Starting phenix.real_space_refine on Fri Jul 19 08:13:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvy_32862/07_2024/7wvy_32862.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvy_32862/07_2024/7wvy_32862.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/7wvy_32862/07_2024/7wvy_32862.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvy_32862/07_2024/7wvy_32862.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvy_32862/07_2024/7wvy_32862.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvy_32862/07_2024/7wvy_32862.cif" } 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= 0.000 sd= 0.004 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 52 5.16 5 C 4564 2.51 5 N 1201 2.21 5 O 1277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L ASP 1": "OD1" <-> "OD2" Residue "R ASP 71": "OD1" <-> "OD2" Residue "R PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 311": "OE1" <-> "OE2" Residue "A ASP 9": "OD1" <-> "OD2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 252": "OD1" <-> "OD2" Residue "A ASP 273": "OD1" <-> "OD2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A ASP 298": "OD1" <-> "OD2" Residue "A ASP 316": "OD1" <-> "OD2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C GLU 42": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 7094 Number of models: 1 Model: "" Number of chains: 5 Chain: "L" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 109 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 15} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2319 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 13, 'TRANS': 284} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1757 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 2531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2531 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 328} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 378 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 5.25, per 1000 atoms: 0.74 Number of scatterers: 7094 At special positions: 0 Unit cell: (113.905, 119.13, 83.6, 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 52 16.00 O 1277 8.00 N 1201 7.00 C 4564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " 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: 2.78 Conformation dependent library (CDL) restraints added in 2.1 seconds 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1724 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 9 sheets defined 49.2% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'R' and resid 20 through 55 Proline residue: R 29 - end of helix removed outlier: 3.741A pdb=" N PHE R 53 " --> pdb=" O TRP R 49 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET R 55 " --> pdb=" O ALA R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 77 removed outlier: 3.720A pdb=" N THR R 77 " --> pdb=" O SER R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 87 removed outlier: 3.618A pdb=" N LEU R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N MET R 87 " --> pdb=" O VAL R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 129 Processing helix chain 'R' and resid 129 through 137 Processing helix chain 'R' and resid 138 through 163 removed outlier: 4.431A pdb=" N GLY R 148 " --> pdb=" O LYS R 144 " (cutoff:3.500A) Proline residue: R 149 - end of helix Proline residue: R 159 - end of helix Processing helix chain 'R' and resid 180 through 185 Processing helix chain 'R' and resid 186 through 209 Processing helix chain 'R' and resid 210 through 232 Processing helix chain 'R' and resid 237 through 267 Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 267 through 273 Processing helix chain 'R' and resid 278 through 303 removed outlier: 3.612A pdb=" N ILE R 282 " --> pdb=" O LYS R 278 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ASN R 285 " --> pdb=" O ASP R 281 " (cutoff:3.500A) Proline residue: R 