Starting phenix.real_space_refine on Sat Apr 6 13:27:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxt_36712/04_2024/8jxt_36712_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxt_36712/04_2024/8jxt_36712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxt_36712/04_2024/8jxt_36712.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxt_36712/04_2024/8jxt_36712.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxt_36712/04_2024/8jxt_36712_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxt_36712/04_2024/8jxt_36712_neut_updated.pdb" } resolution = 3.07 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= -0.003 sd= 0.121 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 P 1 5.49 5 S 54 5.16 5 C 5330 2.51 5 N 1365 2.21 5 O 1548 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8298 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1627 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 79 Chain: "C" Number of atoms: 2489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2489 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 75 Chain: "D" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 336 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "E" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1728 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 38 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: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2105 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 9, 'TRANS': 260} Chain breaks: 1 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 74 Chain: "R" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {'HSM': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.83, per 1000 atoms: 0.58 Number of scatterers: 8298 At special positions: 0 Unit cell: (91.3, 124.3, 127.6, 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) S 54 16.00 P 1 15.00 O 1548 8.00 N 1365 7.00 C 5330 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.03 Conformation dependent library (CDL) restraints added in 1.5 seconds 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 12 sheets defined 33.0% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'B' and resid 7 through 29 Processing helix chain 'B' and resid 46 through 52 Processing helix chain 'B' and resid 212 through 215 Processing helix chain 'B' and resid 242 through 254 Processing helix chain 'B' and resid 257 through 259 No H-bonds generated for 'chain 'B' and resid 257 through 259' Processing helix chain 'B' and resid 272 through 275 No H-bonds generated for 'chain 'B' and resid 272 through 275' Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 296 through 310 removed outlier: 4.046A pdb=" N LEU B 310 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 351 removed outlier: 4.245A pdb=" N VAL B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS B 351 " --> pdb=" O ASN B 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 25 Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 34 through 36 No H-bonds generated for 'chain 'C' and resid 34 through 36' Processing helix chain 'D' and resid 11 through 23 Processing helix chain 'D' and resid 30 through 44 removed outlier: 3.768A pdb=" N HIS D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'R' and resid 15 through 42 removed outlier: 4.064A pdb=" N VAL R 36 " --> pdb=" O GLY R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 77 removed outlier: 3.805A pdb=" N GLY R 65 " --> pdb=" O ASP R 61 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL R 66 " --> pdb=" O PHE R 62 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE R 67 " --> pdb=" O PHE R 63 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER R 68 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ILE R 69 " --> pdb=" O GLY R 65 " (cutoff:3.500A) Proline residue: R 70 - end of helix Proline residue: R 74 - end of helix Processing helix chain 'R' and resid 84 through 117 removed outlier: 4.199A pdb=" N PHE R 89 " --> pdb=" O GLU R 85 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL R 116 " --> pdb=" O ARG R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 120 through 123 No H-bonds generated for 'chain 'R' and resid 120 through 123' Processing helix chain 'R' and resid 131 through 153 removed outlier: 3.977A pdb=" N TRP R 140 " --> pdb=" O MET R 136 " (cutoff:3.500A) removed outlier: 4.039A 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 172 through 180 removed outlier: 4.413A