Starting phenix.real_space_refine on Wed Feb 12 22:17:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxw_36715/02_2025/8jxw_36715_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxw_36715/02_2025/8jxw_36715.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jxw_36715/02_2025/8jxw_36715.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxw_36715/02_2025/8jxw_36715.map" model { file = "/net/cci-nas-00/data/ceres_data/8jxw_36715/02_2025/8jxw_36715_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxw_36715/02_2025/8jxw_36715_neut.cif" } resolution = 3.01 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= 0.118 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 57 5.16 5 Cl 1 4.86 5 C 5390 2.51 5 N 1374 2.21 5 O 1567 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8389 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1727 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 217} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 2432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2432 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 4, 'ARG:plan': 13, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 118 Chain: "D" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 363 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1691 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 217} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 49 Chain: "R" Number of atoms: 2153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2153 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 9, 'TRANS': 261} Chain breaks: 2 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'TRP:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "R" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'VCF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.05, per 1000 atoms: 0.60 Number of scatterers: 8389 At special positions: 0 Unit cell: (91.3, 121, 129.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 57 16.00 O 1567 8.00 N 1374 7.00 C 5390 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.05 Simple disulfide: pdb=" SG CYS R 87 " - pdb=" SG CYS R 164 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.11 Conformation dependent library (CDL) restraints added in 1.0 seconds 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2080 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 12 sheets defined 38.1% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'B' and resid 6 through 30 Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.931A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 216 removed outlier: 3.525A pdb=" N GLU B 216 " --> pdb=" O HIS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 removed outlier: 4.508A pdb=" N ASP B 231 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 232 " --> pdb=" O ASP B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 228 through 232' Processing helix chain 'B' and resid 241 through 255 removed outlier: 3.796A pdb=" N ALA B 245 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 260 removed outlier: 4.097A pdb=" N THR B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 278 removed outlier: 3.624A pdb=" N PHE B 274 " --> pdb=" O LYS B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 295 through 309 removed outlier: 3.885A pdb=" N ALA B 299 " --> pdb=" O THR B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 351 removed outlier: 4.094A pdb=" N VAL B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS B 351 " --> pdb=" O ASN B 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 25 removed outlier: 3.862A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 24 removed outlier: 3.658A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.574A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.763A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.505A pdb=" N ASP E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'R' and resid 14 through 43 removed outlier: 4.124A pdb=" N LEU R 18 " --> pdb=" O THR R 14 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA R 19 " --> pdb=" O ARG R 15 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE R 20 " --> pdb=" O VAL R 16 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE R 21 " --> pdb=" O THR R 17 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP R 43 " --> pdb=" O ALA R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 67 removed outlier: 3.693A pdb=" N VAL R 64 " --> pdb=" O SER R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 78 removed outlier: 3.843A pdb=" N LEU R 71 " --> pdb=" O ILE R 67 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR R 72 " --> pdb=" O SER R 68 