286 - end of helix Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 306 through 316 Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.559A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 208 through 213 removed outlier: 4.197A pdb=" N TRP A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 217 removed outlier: 3.516A pdb=" N GLU A 217 " --> pdb=" O HIS A 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 214 through 217' Processing helix chain 'A' and resid 229 through 233 removed outlier: 3.986A pdb=" N ASP A 232 " --> pdb=" O SER A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 257 removed outlier: 3.511A pdb=" N CYS A 255 " --> pdb=" O PHE A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 261 removed outlier: 4.115A pdb=" N THR A 261 " --> pdb=" O LYS A 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 258 through 261' Processing helix chain 'A' and resid 271 through 282 removed outlier: 4.132A pdb=" N THR A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 removed outlier: 3.971A pdb=" N ILE A 286 " --> pdb=" O PRO A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 312 removed outlier: 3.993A pdb=" N PHE A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 Processing helix chain 'B' and resid 8 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 13 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 Processing sheet with id=AA1, first strand: chain 'R' and resid 167 through 168 Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 192 removed outlier: 3.622A pdb=" N PHE A 190 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 9.314A pdb=" N ALA A 221 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N ALA A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.059A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.795A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.397A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.300A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.754A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.614A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.639A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) 389 hydrogen bonds defined for protein. 1134 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: 1.95 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2265 1.35 - 1.46: 1742 1.46 - 1.58: 3161 1.58 - 1.70: 1 1.70 - 1.81: 75 Bond restraints: 7244 Sorted by residual: bond pdb=" CB PRO A 283 " pdb=" CG PRO A 283 " ideal model delta sigma weight residual 1.492 1.634 -0.142 5.00e-02 4.00e+02 8.07e+00 bond pdb=" CA ILE R 234 " pdb=" CB ILE R 234 " ideal model delta sigma weight residual 1.540 1.527 0.013 1.36e-02 5.41e+03 9.39e-01 bond pdb=" C LEU R 158 " pdb=" N PRO R 159 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.36e-02 5.41e+03 6.32e-01 bond pdb=" CA LEU R 158 " pdb=" C LEU R 158 " ideal model delta sigma weight residual 1.524 1.533 -0.009 1.26e-02 6.30e+03 4.91e-01 bond pdb=" CG PRO R 213 " pdb=" CD PRO R 213 " ideal model delta sigma weight residual 1.503 1.480 0.023 3.40e-02 8.65e+02 4.43e-01 ... (remaining 7239 not shown) Histogram of bond angle deviations from ideal: 97.71 - 104.97: 89 104.97 - 112.23: 3765 112.23 - 119.49: 2220 119.49 - 126.74: 3643 126.74 - 134.00: 110 Bond angle restraints: 9827 Sorted by residual: angle pdb=" CA PRO A 283 " pdb=" N PRO A 283 " pdb=" CD PRO A 283 " ideal model delta sigma weight residual 112.00 104.03 7.97 1.40e+00 5.10e-01 3.24e+01 angle pdb=" N PRO A 283 " pdb=" CD PRO A 283 " pdb=" CG PRO A 283 " ideal model delta sigma weight residual 103.20 97.71 5.49 1.50e+00 4.44e-01 1.34e+01 angle pdb=" CA LEU R 162 " pdb=" CB LEU R 162 " pdb=" CG LEU R 162 " ideal model delta sigma weight residual 116.30 126.30 -10.00 3.50e+00 8.16e-02 8.16e+00 angle pdb=" C PHE R 161 " pdb=" N LEU R 162 " pdb=" CA LEU R 162 " ideal model delta sigma weight residual 