Starting phenix.real_space_refine on Mon Apr 28 18:36:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxv_36714/04_2025/8jxv_36714.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxv_36714/04_2025/8jxv_36714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jxv_36714/04_2025/8jxv_36714.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxv_36714/04_2025/8jxv_36714.map" model { file = "/net/cci-nas-00/data/ceres_data/8jxv_36714/04_2025/8jxv_36714.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxv_36714/04_2025/8jxv_36714.cif" } resolution = 3.21 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= 0.016 sd= 0.078 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 52 5.16 5 Cl 1 4.86 5 C 5111 2.51 5 N 1307 2.21 5 O 1464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 7935 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1550 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 2, 'TRANS': 201} Chain breaks: 4 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 73 Chain: "C" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2293 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 300} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 46 Chain: "D" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 227 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 27} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1749 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "R" Number of atoms: 2093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2093 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 70 Chain: "R" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'VBU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.91, per 1000 atoms: 0.62 Number of scatterers: 7935 At special positions: 0 Unit cell: (83.6, 118.8, 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 52 16.00 O 1464 8.00 N 1307 7.00 C 5111 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=2.04 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: 1.74 Conformation dependent library (CDL) restraints added in 1.0 seconds 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 34.0% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'B' and resid 8 through 31 Processing helix chain 'B' and resid 212 through 216 Processing helix chain 'B' and resid 242 through 255 Processing helix chain 'B' and resid 256 through 260 Processing helix chain 'B' and resid 270 through 281 removed outlier: 3.763A pdb=" N LYS B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 295 through 309 removed outlier: 3.697A pdb=" N ALA B 299 " --> pdb=" O THR B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 348 Processing helix chain 'D' and resid 32 through 44 removed outlier: 3.522A pdb=" N HIS D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.550A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.680A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 43 removed outlier: 4.002A pdb=" N VAL R 36 " --> pdb=" O GLY R 32 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP R 43 " --> pdb=" O ALA R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 63 removed outlier: 3.980A pdb=" N PHE R 63 " --> pdb=" O ILE R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 78 Proline residue: R 74 - end of helix Processing helix chain 'R' and resid 83 through 118 removed outlier: 4.748A pdb=" N PHE R 89 " --> pdb=" O GLU R 85 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL R 116 " --> pdb=" O ARG R 112 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN R 118 " --> pdb=" O LEU R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 148 removed outlier: 4.324A pdb=" N TRP R 140 " --> pdb=" O MET R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 151 No H-bonds generated for 'chain 'R' and resid 149 through 151' Processing helix chain 'R' and resid 155 through 159 removed outlier: 3.670A pdb=" N ASP R 159 " --> pdb=" O SER R 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 170 Processing helix chain 'R' and resid 171 through 181 removed outlier: 3.570A pdb=" N LEU R 175 " --> pdb=" O GLU R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 203 Processing helix chain 'R' and resid 294 through 329 Proline residue: R 318 - end of helix removed outlier: 4.206A pdb=" N TYR R 329 " --> pdb=" O VAL R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 337 through 349 removed outlier: 