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE R 73 " --> pdb=" O ILE R 69 " (cutoff:3.500A) Proline residue: R 74 - end of helix Processing helix chain 'R' and resid 83 through 118 removed outlier: 3.862A pdb=" N VAL R 116 " --> pdb=" O ARG R 112 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN R 118 " --> pdb=" O LEU R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 124 removed outlier: 3.650A pdb=" N TYR R 122 " --> pdb=" O ASN R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 154 removed outlier: 3.974A pdb=" N ASN R 147 " --> pdb=" O ALA R 143 " (cutoff:3.500A) Proline residue: R 149 - end of helix Processing helix chain 'R' and resid 166 through 170 removed outlier: 3.752A pdb=" N PHE R 169 " --> pdb=" O PRO R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 203 removed outlier: 3.823A pdb=" N LEU R 175 " --> pdb=" O GLU R 171 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ILE R 185 " --> pdb=" O LEU R 181 " (cutoff:3.500A) Proline residue: R 186 - end of helix Processing helix chain 'R' and resid 294 through 330 Proline residue: R 318 - end of helix removed outlier: 3.829A pdb=" N TYR R 329 " --> pdb=" O VAL R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 337 through 362 removed outlier: 4.080A pdb=" N ARG R 341 " --> pdb=" O SER R 337 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TRP R 348 " --> pdb=" O PHE R 344 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN R 350 " --> pdb=" O LEU R 346 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER R 351 " --> pdb=" O GLN R 347 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE R 352 " --> pdb=" O TRP R 348 " (cutoff:3.500A) Proline residue: R 355 - end of helix removed outlier: 3.665A pdb=" N TYR R 358 " --> pdb=" O ASN R 354 " (cutoff:3.500A) Proline residue: R 359 - end of helix removed outlier: 3.679A pdb=" N HIS R 362 " --> pdb=" O TYR R 358 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 372 Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 191 removed outlier: 3.775A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.673A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.043A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.955A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 153 removed outlier: 3.739A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N CYS C 166 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N THR C 179 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU C 168 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.855A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.899A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 276 through 278 Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 6.118A pdb=" N GLY E 16 " --> pdb=" O SER E 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.123A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 142 through 143 Processing sheet with id=AB3, first strand: chain 'E' and resid 148 through 149 removed outlier: 3.596A pdb=" N GLU E 247 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU E 179 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU E 188 " --> pdb=" O LEU E 179 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1146 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: 2.48 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2652 1.34 - 1.46: 2161 1.46 - 1.58: 3684 1.58 - 1.70: 1 1.70 - 1.83: 83 Bond restraints: 8581 Sorted by residual: bond pdb=" C08 VCF R 401 " pdb=" N05 VCF R 401 " ideal model delta sigma weight residual 1.358 1.488 -0.130 2.00e-02 2.50e+03 4.21e+01 bond pdb=" C08 VCF R 401 " pdb=" C23 VCF R 401 " ideal model delta sigma weight residual 1.485 1.550 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" N VAL B 233 " pdb=" CA VAL B 233 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.25e-02 6.40e+03 8.39e+00 bond pdb=" N THR R 14 " pdb=" CA THR R 14 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.26e-02 6.30e+03 6.51e+00 bond pdb=" N SER R 13 " pdb=" CA SER R 13 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.14e-02 7.69e+03 6.35e+00 ... (remaining 8576 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 11276 1.91 - 3.82: 335 3.82 - 5.73: 54 5.73 - 7.64: 16 7.64 - 9.55: 7 Bond angle restraints: 11688 Sorted by residual: angle pdb=" CA PRO R 355 " pdb=" N PRO R 355 " pdb=" CD PRO R 355 " ideal model delta sigma weight residual 112.00 102.45 9.55 1.40e+00 5.10e-01 4.66e+01 angle pdb=" CA PRO C 39 " pdb=" N PRO C 39 " pdb=" CD PRO C 39 " ideal model delta sigma weight residual 112.00 102.87 9.13 1.40e+00 5.10e-01 4.25e+01 angle pdb=" N ALA E 92 " pdb=" CA ALA E 92 " pdb=" C ALA E 92 " ideal model