122.60 117.72 4.88 1.88e+00 2.83e-01 6.73e+00 angle pdb=" CA LEU R 158 " pdb=" CB LEU R 158 " pdb=" CG LEU R 158 " ideal model delta sigma weight residual 116.30 125.14 -8.84 3.50e+00 8.16e-02 6.38e+00 ... (remaining 9822 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 3815 15.98 - 31.96: 357 31.96 - 47.93: 74 47.93 - 63.91: 8 63.91 - 79.89: 6 Dihedral angle restraints: 4260 sinusoidal: 1599 harmonic: 2661 Sorted by residual: dihedral pdb=" CG ARG B 48 " pdb=" CD ARG B 48 " pdb=" NE ARG B 48 " pdb=" CZ ARG B 48 " ideal model delta sinusoidal sigma weight residual -180.00 -135.98 -44.02 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CA LEU R 162 " pdb=" C LEU R 162 " pdb=" N PHE R 163 " pdb=" CA PHE R 163 " ideal model delta harmonic sigma weight residual -180.00 -164.38 -15.62 0 5.00e+00 4.00e-02 9.76e+00 dihedral pdb=" CA ASP B 312 " pdb=" CB ASP B 312 " pdb=" CG ASP B 312 " pdb=" OD1 ASP B 312 " ideal model delta sinusoidal sigma weight residual -30.00 -82.04 52.04 1 2.00e+01 2.50e-03 9.24e+00 ... (remaining 4257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 700 0.026 - 0.053: 261 0.053 - 0.079: 111 0.079 - 0.106: 49 0.106 - 0.132: 25 Chirality restraints: 1146 Sorted by residual: chirality pdb=" CA ILE R 169 " pdb=" N ILE R 169 " pdb=" C ILE R 169 " pdb=" CB ILE R 169 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.36e-01 ... (remaining 1143 not shown) Planarity restraints: 1229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " 0.050 5.00e-02 4.00e+02 7.60e-02 9.24e+00 pdb=" N PRO B 39 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 282 " -0.036 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO A 283 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO B 236 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.025 5.00e-02 4.00e+02 ... (remaining 1226 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1477 2.78 - 3.31: 6973 3.31 - 3.84: 12359 3.84 - 4.37: 14213 4.37 - 4.90: 25134 Nonbonded interactions: 60156 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.251 2.440 nonbonded pdb=" OG SER B 67 " pdb=" OD1 ASP B 323 " model vdw 2.294 2.440 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.318 2.440 nonbonded pdb=" O ASN R 135 " pdb=" NH1 ARG A 32 " model vdw 2.348 2.520 nonbonded pdb=" OG SER B 67 " pdb=" OG1 THR B 321 " model vdw 2.354 2.440 ... (remaining 60151 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.340 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 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 0.142 7244 Z= 0.177 Angle : 0.512 10.000 9827 Z= 0.272 Chirality : 0.039 0.132 1146 Planarity : 0.004 0.076 1229 Dihedral : 12.968 79.890 2533 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.13 % Allowed : 0.13 % Favored : 99.73 % 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: 0.72 (0.27), residues: 908 helix: 1.36 (0.25), residues: 411 sheet: 0.82 (0.38), residues: 189 loop : -0.90 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 254 HIS 0.002 0.000 HIS A 189 PHE 0.015 0.001 PHE R 110 TYR 0.008 0.001 TYR B 124 ARG 0.005 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 0.746 Fit side-chains REVERT: R 197 MET cc_start: 0.7231 (tmm) cc_final: 0.6877 (tmm) REVERT: A 25 GLU cc_start: 0.7047 (tm-30) cc_final: 0.6754 (tm-30) REVERT: B 258 ASP cc_start: 0.7249 (t0) cc_final: 0.6525 (t0) REVERT: B 322 ASP cc_start: 0.6612 (m-30) cc_final: 0.6404 (m-30) outliers start: 1 outliers final: 0 residues processed: 144 average time/residue: 0.9336 time to fit residues: 143.5919 Evaluate side-chains 117 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7244 Z= 0.280 Angle : 0.591 10.576 9827 Z= 0.301 Chirality : 0.042 0.133 1146 Planarity : 0.005 0.059 1229 Dihedral : 3.933 18.562 978 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.87 % Allowed : 14.15 % Favored : 83.98 % 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: 