO A 183 " pdb=" CA PRO A 183 " ideal model delta harmonic sigma weight residual 180.00 161.88 18.12 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 54 " pdb=" CB CYS B 54 " ideal model delta sinusoidal sigma weight residual -86.00 -112.86 26.86 1 1.00e+01 1.00e-02 1.04e+01 dihedral pdb=" CG ARG B 37 " pdb=" CD ARG B 37 " pdb=" NE ARG B 37 " pdb=" CZ ARG B 37 " ideal model delta sinusoidal sigma weight residual 180.00 137.02 42.98 2 1.50e+01 4.44e-03 9.92e+00 ... (remaining 4639 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1075 0.064 - 0.128: 128 0.128 - 0.192: 4 0.192 - 0.256: 0 0.256 - 0.320: 2 Chirality restraints: 1209 Sorted by residual: chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA CYS B 22 " pdb=" N CYS B 22 " pdb=" C CYS B 22 " pdb=" CB CYS B 22 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB THR C 329 " pdb=" CA THR C 329 " pdb=" OG1 THR C 329 " pdb=" CG2 THR C 329 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.90e-01 ... (remaining 1206 not shown) Planarity restraints: 1319 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 310 " -0.192 9.50e-02 1.11e+02 8.61e-02 4.55e+00 pdb=" NE ARG A 310 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 310 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 310 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 310 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 21 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" C CYS B 21 " 0.025 2.00e-02 2.50e+03 pdb=" O CYS B 21 " -0.009 2.00e-02 2.50e+03 pdb=" N CYS B 22 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 32 " 0.006 2.00e-02 2.50e+03 1.14e-02 1.29e+00 pdb=" C GLU B 32 " -0.020 2.00e-02 2.50e+03 pdb=" O GLU B 32 " 0.007 2.00e-02 2.50e+03 pdb=" N THR B 33 " 0.007 2.00e-02 2.50e+03 ... (remaining 1316 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 91 2.64 - 3.20: 7121 3.20 - 3.77: 11657 3.77 - 4.33: 16396 4.33 - 4.90: 26985 Nonbonded interactions: 62250 Sorted by model distance: nonbonded pdb=" OG SER D 281 " pdb=" OD2 ASP G 48 " model vdw 2.073 2.440 nonbonded pdb=" OG SER D 147 " pdb=" O MET D 188 " model vdw 2.208 2.440 nonbonded pdb=" OG1 THR D 274 " pdb=" OD1 ASP D 290 " model vdw 2.231 2.440 nonbonded pdb=" OD1 ASP C 251 " pdb=" ND2 ASN C 255 " model vdw 2.243 2.520 nonbonded pdb=" OH TYR A 300 " pdb=" NH1 ARG A 310 " model vdw 2.249 2.520 ... (remaining 62245 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: 0.640 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: 3.590 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 24.890 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:10.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 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 0.061 7754 Z= 0.202 Angle : 0.505 7.367 10495 Z= 0.307 Chirality : 0.040 0.320 1209 Planarity : 0.003 0.086 1319 Dihedral : 11.846 80.207 2803 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.24 % Allowed : 4.63 % Favored : 95.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.26), residues: 955 helix: 0.58 (0.24), residues: 436 sheet: -0.04 (0.38), residues: 189 loop : -1.36 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 74 HIS 0.001 0.000 HIS A 101 PHE 0.015 0.001 PHE D 234 TYR 0.005 0.000 TYR C 296 ARG 0.002 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 232 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8147 (tpp80) cc_final: 0.7915 (tpp80) REVERT: A 298 ILE cc_start: 0.8483 (mt) cc_final: 0.8230 (mp) REVERT: C 209 LYS cc_start: 0.7878 (ttpt) cc_final: 0.7553 (ttpt) REVERT: D 82 TRP cc_start: 0.8506 (m100) cc_final: 0.8273 (m100) REVERT: D 86 THR cc_start: 0.8091 (p) cc_final: 0.7834 (p) REVERT: D 217 MET cc_start: 0.5944 (ttm) cc_final: 0.5647 (ttm) REVERT: D 273 ILE cc_start: 0.7134 (mt) cc_final: 0.6924 (mt) REVERT: D 303 ASP cc_start: 0.6706 (m-30) cc_final: 0.6455 (m-30) outliers start: 2 outliers final: 0 residues processed: 234 average time/residue: 0.9686 time to fit residues: 241.8203 Evaluate side-chains 179 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 54 optimal weight: 0.0470 chunk 85 optimal weight: 2.