delta sigma weight residual 107.88 113.70 -5.82 1.41e+00 5.03e-01 1.70e+01 angle pdb=" CG ARG C 314 " pdb=" CD ARG C 314 " pdb=" NE ARG C 314 " ideal model delta sigma weight residual 112.00 120.22 -8.22 2.20e+00 2.07e-01 1.40e+01 angle pdb=" N GLY C 319 " pdb=" CA GLY C 319 " pdb=" C GLY C 319 " ideal model delta sigma weight residual 110.87 116.17 -5.30 1.54e+00 4.22e-01 1.18e+01 ... (remaining 11683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.99: 4384 13.99 - 27.98: 447 27.98 - 41.96: 118 41.96 - 55.95: 26 55.95 - 69.94: 12 Dihedral angle restraints: 4987 sinusoidal: 1767 harmonic: 3220 Sorted by residual: dihedral pdb=" CB CYS E 160 " pdb=" SG CYS E 160 " pdb=" SG CYS E 230 " pdb=" CB CYS E 230 " ideal model delta sinusoidal sigma weight residual 93.00 138.07 -45.07 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CA ILE R 67 " pdb=" C ILE R 67 " pdb=" N SER R 68 " pdb=" CA SER R 68 " ideal model delta harmonic sigma weight residual -180.00 -155.30 -24.70 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA GLU R 182 " pdb=" C GLU R 182 " pdb=" N PHE R 183 " pdb=" CA PHE R 183 " ideal model delta harmonic sigma weight residual -180.00 -156.83 -23.17 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 4984 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 833 0.039 - 0.078: 382 0.078 - 0.118: 103 0.118 - 0.157: 38 0.157 - 0.196: 3 Chirality restraints: 1359 Sorted by residual: chirality pdb=" CA PRO R 355 " pdb=" N PRO R 355 " pdb=" C PRO R 355 " pdb=" CB PRO R 355 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.59e-01 chirality pdb=" CA VAL R 16 " pdb=" N VAL R 16 " pdb=" C VAL R 16 " pdb=" CB VAL R 16 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.55e-01 chirality pdb=" CA VAL B 233 " pdb=" N VAL B 233 " pdb=" C VAL B 233 " pdb=" CB VAL B 233 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.49e-01 ... (remaining 1356 not shown) Planarity restraints: 1465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 354 " 0.068 5.00e-02 4.00e+02 9.69e-02 1.50e+01 pdb=" N PRO R 355 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO R 355 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO R 355 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 38 " -0.063 5.00e-02 4.00e+02 8.98e-02 1.29e+01 pdb=" N PRO C 39 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO C 39 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 39 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 48 " -0.043 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO D 49 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO D 49 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 49 " -0.036 5.00e-02 4.00e+02 ... (remaining 1462 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 81 2.65 - 3.22: 7412 3.22 - 3.78: 11784 3.78 - 4.34: 15846 4.34 - 4.90: 27557 Nonbonded interactions: 62680 Sorted by model distance: nonbonded pdb=" O HIS C 54 " pdb=" OG SER C 334 " model vdw 2.092 3.040 nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.130 3.040 nonbonded pdb=" OD1 ASP C 247 " pdb=" OG1 THR C 249 " model vdw 2.185 3.040 nonbonded pdb=" O ASP C 163 " pdb=" OG1 THR C 164 " model vdw 2.218 3.040 nonbonded pdb=" OG SER R 179 " pdb=" OG SER R 320 " model vdw 2.243 3.040 ... (remaining 62675 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.970 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.880 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 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 : 0.006 0.130 8581 Z= 0.391 Angle : 0.822 9.553 11688 Z= 0.464 Chirality : 0.048 0.196 1359 Planarity : 0.006 0.097 1465 Dihedral : 13.111 69.938 2901 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.80 % Allowed : 1.03 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.59 (0.24), residues: 1088 helix: 1.24 (0.26), residues: 374 sheet: 0.09 (0.30), residues: 280 loop : -2.25 (0.25), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 211 HIS 0.010 0.002 HIS C 183 PHE 0.017 0.002 PHE R 349 TYR 0.014 0.002 TYR R 329 ARG 0.008 0.001 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 1.042 Fit side-chains REVERT: C 101 MET cc_start: 0.8642 (mtt) cc_final: 0.8392 (mtt) outliers start: 7 outliers final: 4 residues processed: 119 average time/residue: 0.2309 time to fit residues: 37.3374 Evaluate side-chains 98 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 15 ARG Chi-restraints excluded: chain R residue 16 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.8980 chunk 82 optimal weight: 0.0670 chunk 45 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 20.0000 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN C 119 