908 helix: 1.63 (0.25), residues: 410 sheet: 0.43 (0.37), residues: 191 loop : -0.84 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS R 136 PHE 0.015 0.002 PHE R 118 TYR 0.009 0.001 TYR B 59 ARG 0.006 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 0.719 Fit side-chains REVERT: R 197 MET cc_start: 0.7395 (tmm) cc_final: 0.7035 (tmm) REVERT: A 25 GLU cc_start: 0.7197 (tm-30) cc_final: 0.6750 (tm-30) REVERT: A 295 ASN cc_start: 0.7209 (OUTLIER) cc_final: 0.6609 (p0) REVERT: B 214 ARG cc_start: 0.7427 (mpt180) cc_final: 0.6931 (tpp80) REVERT: B 258 ASP cc_start: 0.7489 (t0) cc_final: 0.6647 (t0) REVERT: B 322 ASP cc_start: 0.6815 (m-30) cc_final: 0.6592 (m-30) outliers start: 14 outliers final: 7 residues processed: 144 average time/residue: 0.9299 time to fit residues: 143.3510 Evaluate side-chains 125 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 259 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 0.0370 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 88 optimal weight: 0.0770 chunk 72 optimal weight: 0.0870 chunk 27 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 0.0060 overall best weight: 0.2210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 ASN A 22 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 7244 Z= 0.153 Angle : 0.511 10.341 9827 Z= 0.256 Chirality : 0.040 0.134 1146 Planarity : 0.004 0.052 1229 Dihedral : 3.677 18.469 978 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.40 % Allowed : 17.89 % Favored : 79.71 % 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: 0.93 (0.27), residues: 908 helix: 1.86 (0.25), residues: 409 sheet: 0.41 (0.36), residues: 186 loop : -0.90 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS B 91 PHE 0.012 0.001 PHE R 180 TYR 0.005 0.001 TYR B 59 ARG 0.005 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 0.789 Fit side-chains REVERT: R 197 MET cc_start: 0.7363 (tmm) cc_final: 0.7086 (tmm) REVERT: A 20 ASP cc_start: 0.7756 (m-30) cc_final: 0.7424 (m-30) REVERT: A 25 GLU cc_start: 0.7130 (tm-30) cc_final: 0.6751 (tm-30) REVERT: A 241 MET cc_start: 0.6649 (tpp) cc_final: 0.6381 (tpp) REVERT: B 214 ARG cc_start: 0.7387 (mpt180) cc_final: 0.6938 (tpp80) REVERT: B 219 ARG cc_start: 0.7977 (mtm110) cc_final: 0.7691 (mtp180) REVERT: B 258 ASP cc_start: 0.7612 (t0) cc_final: 0.7004 (t0) outliers start: 18 outliers final: 7 residues processed: 136 average time/residue: 0.9829 time to fit residues: 142.5927 Evaluate side-chains 124 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 54 optimal weight: 0.0020 chunk 82 optimal weight: 0.8980 chunk 86 optimal weight: 0.0010 chunk 77 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN B 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7244 Z= 0.199 Angle : 0.523 9.871 9827 Z= 0.267 Chirality : 0.040 0.133 1146 Planarity : 0.004 0.048 1229 Dihedral : 3.773 19.544 978 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.74 % Allowed : 17.76 % Favored : 78.50 % 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: 0.91 (0.27), residues: 908 helix: 1.81 (0.25), residues: 416 sheet: 0.12 (0.35), residues: 196 loop : -0.76 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS B 311 PHE 0.014 0.001 PHE R 180 TYR 0.006 0.001 TYR B 59 ARG 0.004 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 0.757 Fit side-chains REVERT: A 20 ASP cc_start: 0.7764 (m-30) cc_final: 0.7399 (m-30) REVERT: A 25 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6765 (tm-30) REVERT: A 241 MET cc_start: 0.6737 (tpp) cc_final: 0.6368 (tpp) REVERT: A 295 ASN cc_start: 0.7321 (OUTLIER) cc_final: 0.6916 (p0) REVERT: B 214 ARG cc_start: 0.7452 (mpt180) cc_final: 0.6994 (tpp80) REVERT: B 219 ARG cc_start: 0.7908 (mtm110) cc_final: 0.7620 (mtp180) REVERT: B 258 ASP cc_start: 0.7672 (t0) cc_final: 0.6942 (t0) REVERT: B 280 LYS cc_start: 0.7565 (tptp) cc_final: 0.6997 (tptt) outliers