3.642A pdb=" N ARG R 341 " --> pdb=" O SER R 337 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TRP R 348 " --> pdb=" O PHE R 344 " (cutoff:3.500A) Processing helix chain 'R' and resid 349 through 362 removed outlier: 4.113A pdb=" N VAL R 353 " --> pdb=" O PHE R 349 " (cutoff:3.500A) Proline residue: R 355 - end of helix removed outlier: 4.129A pdb=" N TYR R 358 " --> pdb=" O ASN R 354 " (cutoff:3.500A) Proline residue: R 359 - end of helix removed outlier: 3.968A pdb=" N HIS R 362 " --> pdb=" O TYR R 358 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 372 removed outlier: 3.857A pdb=" N ILE R 372 " --> pdb=" O ALA R 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 191 removed outlier: 6.489A pdb=" N VAL B 34 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N PHE B 199 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LEU B 36 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N HIS B 322 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU B 266 " --> pdb=" O HIS B 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.863A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 336 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.762A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.714A 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: 6.939A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 148 through 151 removed outlier: 3.753A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER C 160 " --> pdb=" O CYS C 148 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.681A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.492A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 276 through 277 removed outlier: 4.250A pdb=" N CYS C 294 " --> pdb=" O LEU C 308 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.862A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.732A pdb=" N VAL E 148 " --> pdb=" O LYS E 245 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU E 247 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU E 179 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LEU E 188 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.732A pdb=" N VAL E 148 " --> pdb=" O LYS E 245 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU E 247 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN E 232 " --> pdb=" O THR E 239 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR E 239 " --> pdb=" O GLN E 232 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 156 through 161 373 hydrogen bonds defined for protein. 1026 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: 2.46 Time building geometry restraints manager: 2.10 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: 2491 1.34 - 1.46: 2032 1.46 - 1.58: 3522 1.58 - 1.70: 2 1.70 - 1.82: 74 Bond restraints: 8121 Sorted by residual: bond pdb=" C10 VBU R 401 " pdb=" N02 VBU R 401 " ideal model delta sigma weight residual 1.351 1.618 -0.267 2.00e-02 2.50e+03 1.79e+02 bond pdb=" C10 VBU R 401 " pdb=" C11 VBU R 401 " ideal model delta sigma weight residual 1.486 1.624 -0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" C14 VBU R 401 " pdb=" N04 VBU R 401 " ideal model delta sigma weight residual 1.377 1.481 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" C07 VBU R 401 " pdb=" N02 VBU R 401 " ideal model delta sigma weight residual 1.453 1.543 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C06 VBU R 401 " pdb=" N02 VBU R 401 " ideal model delta sigma weight residual 1.458 1.534 -0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 8116 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 10862 2.54 - 5.08: 161 5.08 - 7.61: 21 7.61 - 10.15: 6 10.15 - 12.69: 4 Bond angle restraints: 11054 Sorted by residual: angle pdb=" C08 VBU R 401 " pdb=" N03 VBU R 401 " pdb=" C09 VBU R 401 " ideal model delta sigma weight residual 113.13 100.44 12.69 3.00e+00 1.11e-01 1.79e+01 angle pdb=" C10 VBU R 401 " pdb=" N04 VBU R 401 " pdb=" C14 VBU R 401 " ideal model delta sigma weight residual 123.92 135.64 -11.72 3.00e+00 1.11e-01 1.53e+01 angle pdb=" C13 VBU R 401 " pdb=" N05 VBU R 401 " pdb=" C15 VBU R 401 " ideal model delta sigma weight residual 112.77 124.09 -11.32 3.00e+00 1.11e-01 1.42e+01 angle pdb=" N VAL R 153 " pdb=" CA VAL R 153 " pdb=" C VAL R 153 " ideal model delta sigma weight residual 112.80 108.89 3.91 1.15e+00 7.56e-01 1.15e+01 angle pdb=" C19 VBU R 401 " pdb=" C14 VBU R 401 " pdb=" N04 VBU R 401 " ideal model delta sigma weight residual 117.94 127.49 -9.55 3.00e+00 1.11e-01 1.01e+01 ... (remaining 11049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 4278 16.79 - 33.57: 344 33.57 - 50.36: 71 50.36 - 67.15: 10 67.15 - 83.93: 3 Dihedral angle restraints: 4706 sinusoidal: 1690 harmonic: 3016 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 93.00 138.04 -45.04 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CA PHE E 80 " pdb=" C PHE E 80 " pdb=" N LEU E 81 " pdb=" CA LEU E 81 " ideal model delta harmonic sigma weight residual 180.00 160.54 19.46 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ARG E 192 " pdb=" C ARG E 192 " pdb=" N MET E 193 " pdb=" CA MET E 193 " ideal model delta harmonic sigma weight residual 180.00 161.08 18.92 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 4703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 805 0.038 - 0.076: 332 0.076 - 0.114: 110 0.114 - 0.153: 24 0.153 - 0.191: 4 Chirality restraints: 1275 Sorted by residual: chirality pdb=" CA PRO R 186 " pdb=" N PRO R 186 " pdb=" C PRO R 186 " pdb=" CB PRO R 186 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.10e-01 chirality pdb=" CA TRP R 316 " pdb=" N TRP R 316 " pdb=" C TRP R 316 " pdb=" CB TRP R 316 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CA TYR C 59 " pdb=" N TYR C 59 " pdb=" C TYR C 59 " pdb=" CB TYR C 59 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.92e-01 ... (remaining 1272 not shown) Planarity restraints: 1379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 306 " -0.014 2.00e-02 2.50e+03 2.89e-02 8.37e+00 pdb=" C GLY C 306 " 0.050 2.00e-02 2.50e+03 pdb=" O GLY C 306 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL C 307 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 332 " -0.019 2.00e-02 2.50e+03 1.64e-02 6.73e+00 pdb=" CG TRP C 332 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP C 332 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C 332 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 332 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 332 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 332 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 332 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 332 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 332 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 354 " 0.041 5.00e-02 4.00e+02 6.12e-02 5.99e+00 pdb=" N PRO R 355 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO R 355 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 355 " 0.034 5.00e-02 4.00e+02 ... (remaining 1376 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 87 2.63 - 3.20: 7208 3.20 - 3.77: 11921 3.77 - 4.33: 16091 4.33 - 4.90: 27251 Nonbonded interactions: 62558 Sorted by model distance: nonbonded pdb=" OG SER C 275 " pdb=" O SER C 316 " model vdw 2.068 3.040 nonbonded pdb=" O ARG E 67 " pdb=" OG1 THR E 84 " model vdw 2.202 3.040 nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.220 3.040 nonbonded pdb=" O CYS C 103 " pdb=" NH1 ARG C 150 " model vdw 2.227 3.120 nonbonded pdb=" OG1 THR C 86 " pdb=" OD1 ASN C 88 " model vdw 2.241 3.040 ... (remaining 62553 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: 1.100 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.410 Find NCS groups from input model: 0.120 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 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 : 0.007 0.267 8123 Z= 0.316 Angle : 0.827 12.690 11058 Z= 0.431 Chirality : 0.046 0.191 1275 Planarity : 0.004 0.061 1379 Dihedral : 13.108 83.932 2752 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.75 (0.26), residues: 1016 helix: 1.11 (0.30), residues: 302 sheet: -0.28 (0.33), residues: 243 loop : -1.71 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP C 332 HIS 0.004 0.001 HIS B 322 PHE 0.021 0.002 PHE C 234 TYR 0.012 0.002 TYR E 95 ARG 0.006 0.001 ARG B 32 Details of bonding type rmsd hydrogen bonds : bond 0.14949 ( 369) hydrogen bonds : angle 6.19377 ( 1026) SS BOND : bond 0.00567 ( 2) SS BOND : angle 1.20366 ( 4) covalent geometry : bond 0.00684 ( 8121) covalent geometry : angle 0.82699 (11054) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.893 Fit side-chains REVERT: C 332 TRP cc_start: 0.6650 (m-10) cc_final: 0.6368 (m-10) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1931 