ASN ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 33 ASN R 147 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.178067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.125803 restraints weight = 9934.518| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.76 r_work: 0.3373 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8581 Z= 0.179 Angle : 0.584 7.298 11688 Z= 0.310 Chirality : 0.042 0.152 1359 Planarity : 0.004 0.050 1465 Dihedral : 5.724 55.713 1197 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.49 % Allowed : 7.34 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.17 (0.25), residues: 1088 helix: 2.11 (0.27), residues: 373 sheet: 0.28 (0.31), residues: 278 loop : -1.86 (0.26), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.005 0.001 HIS C 183 PHE 0.021 0.002 PHE R 322 TYR 0.015 0.001 TYR R 329 ARG 0.006 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.939 Fit side-chains REVERT: C 101 MET cc_start: 0.8731 (mtt) cc_final: 0.8508 (mtt) REVERT: R 33 ASN cc_start: 0.6754 (m-40) cc_final: 0.6524 (m-40) outliers start: 13 outliers final: 11 residues processed: 116 average time/residue: 0.2259 time to fit residues: 35.9295 Evaluate side-chains 117 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain R residue 15 ARG Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 321 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 53 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.174331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.129361 restraints weight = 10057.747| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.80 r_work: 0.3315 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8581 Z= 0.264 Angle : 0.625 8.003 11688 Z= 0.331 Chirality : 0.044 0.139 1359 Planarity : 0.004 0.043 1465 Dihedral : 5.279 48.691 1194 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.64 % Allowed : 9.40 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.29 (0.26), residues: 1088 helix: 2.17 (0.27), residues: 375 sheet: 0.30 (0.31), residues: 280 loop : -1.73 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 82 HIS 0.005 0.001 HIS E 233 PHE 0.015 0.002 PHE B 189 TYR 0.013 0.002 TYR E 103 ARG 0.005 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.898 Fit side-chains REVERT: C 101 MET cc_start: 0.8777 (mtt) cc_final: 0.8560 (mtt) REVERT: D 48 ASP cc_start: 0.8367 (t70) cc_final: 0.8055 (t70) outliers start: 23 outliers final: 21 residues processed: 114 average time/residue: 0.2304 time to fit residues: 35.3838 Evaluate side-chains 121 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain R residue 15 ARG Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 325 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 40 optimal weight: 0.0670 chunk 99 optimal weight: 0.3980 chunk 14 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.179836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.127095 restraints weight = 10013.431| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.78 r_work: 0.3381 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8581 Z= 0.148 Angle : 0.527 7.583 11688 Z= 0.279 Chirality : 0.041 0.141 1359 Planarity : 0.004 0.041 1465 Dihedral : 4.768 43.795 1194 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.41 % Allowed : 10.21 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.59 (0.26), residues: 1088 helix: 2.42 (0.27), residues: 380 sheet: 0.41 (0.31), residues: 280 loop : -1.57 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS C 183 PHE 0.012 0.001 PHE R 168 TYR 0.010 0.001 TYR R 329 ARG 0.003 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.868 Fit side-chains REVERT: C 101 MET cc_start: 0.8702 (mtt) cc_final: 0.8449 (mtt) REVERT: R 15 ARG cc_start: 0.6756 (OUTLIER) cc_final: 0.6474 (mmt180) REVERT: R 33 ASN cc_start: 0.6648 (m-40) cc_final: 0.6407 (m-40) outliers start: 21 outliers final: 17 residues processed: 116 average time/residue: 0.2186 time to fit residues: 34.5916 Evaluate side-chains 116 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain R residue 15 ARG Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 353 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 85 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.172136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.118957 restraints weight = 9942.761| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.73 r_work: 0.3290 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 8581 Z= 0.393 Angle : 0.701 8.671 11688 Z= 0.371 Chirality : 0.047 0.147 1359 Planarity : 0.005 0.047 1465 Dihedral : 5.170 40.029 1193 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.67 % Allowed : 