start: 28 outliers final: 14 residues processed: 133 average time/residue: 1.0553 time to fit residues: 149.1628 Evaluate side-chains 125 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 46 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 0.0870 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 7244 Z= 0.488 Angle : 0.671 8.678 9827 Z= 0.348 Chirality : 0.046 0.162 1146 Planarity : 0.005 0.044 1229 Dihedral : 4.425 21.862 978 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.14 % Allowed : 20.69 % Favored : 75.17 % 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: 0.44 (0.28), residues: 908 helix: 1.50 (0.26), residues: 412 sheet: -0.40 (0.35), residues: 203 loop : -0.85 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 91 HIS 0.006 0.001 HIS B 311 PHE 0.014 0.002 PHE R 96 TYR 0.012 0.002 TYR B 59 ARG 0.004 0.000 ARG R 57 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 124 time to evaluate : 0.764 Fit side-chains REVERT: A 25 GLU cc_start: 0.7294 (tm-30) cc_final: 0.6853 (tm-30) REVERT: A 187 GLU cc_start: 0.7087 (tt0) cc_final: 0.6780 (tm-30) REVERT: A 241 MET cc_start: 0.6878 (tpp) cc_final: 0.6422 (tpp) REVERT: A 296 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7815 (mmmt) REVERT: B 186 ASP cc_start: 0.7277 (OUTLIER) cc_final: 0.6839 (m-30) REVERT: B 214 ARG cc_start: 0.7470 (mpt180) cc_final: 0.7140 (tpp80) REVERT: B 258 ASP cc_start: 0.7869 (t0) cc_final: 0.7068 (t0) REVERT: B 280 LYS cc_start: 0.7807 (tptp) cc_final: 0.7582 (tttm) outliers start: 31 outliers final: 23 residues processed: 141 average time/residue: 1.0677 time to fit residues: 159.6992 Evaluate side-chains 129 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 104 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain R residue 297 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 46 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 7244 Z= 0.264 Angle : 0.564 9.245 9827 Z= 0.288 Chirality : 0.042 0.186 1146 Planarity : 0.004 0.043 1229 Dihedral : 4.205 21.882 978 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.74 % Allowed : 23.50 % Favored : 72.76 % 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: 0.50 (0.28), residues: 908 helix: 1.60 (0.26), residues: 412 sheet: -0.43 (0.36), residues: 199 loop : -0.84 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 82 HIS 0.003 0.001 HIS B 54 PHE 0.013 0.001 PHE A 197 TYR 0.010 0.001 TYR B 59 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 110 time to evaluate : 0.776 Fit side-chains REVERT: A 25 GLU cc_start: 0.7189 (tm-30) cc_final: 0.6775 (tm-30) REVERT: A 194 ASP cc_start: 0.7157 (m-30) cc_final: 0.6897 (m-30) REVERT: A 241 MET cc_start: 0.6747 (tpp) cc_final: 0.6326 (tpp) REVERT: A 277 GLU cc_start: 0.7712 (pt0) cc_final: 0.7353 (mp0) REVERT: A 332 ASN cc_start: 0.7977 (m-40) cc_final: 0.7770 (m-40) REVERT: B 52 ARG cc_start: 0.8024 (ptp-110) cc_final: 0.7806 (ptm160) REVERT: B 186 ASP cc_start: 0.7164 (OUTLIER) cc_final: 0.6722 (m-30) REVERT: B 214 ARG cc_start: 0.7480 (mpt180) cc_final: 0.7144 (tpp80) REVERT: B 258 ASP cc_start: 0.7715 (t0) cc_final: 0.6809 (t0) REVERT: B 280 LYS cc_start: 0.7733 (tptp) cc_final: 0.7452 (tttm) outliers start: 28 outliers final: 18 residues processed: 126 average time/residue: 0.9357 time to fit residues: 125.9899 Evaluate side-chains 119 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain R residue 297 LEU Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 46 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 54 optimal weight: 0.0570 chunk 52 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 7244 Z= 0.316 Angle : 0.606 12.210 9827 Z= 0.307 Chirality : 0.043 0.173 1146 Planarity : 0.004 0.042 1229 Dihedral : 4.274 21.831 978 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.87 % Allowed : 23.36 % Favored : 72.76 % 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: 