time to fit residues: 31.1992 Evaluate side-chains 106 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 26 optimal weight: 0.0970 chunk 52 optimal weight: 0.2980 chunk 41 optimal weight: 0.7980 chunk 79 optimal weight: 0.0980 chunk 30 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 350 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.149018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.126620 restraints weight = 13197.468| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 2.44 r_work: 0.3844 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8123 Z= 0.131 Angle : 0.625 11.150 11058 Z= 0.322 Chirality : 0.042 0.152 1275 Planarity : 0.004 0.045 1379 Dihedral : 5.012 19.193 1123 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.48 % Allowed : 7.26 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.33 (0.26), residues: 1016 helix: 1.66 (0.30), residues: 297 sheet: -0.29 (0.31), residues: 279 loop : -1.51 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 345 HIS 0.002 0.001 HIS C 311 PHE 0.015 0.002 PHE R 168 TYR 0.011 0.001 TYR R 329 ARG 0.002 0.000 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.05764 ( 369) hydrogen bonds : angle 5.32338 ( 1026) SS BOND : bond 0.00513 ( 2) SS BOND : angle 0.41326 ( 4) covalent geometry : bond 0.00264 ( 8121) covalent geometry : angle 0.62473 (11054) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 119 time to evaluate : 0.785 Fit side-chains REVERT: C 264 TYR cc_start: 0.5791 (m-10) cc_final: 0.5552 (m-10) REVERT: E 98 ARG cc_start: 0.7024 (mtm110) cc_final: 0.6560 (mtm110) outliers start: 4 outliers final: 3 residues processed: 121 average time/residue: 0.1918 time to fit residues: 31.9369 Evaluate side-chains 113 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 110 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 88 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 98 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 143 GLN ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.148576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.125935 restraints weight = 13363.950| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 2.28 r_work: 0.3853 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8123 Z= 0.137 Angle : 0.606 10.631 11058 Z= 0.311 Chirality : 0.042 0.144 1275 Planarity : 0.004 0.043 1379 Dihedral : 4.809 17.757 1123 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.09 % Allowed : 9.69 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.15 (0.26), residues: 1016 helix: 1.83 (0.30), residues: 298 sheet: -0.15 (0.31), residues: 272 loop : -1.43 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 345 HIS 0.003 0.001 HIS C 142 PHE 0.025 0.002 PHE E 29 TYR 0.009 0.001 TYR R 329 ARG 0.005 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.05663 ( 369) hydrogen bonds : angle 5.12806 ( 1026) SS BOND : bond 0.00631 ( 2) SS BOND : angle 0.28612 ( 4) covalent geometry : bond 0.00292 ( 8121) covalent geometry : angle 0.60585 (11054) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.802 Fit side-chains REVERT: C 264 TYR cc_start: 0.5928 (m-10) cc_final: 0.5668 (m-10) REVERT: E 98 ARG cc_start: 0.7060 (mtm110) cc_final: 0.6667 (mtm110) REVERT: E 177 TRP cc_start: 0.6054 (m100) cc_final: 0.5492 (m100) REVERT: R 150 MET cc_start: 0.8366 (tpp) cc_final: 0.7785 (mmt) outliers start: 9 outliers final: 5 residues processed: 119 average time/residue: 0.1866 time to fit residues: 30.8387 Evaluate side-chains 112 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 338 VAL Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 42 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 66 optimal weight: 20.0000 chunk 69 optimal weight: 6.9990 chunk 95 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 ASN ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.146364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.123426 restraints weight = 13208.702| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 2.41 r_work: 0.3785 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8123 Z= 0.182 Angle : 0.650 10.848 11058 Z= 0.333 Chirality : 0.043 0.156 1275 Planarity : 0.005 0.051 1379 Dihedral : 4.889 17.835 1123 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.33 % Allowed : 12.47 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.18 (0.26), residues: 1016 helix: 1.77 (0.30), residues: 298 sheet: -0.12 (0.33), residues: 247 loop : -1.40 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 99 HIS 0.003 0.001 HIS C 142 PHE 0.024 0.002 PHE R 180 TYR 0.019 0.002 TYR E 60 ARG 0.005 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.06395 ( 369) hydrogen bonds : angle 5.13506 ( 1026) SS BOND : bond 0.00537 ( 2) SS BOND : angle 0.55023 ( 4) covalent geometry : bond 0.00413 ( 8121) covalent geometry : angle 0.65042 (11054) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.905 Fit side-chains REVERT: B 266 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6300 (tt) REVERT: C 327 VAL cc_start: 0.7483 (OUTLIER) cc_final: 0.7059 (p) REVERT: E 98 ARG cc_start: 0.7046 (mtm110) cc_final: 0.6651 (mtm110) REVERT: E 224 ASP cc_start: 0.6375 (m-30) cc_final: 0.6151 (m-30) outliers start: 11 outliers final: 6 residues processed: 112 average time/residue: 0.1907 time to fit residues: 29.6998 Evaluate side-chains 112 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 338 VAL Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 95 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 79 optimal weight: 0.2980 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 99 optimal weight: 0.0870 chunk 47 optimal weight: 6.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 ASN ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 350 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.148855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.125971 restraints weight = 13245.364| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 2.27 r_work: 0.3859 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8123 Z= 0.127 Angle : 0.585 10.134 11058 Z= 0.301 Chirality : 0.041 0.149 1275 Planarity : 0.004 0.046 1379 Dihedral : 4.644 16.463 1123 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.06 % Allowed : 13.44 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.10 (0.27), residues: 1016 helix: 1.98 (0.30), residues: 303 sheet: 0.00 (0.33), residues: 258 loop : -1.24 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 345 HIS 0.003 0.001 HIS C 142 PHE 0.024 0.002 PHE R 180 TYR 0.011 0.001 TYR E 60 ARG 0.003 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.05326 ( 369) hydrogen bonds : angle 4.88368 ( 1026) SS BOND : bond 0.00582 ( 2) SS BOND : angle 0.20264 ( 4) covalent geometry : bond 0.00269 ( 8121) covalent geometry : angle 0.58463 (11054) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.797 Fit side-chains REVERT: B 266 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.6067 (tt) REVERT: C 327 VAL cc_start: 0.7309 (OUTLIER) cc_final: 0.7034 (t) REVERT: E 98 ARG cc_start: 0.7037 (mtm110) cc_final: 0.6634 (mtm110) outliers start: 17 outliers final: 8 residues processed: 117 average time/residue: 0.1809 time to fit residues: 29.5855 Evaluate side-chains 113 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 61 ASP Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.0070 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 79 optimal weight: 0.3980 chunk 38 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.148994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.127068 restraints weight = 13207.047| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 2.22 r_work: 0.3866 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8123 Z= 0.128 Angle : 0.593 9.858 11058 Z= 0.303 Chirality : 0.041 0.143 1275 Planarity : 0.004 0.045 1379 Dihedral : 4.558 16.694 1123 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.82 % Allowed : 15.25 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.19 (0.27), residues: 1016 helix: 2.02 (0.31), residues: 301 sheet: 0.12 (0.33), residues: 257 loop : -1.18 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 345 HIS 0.002 0.001 HIS C 142 PHE 0.022 0.002 PHE R 180 TYR 0.009 0.001 TYR E 191 ARG 0.003 0.000 ARG R 112 Details of bonding type rmsd hydrogen bonds : bond 0.05292 ( 369) hydrogen bonds : angle 4.82443 ( 1026) SS BOND : bond 0.00656 ( 2) SS BOND : angle 0.25538 ( 4) covalent geometry : bond 0.00272 ( 8121) covalent geometry : angle 0.59266 (11054) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 1.021 Fit side-chains REVERT: B 4 THR cc_start: 0.6923 (OUTLIER) cc_final: 0.6627 (m) REVERT: B 266 LEU cc_start: 0.6733 (OUTLIER) cc_final: 0.6177 (tt) REVERT: E 98 ARG cc_start: 0.7075 (mtm110) cc_final: 