12.16 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.22 (0.26), residues: 1088 helix: 2.04 (0.27), residues: 383 sheet: 0.21 (0.33), residues: 259 loop : -1.65 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 172 HIS 0.006 0.002 HIS E 35 PHE 0.018 0.002 PHE B 189 TYR 0.026 0.002 TYR C 105 ARG 0.004 0.001 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: C 101 MET cc_start: 0.8797 (mtt) cc_final: 0.8577 (mtt) REVERT: C 234 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.7907 (t80) REVERT: R 15 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.6090 (mmp-170) outliers start: 32 outliers final: 26 residues processed: 120 average time/residue: 0.2265 time to fit residues: 37.2303 Evaluate side-chains 125 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain R residue 15 ARG Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 182 GLU Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 353 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 31 optimal weight: 0.6980 chunk 70 optimal weight: 0.3980 chunk 11 optimal weight: 4.9990 chunk 67 optimal weight: 0.3980 chunk 62 optimal weight: 0.5980 chunk 89 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 36 optimal weight: 0.2980 chunk 61 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.179999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.127159 restraints weight = 9978.169| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.78 r_work: 0.3384 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8581 Z= 0.137 Angle : 0.528 7.453 11688 Z= 0.278 Chirality : 0.041 0.142 1359 Planarity : 0.004 0.045 1465 Dihedral : 4.620 37.757 1193 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.87 % Allowed : 12.84 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.26), residues: 1088 helix: 2.39 (0.27), residues: 386 sheet: 0.45 (0.31), residues: 278 loop : -1.55 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE R 168 TYR 0.009 0.001 TYR E 102 ARG 0.009 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: C 101 MET cc_start: 0.8636 (mtt) cc_final: 0.8391 (mtt) REVERT: R 15 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.6531 (mpt90) REVERT: R 33 ASN cc_start: 0.6592 (m-40) cc_final: 0.6381 (m-40) outliers start: 25 outliers final: 23 residues processed: 115 average time/residue: 0.2154 time to fit residues: 34.0568 Evaluate side-chains 120 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain R residue 15 ARG Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 182 GLU Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 353 VAL Chi-restraints excluded: chain R residue 362 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 58 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.174044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.120936 restraints weight = 10127.848| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.77 r_work: 0.3305 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8581 Z= 0.284 Angle : 0.633 8.069 11688 Z= 0.332 Chirality : 0.044 0.136 1359 Planarity : 0.004 0.045 1465 Dihedral : 4.832 35.181 1193 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.21 % Allowed : 13.42 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.26), residues: 1088 helix: 2.33 (0.27), residues: 381 sheet: 0.34 (0.32), residues: 264 loop : -1.56 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 82 HIS 0.005 0.001 HIS E 35 PHE 0.015 0.002 PHE B 189 TYR 0.017 0.002 TYR C 105 ARG 0.008 0.001 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: C 101 MET cc_start: 0.8715 (mtt) cc_final: 0.8488 (mtt) REVERT: C 234 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.7873 (t80) REVERT: E 83 MET cc_start: 0.7077 (mtp) cc_final: 0.6748 (mtm) REVERT: R 15 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.6414 (mmp-170) outliers start: 28 outliers final: 24 residues processed: 118 average time/residue: 0.2389 time to fit residues: 37.9095 Evaluate side-chains 128 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain R residue 15 ARG Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 182 GLU Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 353 VAL Chi-restraints excluded: chain R residue 362 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 93 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 50 optimal weight: 0.0970 chunk 7 optimal weight: 0.6980 chunk 65 optimal weight: 0.1980 chunk 11 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.180864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.128004 restraints weight = 10123.559| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.80 r_work: 0.3394 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8581 