0.44 (0.28), residues: 908 helix: 1.54 (0.25), residues: 418 sheet: -0.59 (0.37), residues: 199 loop : -0.81 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 183 HIS 0.004 0.001 HIS B 311 PHE 0.013 0.002 PHE A 197 TYR 0.011 0.001 TYR B 59 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 105 time to evaluate : 0.766 Fit side-chains REVERT: A 25 GLU cc_start: 0.7189 (tm-30) cc_final: 0.6769 (tm-30) REVERT: A 32 ARG cc_start: 0.7359 (ttp-110) cc_final: 0.6827 (mtt90) REVERT: A 194 ASP cc_start: 0.7164 (m-30) cc_final: 0.6915 (m-30) REVERT: A 241 MET cc_start: 0.6800 (tpp) cc_final: 0.6393 (tpp) REVERT: A 244 MET cc_start: 0.8265 (tpp) cc_final: 0.7941 (mtp) REVERT: A 277 GLU cc_start: 0.7707 (pt0) cc_final: 0.7459 (mp0) REVERT: A 295 ASN cc_start: 0.6549 (m-40) cc_final: 0.6281 (m-40) REVERT: A 332 ASN cc_start: 0.7995 (m-40) cc_final: 0.7784 (m-40) REVERT: B 186 ASP cc_start: 0.7229 (OUTLIER) cc_final: 0.6817 (m-30) REVERT: B 214 ARG cc_start: 0.7400 (mpt180) cc_final: 0.7097 (tpp80) REVERT: B 258 ASP cc_start: 0.7860 (t0) cc_final: 0.6986 (t0) outliers start: 29 outliers final: 21 residues processed: 124 average time/residue: 0.9670 time to fit residues: 127.9785 Evaluate side-chains 122 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain R residue 297 LEU Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 46 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 55 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 7244 Z= 0.276 Angle : 0.581 12.731 9827 Z= 0.294 Chirality : 0.042 0.169 1146 Planarity : 0.004 0.041 1229 Dihedral : 4.219 21.685 978 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.60 % Allowed : 24.17 % Favored : 72.23 % 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: 0.49 (0.28), residues: 908 helix: 1.61 (0.25), residues: 418 sheet: -0.59 (0.37), residues: 199 loop : -0.80 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 82 HIS 0.003 0.001 HIS B 311 PHE 0.013 0.001 PHE A 197 TYR 0.013 0.001 TYR R 175 ARG 0.004 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 103 time to evaluate : 0.728 Fit side-chains REVERT: A 25 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6764 (tm-30) REVERT: A 32 ARG cc_start: 0.7329 (ttp-110) cc_final: 0.6805 (mtt90) REVERT: A 194 ASP cc_start: 0.7172 (m-30) cc_final: 0.6919 (m-30) REVERT: A 241 MET cc_start: 0.6797 (tpp) cc_final: 0.6367 (tpp) REVERT: A 277 GLU cc_start: 0.7649 (pt0) cc_final: 0.7365 (mp0) REVERT: A 316 ASP cc_start: 0.7191 (OUTLIER) cc_final: 0.6678 (p0) REVERT: B 186 ASP cc_start: 0.7210 (OUTLIER) cc_final: 0.6791 (m-30) REVERT: B 214 ARG cc_start: 0.7391 (mpt180) cc_final: 0.7096 (tpp80) REVERT: B 258 ASP cc_start: 0.7948 (t0) cc_final: 0.7067 (t0) outliers start: 27 outliers final: 17 residues processed: 120 average time/residue: 1.0213 time to fit residues: 130.9753 Evaluate side-chains 120 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain R residue 297 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 28 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 48 optimal weight: 0.0270 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 0.0980 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.5842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 7244 Z= 0.246 Angle : 0.593 12.525 9827 Z= 0.295 Chirality : 0.041 0.169 1146 Planarity : 0.004 0.041 1229 Dihedral : 4.151 21.435 978 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.07 % Allowed : 24.70 % Favored : 72.23 % 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: 0.53 (0.28), residues: 908 helix: 1.67 (0.26), residues: 412 sheet: -0.55 (0.37), residues: 199 loop : -0.77 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS B 311 PHE 0.013 0.001 PHE R 53 TYR 0.013 0.001 TYR R 175 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 108 time to evaluate : 0.783 Fit side-chains REVERT: R 28 LEU cc_start: 0.7304 (tp) cc_final: 