0.6711 (mtm110) outliers start: 15 outliers final: 8 residues processed: 113 average time/residue: 0.1970 time to fit residues: 31.0038 Evaluate side-chains 112 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain R residue 61 ASP Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 338 VAL Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 50 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.148309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.125376 restraints weight = 13376.557| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 2.43 r_work: 0.3842 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8123 Z= 0.143 Angle : 0.606 9.833 11058 Z= 0.310 Chirality : 0.042 0.157 1275 Planarity : 0.004 0.046 1379 Dihedral : 4.581 17.532 1123 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.30 % Allowed : 15.98 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.26 (0.27), residues: 1016 helix: 2.03 (0.31), residues: 301 sheet: 0.17 (0.33), residues: 261 loop : -1.12 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 332 HIS 0.002 0.001 HIS C 311 PHE 0.023 0.002 PHE R 180 TYR 0.010 0.001 TYR E 102 ARG 0.003 0.000 ARG R 112 Details of bonding type rmsd hydrogen bonds : bond 0.05545 ( 369) hydrogen bonds : angle 4.85283 ( 1026) SS BOND : bond 0.00689 ( 2) SS BOND : angle 0.30412 ( 4) covalent geometry : bond 0.00313 ( 8121) covalent geometry : angle 0.60601 (11054) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: B 4 THR cc_start: 0.6885 (OUTLIER) cc_final: 0.6585 (m) REVERT: B 266 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6057 (tt) REVERT: C 327 VAL cc_start: 0.7310 (OUTLIER) cc_final: 0.7016 (t) outliers start: 19 outliers final: 13 residues processed: 112 average time/residue: 0.1868 time to fit residues: 29.5377 Evaluate side-chains 115 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 61 ASP Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 338 VAL Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 79 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 39 optimal weight: 0.0980 chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 0.0970 chunk 100 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 82 optimal weight: 0.0030 chunk 73 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.151399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.128753 restraints weight = 13347.300| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 2.27 r_work: 0.3894 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8123 Z= 0.109 Angle : 0.567 9.040 11058 Z= 0.289 Chirality : 0.041 0.148 1275 Planarity : 0.004 0.044 1379 Dihedral : 4.387 16.907 1123 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.45 % Allowed : 17.07 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.27), residues: 1016 helix: 2.27 (0.31), residues: 304 sheet: 0.38 (0.32), residues: 266 loop : -1.10 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 345 HIS 0.002 0.000 HIS E 35 PHE 0.026 0.002 PHE R 180 TYR 0.009 0.001 TYR R 72 ARG 0.009 0.000 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.04528 ( 369) hydrogen bonds : angle 4.66092 ( 1026) SS BOND : bond 0.00524 ( 2) SS BOND : angle 0.13410 ( 4) covalent geometry : bond 0.00223 ( 8121) covalent geometry : angle 0.56712 (11054) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: B 4 THR cc_start: 0.6838 (OUTLIER) cc_final: 0.6533 (m) REVERT: B 266 LEU cc_start: 0.6504 (OUTLIER) cc_final: 0.5975 (tt) REVERT: C 125 ASN cc_start: 0.6671 (t0) cc_final: 0.5970 (p0) outliers start: 12 outliers final: 7 residues processed: 114 average time/residue: 0.1825 time to fit residues: 29.1920 Evaluate side-chains 111 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain R residue 61 ASP Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 75 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 66 optimal weight: 0.0060 chunk 85 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 101 optimal weight: 0.0870 chunk 41 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 overall best weight: 0.5374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.150781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.128020 restraints weight = 13432.598| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 2.26 r_work: 0.3871 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8123 Z= 0.121 Angle : 0.588 8.798 11058 Z= 0.299 