Z= 0.132 Angle : 0.518 7.493 11688 Z= 0.271 Chirality : 0.041 0.140 1359 Planarity : 0.004 0.048 1465 Dihedral : 4.427 32.463 1193 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.52 % Allowed : 14.22 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.76 (0.26), residues: 1088 helix: 2.46 (0.27), residues: 388 sheet: 0.52 (0.31), residues: 278 loop : -1.44 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE C 151 TYR 0.010 0.001 TYR R 192 ARG 0.010 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.963 Fit side-chains REVERT: C 101 MET cc_start: 0.8694 (mtt) cc_final: 0.8471 (mtt) REVERT: E 83 MET cc_start: 0.7144 (mtp) cc_final: 0.6854 (mtm) REVERT: R 201 LEU cc_start: 0.5800 (tt) cc_final: 0.5330 (tt) outliers start: 22 outliers final: 19 residues processed: 114 average time/residue: 0.2221 time to fit residues: 34.7227 Evaluate side-chains 119 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 362 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 50 optimal weight: 0.0030 chunk 14 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.181363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.128358 restraints weight = 10093.874| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.78 r_work: 0.3398 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8581 Z= 0.139 Angle : 0.524 7.918 11688 Z= 0.273 Chirality : 0.041 0.140 1359 Planarity : 0.004 0.046 1465 Dihedral : 4.190 25.287 1189 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.06 % Allowed : 14.79 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.81 (0.26), residues: 1088 helix: 2.48 (0.27), residues: 388 sheet: 0.55 (0.32), residues: 267 loop : -1.35 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE R 168 TYR 0.009 0.001 TYR E 191 ARG 0.005 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.971 Fit side-chains REVERT: C 101 MET cc_start: 0.8690 (mtt) cc_final: 0.8464 (mtt) REVERT: E 83 MET cc_start: 0.7124 (mtp) cc_final: 0.6809 (mtm) REVERT: R 201 LEU cc_start: 0.5816 (tt) cc_final: 0.5357 (tt) outliers start: 18 outliers final: 16 residues processed: 109 average time/residue: 0.2279 time to fit residues: 33.8154 Evaluate side-chains 116 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 362 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 65 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 88 optimal weight: 0.0970 chunk 68 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.179118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.126095 restraints weight = 10010.122| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.77 r_work: 0.3369 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8581 Z= 0.178 Angle : 0.546 7.753 11688 Z= 0.286 Chirality : 0.041 0.134 1359 Planarity : 0.004 0.048 1465 Dihedral : 4.229 21.998 1189 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.95 % Allowed : 15.60 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.80 (0.26), residues: 1088 helix: 2.45 (0.27), residues: 390 sheet: 0.49 (0.32), residues: 268 loop : -1.32 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE B 250 TYR 0.012 0.001 TYR E 191 ARG 0.005 0.000 ARG C 304 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.876 Fit side-chains REVERT: C 101 MET cc_start: 0.8647 (mtt) cc_final: 0.8432 (mtt) REVERT: E 83 MET cc_start: 0.7098 (mtp) cc_final: 0.6776 (mtm) REVERT: R 201 LEU cc_start: 0.6037 (tt) cc_final: 0.5561 (tt) outliers start: 17 outliers final: 17 residues processed: 109 average time/residue: 0.2255 time to fit residues: 33.7555 Evaluate side-chains 118 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 362 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 107 optimal weight: 0.0980 chunk 69 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.180603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.128090 restraints weight = 10194.480| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.77 r_work: 0.3390 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8581 Z= 0.150 Angle : 0.523 7.747 11688 Z= 0.273 Chirality : 0.041 0.134 1359 Planarity : 0.004 0.046 1465 Dihedral : 4.136 21.282 1189 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.06 % Allowed : 15.48 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.26), residues: 1088 helix: 2.56 (0.27), residues: 387 sheet: 0.59 (0.32), residues: 265 loop : -1.31 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.004 0.001 HIS E 35 PHE 0.012 0.001 PHE B 250 TYR 0.010 0.001 TYR E 191 ARG 0.006 0.000 ARG C 304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4505.29 seconds wall clock time: 80 minutes 42.76 seconds (4842.76 seconds total)