0.7076 (tm) REVERT: A 25 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6761 (tm-30) REVERT: A 32 ARG cc_start: 0.7316 (ttp-110) cc_final: 0.6795 (mtt90) REVERT: A 194 ASP cc_start: 0.7163 (m-30) cc_final: 0.6908 (m-30) REVERT: A 241 MET cc_start: 0.6781 (tpp) cc_final: 0.6406 (tpp) REVERT: A 277 GLU cc_start: 0.7631 (pt0) cc_final: 0.7396 (mp0) REVERT: B 186 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6792 (m-30) REVERT: B 214 ARG cc_start: 0.7419 (mpt180) cc_final: 0.7109 (tpp80) REVERT: B 258 ASP cc_start: 0.7860 (t0) cc_final: 0.7091 (t0) outliers start: 23 outliers final: 17 residues processed: 124 average time/residue: 0.9713 time to fit residues: 129.6314 Evaluate side-chains 121 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain R residue 297 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 28 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.0030 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 0.0470 chunk 82 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 overall best weight: 0.4088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 7244 Z= 0.210 Angle : 0.553 12.050 9827 Z= 0.278 Chirality : 0.041 0.164 1146 Planarity : 0.004 0.041 1229 Dihedral : 4.043 21.077 978 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.20 % Allowed : 24.70 % Favored : 72.10 % 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: 0.63 (0.28), residues: 908 helix: 1.76 (0.26), residues: 411 sheet: -0.45 (0.37), residues: 194 loop : -0.78 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS B 311 PHE 0.011 0.001 PHE A 197 TYR 0.013 0.001 TYR R 175 ARG 0.003 0.000 ARG B 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 107 time to evaluate : 0.759 Fit side-chains REVERT: A 25 GLU cc_start: 0.7189 (tm-30) cc_final: 0.6774 (tm-30) REVERT: A 32 ARG cc_start: 0.7295 (ttp-110) cc_final: 0.6825 (mtt90) REVERT: A 194 ASP cc_start: 0.7160 (m-30) cc_final: 0.6902 (m-30) REVERT: A 233 LEU cc_start: 0.8236 (mm) cc_final: 0.7941 (mp) REVERT: A 241 MET cc_start: 0.6796 (tpp) cc_final: 0.6412 (tpp) REVERT: A 302 SER cc_start: 0.8027 (m) cc_final: 0.7079 (p) REVERT: A 316 ASP cc_start: 0.7163 (OUTLIER) cc_final: 0.6830 (t70) REVERT: B 186 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6767 (m-30) REVERT: B 214 ARG cc_start: 0.7448 (mpt180) cc_final: 0.7113 (tpp80) REVERT: B 217 MET cc_start: 0.7471 (pmm) cc_final: 0.7262 (ppp) REVERT: B 258 ASP cc_start: 0.7897 (t0) cc_final: 0.7127 (t0) outliers start: 24 outliers final: 16 residues processed: 123 average time/residue: 0.9787 time to fit residues: 129.1701 Evaluate side-chains 122 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain R residue 297 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 28 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.0980 chunk 71 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 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 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.149187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.112656 restraints weight = 8149.811| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.21 r_work: 0.3080 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 7244 Z= 0.279 Angle : 0.595 12.296 9827 Z= 0.299 Chirality : 0.042 0.163 1146 Planarity : 0.004 0.042 1229 Dihedral : 4.139 21.030 978 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.94 % Allowed : 25.23 % Favored : 71.83 % 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: 0.56 (0.28), residues: 908 helix: 1.69 (0.25), residues: 412 sheet: -0.56 (0.36), residues: 199 loop : -0.74 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 183 HIS 0.003 0.001 HIS B 311 PHE 0.017 0.002 PHE R 163 TYR 0.013 0.001 TYR R 175 ARG 0.004 0.000 ARG B 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3026.36 seconds wall clock time: 53 minutes 49.78 seconds (3229.78 seconds total)