Chirality : 0.041 0.141 1275 Planarity : 0.004 0.044 1379 Dihedral : 4.387 17.778 1123 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.57 % Allowed : 17.43 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.27), residues: 1016 helix: 2.42 (0.30), residues: 298 sheet: 0.36 (0.32), residues: 266 loop : -1.10 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 332 HIS 0.002 0.001 HIS E 35 PHE 0.024 0.002 PHE R 180 TYR 0.045 0.002 TYR E 60 ARG 0.014 0.000 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.04740 ( 369) hydrogen bonds : angle 4.66673 ( 1026) SS BOND : bond 0.00644 ( 2) SS BOND : angle 0.10315 ( 4) covalent geometry : bond 0.00257 ( 8121) covalent geometry : angle 0.58779 (11054) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: B 4 THR cc_start: 0.6928 (OUTLIER) cc_final: 0.6607 (m) REVERT: B 243 MET cc_start: 0.5412 (mmp) cc_final: 0.5147 (mmt) REVERT: B 266 LEU cc_start: 0.6608 (OUTLIER) cc_final: 0.6069 (tt) REVERT: C 125 ASN cc_start: 0.6688 (t0) cc_final: 0.6047 (p0) REVERT: E 98 ARG cc_start: 0.6726 (mtm110) cc_final: 0.6515 (mtm180) outliers start: 13 outliers final: 8 residues processed: 111 average time/residue: 0.1900 time to fit residues: 29.7053 Evaluate side-chains 111 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain R residue 61 ASP Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 55 optimal weight: 0.0570 chunk 11 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 53 optimal weight: 0.0870 chunk 18 optimal weight: 0.0570 chunk 100 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 195 ASN ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.152700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.130276 restraints weight = 13329.918| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 2.26 r_work: 0.3909 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8123 Z= 0.112 Angle : 0.595 9.543 11058 Z= 0.299 Chirality : 0.041 0.182 1275 Planarity : 0.004 0.044 1379 Dihedral : 4.313 20.553 1123 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.45 % Allowed : 17.43 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.60 (0.27), residues: 1016 helix: 2.51 (0.30), residues: 296 sheet: 0.36 (0.32), residues: 267 loop : -1.04 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 345 HIS 0.002 0.000 HIS C 54 PHE 0.026 0.002 PHE R 180 TYR 0.023 0.001 TYR E 60 ARG 0.014 0.000 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 369) hydrogen bonds : angle 4.59694 ( 1026) SS BOND : bond 0.00592 ( 2) SS BOND : angle 0.19148 ( 4) covalent geometry : bond 0.00225 ( 8121) covalent geometry : angle 0.59477 (11054) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 4 THR cc_start: 0.6889 (OUTLIER) cc_final: 0.6567 (m) REVERT: B 243 MET cc_start: 0.5366 (mmp) cc_final: 0.5099 (mmt) REVERT: B 266 LEU cc_start: 0.6515 (OUTLIER) cc_final: 0.5992 (tt) REVERT: C 125 ASN cc_start: 0.6622 (t0) cc_final: 0.6021 (p0) outliers start: 12 outliers final: 6 residues processed: 113 average time/residue: 0.1888 time to fit residues: 30.2312 Evaluate side-chains 111 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain R residue 61 ASP Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 195 ASN ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.149727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.126826 restraints weight = 13310.140| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 2.31 r_work: 0.3873 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8123 Z= 0.145 Angle : 0.634 9.362 11058 Z= 0.319 Chirality : 0.042 0.163 1275 Planarity : 0.004 0.045 1379 Dihedral : 4.418 21.769 1123 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.09 % Allowed : 18.28 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.27), residues: 1016 helix: 2.40 (0.30), residues: 295 sheet: 0.30 (0.32), residues: 266 loop : -1.03 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 332 HIS 0.003 0.001 HIS C 142 PHE 0.028 0.002 PHE R 180 TYR 0.024 0.002 TYR E 60 ARG 0.003 0.000 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.05248 ( 369) hydrogen bonds : angle 4.67358 ( 1026) SS BOND : bond 0.00612 ( 2) SS BOND : angle 0.20056 ( 4) covalent geometry : bond 0.00321 ( 8121) covalent geometry : angle 0.63431 (11054) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4975.65 seconds wall clock time: 85 minutes 39.13 seconds (5139.13 seconds total)