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 194 HIS B 67 HIS ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7754 Z= 0.191 Angle : 0.522 7.687 10495 Z= 0.265 Chirality : 0.041 0.140 1209 Planarity : 0.003 0.033 1319 Dihedral : 4.113 46.592 1069 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.44 % Allowed : 14.62 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.27), residues: 955 helix: 1.64 (0.25), residues: 435 sheet: 0.42 (0.38), residues: 177 loop : -0.87 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 169 HIS 0.010 0.001 HIS B 67 PHE 0.016 0.002 PHE A 93 TYR 0.010 0.001 TYR A 290 ARG 0.009 0.001 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 197 time to evaluate : 0.901 Fit side-chains REVERT: A 228 ARG cc_start: 0.8278 (tpp80) cc_final: 0.8027 (tpp80) REVERT: C 29 LYS cc_start: 0.8104 (tppp) cc_final: 0.7789 (mtpp) REVERT: C 197 LYS cc_start: 0.7856 (tttt) cc_final: 0.7614 (tttm) REVERT: C 209 LYS cc_start: 0.7855 (ttpt) cc_final: 0.7560 (ttpt) REVERT: C 216 GLU cc_start: 0.7205 (tt0) cc_final: 0.7004 (tt0) REVERT: C 268 LEU cc_start: 0.7607 (mt) cc_final: 0.7393 (mm) REVERT: C 271 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.8035 (ttpp) REVERT: C 330 LYS cc_start: 0.7592 (mttt) cc_final: 0.7204 (ttmm) REVERT: D 197 ARG cc_start: 0.7136 (mtp85) cc_final: 0.6926 (mtp180) REVERT: D 246 ASP cc_start: 0.7825 (m-30) cc_final: 0.7566 (m-30) REVERT: D 303 ASP cc_start: 0.6685 (m-30) cc_final: 0.6397 (m-30) outliers start: 20 outliers final: 7 residues processed: 205 average time/residue: 0.9828 time to fit residues: 214.8691 Evaluate side-chains 192 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 184 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 234 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 HIS C 188 HIS ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7754 Z= 0.292 Angle : 0.561 7.780 10495 Z= 0.287 Chirality : 0.043 0.164 1209 Planarity : 0.004 0.043 1319 Dihedral : 4.574 43.778 1069 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.65 % Allowed : 17.78 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.27), residues: 955 helix: 1.55 (0.25), residues: 432 sheet: 0.59 (0.37), residues: 178 loop : -0.75 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 74 HIS 0.009 0.002 HIS B 67 PHE 0.024 0.002 PHE C 334 TYR 0.022 0.002 TYR A 258 ARG 0.005 0.000 ARG D 304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 184 time to evaluate : 0.781 Fit side-chains REVERT: A 236 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7378 (ttp80) REVERT: A 298 ILE cc_start: 0.8545 (mt) cc_final: 0.8305 (mp) REVERT: C 29 LYS cc_start: 0.8127 (tppp) cc_final: 0.7909 (mtpp) REVERT: C 197 LYS cc_start: 0.7896 (tttt) cc_final: 0.7603 (tttm) REVERT: C 209 LYS cc_start: 0.7886 (ttpt) cc_final: 0.7599 (ttpt) REVERT: C 330 LYS cc_start: 0.7721 (mttt) cc_final: 0.7330 (ttmm) REVERT: D 72 SER cc_start: 0.7943 (t) cc_final: 0.7706 (p) REVERT: D 197 ARG cc_start: 0.7210 (mtp85) cc_final: 0.7007 (mtp180) REVERT: D 246 ASP cc_start: 0.7820 (m-30) cc_final: 0.7512 (m-30) REVERT: D 303 ASP cc_start: 0.6774 (m-30) cc_final: 0.6484 (m-30) outliers start: 30 outliers final: 14 residues processed: 200 average time/residue: 0.9741 time to fit residues: 208.2555 Evaluate side-chains 194 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 179 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.1980 chunk 64 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 90 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 HIS ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7754 Z= 0.216 Angle : 0.510 7.159 10495 Z= 0.261 Chirality : 0.041 0.132 1209 Planarity : 0.003 0.041 1319 Dihedral : 4.375 41.283 1069 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.29 % Allowed : 19.85 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.27), residues: 955 helix: 1.64 (0.25), residues: 432 sheet: 0.56 (0.37), residues: 182 loop : -0.73 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 74 HIS 0.004 0.001 HIS C 322 PHE 0.015 0.002 PHE A 182 TYR 0.011 0.001 TYR A 258 ARG 0.004 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 184 time to evaluate : 0.803 Fit side-chains REVERT: A 92 LEU cc_start: 0.8028 (mp) cc_final: 0.7781 (mt) REVERT: A 236 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.6662 (ttp80) REVERT: C 29 LYS cc_start: 0.8150 (tppp) cc_final: 0.7922 (mtpp) REVERT: C 197 LYS cc_start: 0.7894 (tttt) cc_final: 0.7671 (mtpp) REVERT: C 209 LYS cc_start: 0.7881 (ttpt) cc_final: 0.7587 (ttpt) REVERT: C 330 LYS cc_start: 0.7702 (mttt) cc_final: 0.7313 (ttmm) REVERT: D 72 SER cc_start: 0.7969 (t) cc_final: 0.7643 (p) REVERT: D 246 ASP cc_start: 0.7792 (m-30) cc_final: 0.7503 (m-30) REVERT: D 303 ASP cc_start: 0.6666 (m-30) cc_final: 0.6361 (m-30) outliers start: 27 outliers final: 11 residues processed: 200 average time/residue: 0.9718 time to fit residues: 207.6205 Evaluate side-chains 188 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 176 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 0.0970 chunk 1 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 0.0980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 HIS ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7754 Z= 0.157 Angle : 0.490 7.245 10495 Z= 0.251 Chirality : 0.040 0.131 1209 Planarity : 0.003 0.040 1319 Dihedral : 4.229 39.492 1069 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.29 % Allowed : 20.22 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.27), residues: 955 helix: 1.78 (0.25), residues: 433 sheet: 0.52 (0.37), residues: 183 loop : -0.75 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 74 HIS 0.002 0.001 HIS C 322 PHE 0.015 0.002 PHE C 334 TYR 0.010 0.001 TYR A 290 ARG 0.004 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 185 time to evaluate : 0.888 Fit side-chains REVERT: A 92 LEU cc_start: 0.7999 (mp) cc_final: 0.7753 (mt) REVERT: A 236 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.6666 (ttp80) REVERT: A 276 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7537 (mt) REVERT: C 29 LYS cc_start: 0.8134 (tppp) cc_final: 0.7894 (mtpp) REVERT: C 188 HIS cc_start: 0.7855 (OUTLIER) cc_final: 0.7586 (m170) REVERT: C 197 LYS cc_start: 0.7879 (tttt) cc_final: 0.7648 (mtpp) REVERT: C 209 LYS cc_start: 0.7863 (ttpt) cc_final: 0.7547 (ttpt) REVERT: C 308 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7244 (mt-10) REVERT: C 330 LYS cc_start: 0.7720 (mttt) cc_final: 0.7313 (ttmm) REVERT: D 72 SER cc_start: 0.7915 (t) cc_final: 0.7574 (p) REVERT: D 100 VAL cc_start: 0.8289 (OUTLIER) cc_final: 0.8087 (t) REVERT: D 170 ASP cc_start: 0.7079 (m-30) cc_final: 0.6867 (m-30) REVERT: D 197 ARG cc_start: 0.7193 (mtp85) cc_final: 0.6990 (mtp180) REVERT: D 246 ASP cc_start: 0.7799 (m-30) cc_final: 0.7487 (m-30) REVERT: D 303 ASP cc_start: 0.6626 (m-30) cc_final: 0.6316 (m-30) outliers start: 27 outliers final: 12 residues processed: 200 average time/residue: 1.0144 time to fit residues: 216.2800 Evaluate side-chains 199 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 183 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 188 HIS Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 90 optimal weight: 30.0000 chunk 75 optimal weight: 0.0170 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 0.0470 chunk 47 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 overall best weight: 0.7918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7754 Z= 0.214 Angle : 0.510 7.973 10495 Z= 0.262 Chirality : 0.040 0.137 1209 Planarity : 0.003 0.042 1319 Dihedral : 4.273 38.325 1069 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.80 % Allowed : 20.95 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.27), residues: 955 helix: 1.80 (0.25), residues: 432 sheet: 0.52 (0.36), residues: 183 loop : -0.67 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 74 HIS 0.004 0.001 HIS C 188 PHE 0.015 0.002 PHE C 196 TYR 0.026 0.002 TYR D 59 ARG 0.005 0.000 ARG D 251 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 183 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8026 (mp) cc_final: 0.7778 (mt) REVERT: A 236 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.6669 (ttp80) REVERT: A 276 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7558 (mt) REVERT: C 29 LYS cc_start: 0.8143 (tppp) cc_final: 0.7906 (mtpp) REVERT: C 186 GLU cc_start: 0.6494 (pt0) cc_final: 0.6121 (pt0) REVERT: C 197 LYS cc_start: 0.7842 (tttt) cc_final: 0.7476 (tttm) REVERT: C 267 PHE cc_start: 0.7921 (m-80) cc_final: 0.7141 (m-80) REVERT: C 277 LYS cc_start: 0.7931 (ttmt) cc_final: 0.7725 (ttmt) REVERT: C 330 LYS cc_start: 0.7743 (mttt) cc_final: 0.7339 (ttmm) REVERT: D 59 TYR cc_start: 0.8269 (m-80) cc_final: 0.7974 (m-80) REVERT: D 72 SER cc_start: 0.7944 (t) cc_final: 0.7640 (p) REVERT: D 246 ASP cc_start: 0.7829 (m-30) cc_final: 0.7521 (m-30) REVERT: D 279 SER cc_start: 0.7615 (m) cc_final: 0.7388 (p) REVERT: D 303 ASP cc_start: 0.6635 (m-30) cc_final: 0.6318 (m-30) outliers start: 23 outliers final: 18 residues processed: 195 average time/residue: 0.9769 time to fit residues: 203.5147 Evaluate side-chains 202 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 182 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 30.0000 chunk 56 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7754 Z= 0.203 Angle : 0.509 8.278 10495 Z= 0.261 Chirality : 0.040 0.141 1209 Planarity : 0.003 0.043 1319 Dihedral : 4.264 35.931 1069 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.78 % Allowed : 20.22 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.27), residues: 955 helix: 1.77 (0.25), residues: 433 sheet: 0.51 (0.36), residues: 185 loop : -0.71 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 74 HIS 0.003 0.001 HIS C 322 PHE 0.014 0.002 PHE C 334 TYR 0.013 0.001 TYR D 59 ARG 0.006 0.000 ARG D 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 180 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8007 (mp) cc_final: 0.7750 (mt) REVERT: A 110 SER cc_start: 0.7413 (m) cc_final: 0.7184 (t) REVERT: A 236 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.6681 (ttp80) REVERT: C 29 LYS cc_start: 0.8152 (tppp) cc_final: 0.7880 (mtpp) REVERT: C 186 GLU cc_start: 0.6593 (pt0) cc_final: 0.6252 (pt0) REVERT: C 197 LYS cc_start: 0.7866 (tttt) cc_final: 0.7456 (tttm) REVERT: C 267 PHE cc_start: 0.7830 (m-80) cc_final: 0.7191 (m-80) REVERT: C 277 LYS cc_start: 0.7975 (ttmt) cc_final: 0.7757 (ttmt) REVERT: C 330 LYS cc_start: 0.7755 (mttt) cc_final: 0.7349 (ttmm) REVERT: D 72 SER cc_start: 0.7969 (t) cc_final: 0.7667 (p) REVERT: D 246 ASP cc_start: 0.7849 (m-30) cc_final: 0.7531 (m-30) REVERT: D 255 LEU cc_start: 0.6773 (mt) cc_final: 0.6550 (mt) REVERT: D 279 SER cc_start: 0.7590 (m) cc_final: 0.7348 (p) REVERT: D 303 ASP cc_start: 0.6589 (m-30) cc_final: 0.6287 (m-30) outliers start: 31 outliers final: 22 residues processed: 192 average time/residue: 0.9656 time to fit residues: 198.3473 Evaluate side-chains 200 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 177 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7754 Z= 0.244 Angle : 0.532 8.429 10495 Z= 0.273 Chirality : 0.041 0.154 1209 Planarity : 0.004 0.045 1319 Dihedral : 4.376 33.566 1069 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.78 % Allowed : 20.83 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.27), residues: 955 helix: 1.75 (0.25), residues: 432 sheet: 0.58 (0.37), residues: 184 loop : -0.68 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 74 HIS 0.004 0.001 HIS C 322 PHE 0.015 0.002 PHE C 196 TYR 0.013 0.001 TYR A 258 ARG 0.009 0.000 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 185 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8029 (mp) cc_final: 0.7772 (mt) REVERT: A 110 SER cc_start: 0.7479 (m) cc_final: 0.7270 (t) REVERT: A 236 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.6789 (ttp80) REVERT: C 29 LYS cc_start: 0.8177 (tppp) cc_final: 0.7882 (mtpp) REVERT: C 186 GLU cc_start: 0.6602 (pt0) cc_final: 0.6258 (pt0) REVERT: C 197 LYS cc_start: 0.7866 (tttt) cc_final: 0.7488 (tttm) REVERT: C 267 PHE cc_start: 0.7884 (m-80) cc_final: 0.7166 (m-80) REVERT: C 277 LYS cc_start: 0.8046 (ttmt) cc_final: 0.7803 (ttmt) REVERT: C 330 LYS cc_start: 0.7739 (mttt) cc_final: 0.7343 (ttmm) REVERT: D 72 SER cc_start: 0.7936 (t) cc_final: 0.7667 (p) REVERT: D 246 ASP cc_start: 0.7874 (m-30) cc_final: 0.7558 (m-30) REVERT: D 255 LEU cc_start: 0.6948 (mt) cc_final: 0.6695 (mt) REVERT: D 279 SER cc_start: 0.7651 (m) cc_final: 0.7392 (p) REVERT: D 303 ASP cc_start: 0.6556 (m-30) cc_final: 0.6226 (m-30) outliers start: 31 outliers final: 22 residues processed: 199 average time/residue: 0.9962 time to fit residues: 211.5591 Evaluate side-chains 205 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 182 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 55 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7754 Z= 0.186 Angle : 0.514 7.681 10495 Z= 0.262 Chirality : 0.040 0.151 1209 Planarity : 0.003 0.043 1319 Dihedral : 4.230 30.772 1069 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.29 % Allowed : 21.32 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.27), residues: 955 helix: 1.81 (0.25), residues: 432 sheet: 0.63 (0.37), residues: 179 loop : -0.76 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 74 HIS 0.003 0.001 HIS C 322 PHE 0.013 0.002 PHE C 334 TYR 0.012 0.001 TYR D 59 ARG 0.005 0.000 ARG D 251 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 186 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.7992 (mp) cc_final: 0.7742 (mt) REVERT: A 236 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.6778 (ttp80) REVERT: C 29 LYS cc_start: 0.8159 (tppp) cc_final: 0.7880 (mtpp) REVERT: C 186 GLU cc_start: 0.6578 (pt0) cc_final: 0.6218 (pt0) REVERT: C 197 LYS cc_start: 0.7873 (tttt) cc_final: 0.7511 (mtpp) REVERT: C 267 PHE cc_start: 0.7818 (m-80) cc_final: 0.7198 (m-80) REVERT: C 277 LYS cc_start: 0.8051 (ttmt) cc_final: 0.7840 (ttmt) REVERT: C 330 LYS cc_start: 0.7740 (mttt) cc_final: 0.7332 (ttmm) REVERT: D 72 SER cc_start: 0.7945 (t) cc_final: 0.7651 (p) REVERT: D 88 ASN cc_start: 0.7938 (m-40) cc_final: 0.7709 (m110) REVERT: D 234 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.7420 (t80) REVERT: D 246 ASP cc_start: 0.7856 (m-30) cc_final: 0.7546 (m-30) REVERT: D 279 SER cc_start: 0.7572 (m) cc_final: 0.7356 (p) REVERT: D 303 ASP cc_start: 0.6518 (m-30) cc_final: 0.6188 (m-30) outliers start: 27 outliers final: 21 residues processed: 197 average time/residue: 1.0116 time to fit residues: 212.2869 Evaluate side-chains 203 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 180 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 255 ASN ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7754 Z= 0.313 Angle : 0.570 9.538 10495 Z= 0.293 Chirality : 0.042 0.164 1209 Planarity : 0.004 0.049 1319 Dihedral : 4.483 28.876 1069 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.68 % Allowed : 22.05 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.27), residues: 955 helix: 1.67 (0.25), residues: 431 sheet: 0.42 (0.37), residues: 184 loop : -0.66 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 74 HIS 0.005 0.002 HIS C 322 PHE 0.018 0.002 PHE D 235 TYR 0.016 0.002 TYR A 258 ARG 0.011 0.001 ARG B 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 182 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 65 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6671 (mm-30) REVERT: A 92 LEU cc_start: 0.8042 (mp) cc_final: 0.7792 (mt) REVERT: A 236 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.6822 (ttp80) REVERT: C 29 LYS cc_start: 0.8193 (tppp) cc_final: 0.7896 (mtpp) REVERT: C 186 GLU cc_start: 0.6582 (pt0) cc_final: 0.6154 (pt0) REVERT: C 191 PHE cc_start: 0.8652 (t80) cc_final: 0.8287 (t80) REVERT: C 197 LYS cc_start: 0.7882 (tttt) cc_final: 0.7478 (tttm) REVERT: C 247 MET cc_start: 0.7758 (mtp) cc_final: 0.7504 (mtt) REVERT: C 267 PHE cc_start: 0.7887 (m-80) cc_final: 0.7197 (m-80) REVERT: C 330 LYS cc_start: 0.7748 (mttt) cc_final: 0.7362 (ttmm) REVERT: D 246 ASP cc_start: 0.7894 (m-30) cc_final: 0.7616 (m-30) REVERT: D 255 LEU cc_start: 0.7068 (mt) cc_final: 0.6839 (mt) REVERT: D 279 SER cc_start: 0.7682 (m) cc_final: 0.7416 (p) REVERT: D 303 ASP cc_start: 0.6574 (m-30) cc_final: 0.6247 (m-30) outliers start: 22 outliers final: 21 residues processed: 193 average time/residue: 1.0492 time to fit residues: 215.2751 Evaluate side-chains 200 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 178 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 255 ASN ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.135696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.118890 restraints weight = 10168.145| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.81 r_work: 0.3439 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7754 Z= 0.219 Angle : 0.548 11.481 10495 Z= 0.277 Chirality : 0.041 0.155 1209 Planarity : 0.003 0.047 1319 Dihedral : 4.343 26.961 1069 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.80 % Allowed : 22.41 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.27), residues: 955 helix: 1.72 (0.25), residues: 431 sheet: 0.39 (0.37), residues: 184 loop : -0.67 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 74 HIS 0.003 0.001 HIS C 322 PHE 0.014 0.002 PHE A 182 TYR 0.012 0.002 TYR D 59 ARG 0.006 0.000 ARG B 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3722.77 seconds wall clock time: 66 minutes 28.26 seconds (3988.26 seconds total)