pdb=" N ILE R 177 " --> pdb=" O TYR R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 184 through 202 Processing helix chain 'R' and resid 294 through 328 removed outlier: 4.435A pdb=" N PHE R 312 " --> pdb=" O LEU R 308 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing helix chain 'R' and resid 338 through 361 removed outlier: 3.904A pdb=" N TRP R 345 " --> pdb=" O ARG R 341 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN R 347 " --> pdb=" O ALA R 343 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TRP R 348 " --> pdb=" O PHE R 344 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE R 349 " --> pdb=" O TRP R 345 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN R 350 " --> pdb=" O LEU R 346 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N SER R 351 " --> pdb=" O GLN R 347 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE R 352 " --> pdb=" O TRP R 348 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL R 353 " --> pdb=" O PHE R 349 " (cutoff:3.500A) Proline residue: R 355 - end of helix removed outlier: 3.548A pdb=" N TYR R 358 " --> pdb=" O ASN R 354 " (cutoff:3.500A) Proline residue: R 359 - end of helix Processing helix chain 'R' and resid 363 through 370 Processing sheet with id= A, first strand: chain 'B' and resid 319 through 323 removed outlier: 6.917A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N HIS B 322 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU B 266 " --> pdb=" O HIS B 322 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.070A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.042A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 146 through 151 removed outlier: 7.109A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.747A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.745A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 294 through 298 removed outlier: 3.725A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 47 through 51 removed outlier: 7.054A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.601A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 147 through 149 removed outlier: 7.157A pdb=" N LYS E 245 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU E 179 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU E 188 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 156 through 161 375 hydrogen bonds defined for protein. 1077 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: 2.64 Time building geometry restraints manager: 3.31 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: 2636 1.34 - 1.46: 2224 1.46 - 1.59: 3550 1.59 - 1.71: 0 1.71 - 1.83: 77 Bond restraints: 8487 Sorted by residual: bond pdb=" O3 PO4 R 402 " pdb=" P PO4 R 402 " ideal model delta sigma weight residual 1.569 1.524 0.045 2.00e-02 2.50e+03 5.02e+00 bond pdb=" CB HSM R 401 " pdb=" CG HSM R 401 " ideal model delta sigma weight residual 1.496 1.452 0.044 2.00e-02 2.50e+03 4.88e+00 bond pdb=" O2 PO4 R 402 " pdb=" P PO4 R 402 " ideal model delta sigma weight residual 1.567 1.523 0.044 2.00e-02 2.50e+03 4.76e+00 bond pdb=" O4 PO4 R 402 " pdb=" P PO4 R 402 " ideal model delta sigma weight residual 1.568 1.525 0.043 2.00e-02 2.50e+03 4.60e+00 bond pdb=" O1 PO4 R 402 " pdb=" P PO4 R 402 " ideal model delta sigma weight residual 1.565 1.524 0.041 2.00e-02 2.50e+03 4.27e+00 ... (remaining 8482 not shown) Histogram of bond angle deviations from ideal: 99.74 - 106.59: 183 106.59 - 113.44: 4656 113.44 - 120.28: 3098 120.28 - 127.13: 3545 127.13 - 133.98: 92 Bond angle restraints: 11574 Sorted by residual: angle pdb=" CA MET E 193 " pdb=" CB MET E 193 " pdb=" CG MET E 193 " ideal model delta sigma weight residual 114.10 120.62 -6.52 2.00e+00 2.50e-01 1.06e+01 angle pdb=" CA TRP C 82 " pdb=" CB TRP C 82 " pdb=" CG TRP C 82 " ideal model delta sigma weight residual 113.60 119.78 -6.18 1.90e+00 2.77e-01 1.06e+01 angle pdb=" CA HSM R 401 " pdb=" CB HSM R 401 " pdb=" CG HSM R 401 " ideal model delta sigma weight residual 114.47 105.20 9.27 3.00e+00 1.11e-01 9.54e+00 angle pdb=" N MET E 193 " pdb=" CA MET E 193 " pdb=" CB MET E 193 " ideal model delta sigma weight residual 114.27 109.28 4.99 1.64e+00 3.72e-01 9.26e+00 angle pdb=" CG MET E 193 " pdb=" SD MET E 193 " pdb=" CE MET E 193 " ideal model delta sigma weight residual 100.90 107.53 -6.63 2.20e+00 2.07e-01 9.09e+00 ... (remaining 11569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 4515 17.57 - 35.14: 334 35.14 - 52.70: 49 52.70 - 70.27: 7 70.27 - 87.84: 1 Dihedral angle restraints: 4906 sinusoidal: 1690 harmonic: 3216 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 93.00 136.07 -43.07 1 1.00e+01 1.00e-02 2.59e+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 180.00 155.69 24.31 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA TRP C 339 " pdb=" C TRP C 339 " pdb=" N ASN C 340 " pdb=" CA ASN C 340 " ideal model delta harmonic sigma weight residual 180.00 161.10 18.90 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 4903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 735 0.030 - 0.059: 392 0.059 - 0.089: 145 0.089 - 0.119: 65 0.119 - 0.148: 16 Chirality restraints: 1353 Sorted by residual: chirality pdb=" CA PRO R 318 " pdb=" N PRO R 318 " pdb=" C PRO R 318 " pdb=" CB PRO R 318 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA ILE C 58 " pdb=" N ILE C 58 " pdb=" C ILE C 58 " pdb=" CB ILE C 58 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA ILE C 229 " pdb=" N ILE C 229 " pdb=" C ILE C 229 " pdb=" CB ILE C 229 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 1350 not shown) Planarity restraints: 1454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU R 165 " 0.058 5.00e-02 4.00e+02 8.80e-02 1.24e+01 pdb=" N PRO R 166 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO R 166 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO R 166 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " 0.045 5.00e-02 4.00e+02 6.83e-02 7.45e+00 pdb=" N PRO C 236 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 48 " 0.036 5.00e-02 4.00e+02 5.42e-02 4.71e+00 pdb=" N PRO D 49 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 49 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 49 " 0.030 5.00e-02 4.00e+02 ... (remaining 1451 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1406 2.76 - 3.30: 7413 3.30 - 3.83: 12765 3.83 - 4.37: 13835 4.37 - 4.90: 25255 Nonbonded interactions: 60674 Sorted by model distance: nonbonded pdb=" OG1 THR C 86 " pdb=" OD1 ASN C 88 " model vdw 2.228 2.440 nonbonded pdb=" O GLY E 210 " pdb=" OG1 THR E 211 " model vdw 2.264 2.440 nonbonded pdb=" OD1 ASP C 290 " pdb=" NE ARG C 314 " model vdw 2.284 2.520 nonbonded pdb=" NH2 ARG E 203 " pdb=" OE2 GLU E 221 " model vdw 2.288 2.520 nonbonded pdb=" NH1 ARG E 38 " pdb=" OD1 ASP E 90 " model vdw 2.298 2.520 ... (remaining 60669 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 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: 3.940 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.140 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 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 : 0.005 0.045 8487 Z= 0.303 Angle : 0.685 9.267 11574 Z= 0.388 Chirality : 0.045 0.148 1353 Planarity : 0.005 0.088 1454 Dihedral : 12.498 87.839 2824 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.24 % Allowed : 0.24 % Favored : 99.53 % 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: -0.33 (0.26), residues: 1089 helix: 1.28 (0.28), residues: 357 sheet: 0.34 (0.32), residues: 274 loop : -1.83 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 82 HIS 0.007 0.002 HIS R 75 PHE 0.027 0.002 PHE C 199 TYR 0.017 0.002 TYR E 50 ARG 0.012 0.001 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 149 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: C 262 MET cc_start: 0.7771 (mmt) cc_final: 0.7513 (mpp) REVERT: E 205 SER cc_start: 0.7476 (t) cc_final: 0.7198 (m) outliers start: 2 outliers final: 0 residues processed: 150 average time/residue: 0.2233 time to fit residues: 45.3590 Evaluate side-chains 109 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.4980 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 268 ASN E 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8487 Z= 0.181 Angle : 0.549 6.717 11574 Z= 0.293 Chirality : 0.043 0.137 1353 Planarity : 0.004 0.062 1454 Dihedral : 4.286 17.998 1178 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.71 % Allowed : 7.44 % Favored : 91.85 % 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: -0.11 (0.26), residues: 1089 helix: 1.45 (0.29), residues: 364 sheet: 0.28 (0.31), residues: 285 loop : -1.66 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 82 HIS 0.005 0.001 HIS E 233 PHE 0.021 0.001 PHE R 144 TYR 0.012 0.001 TYR E 50 ARG 0.004 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 113 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: C 280 LYS cc_start: 0.7894 (tttm) cc_final: 0.7605 (tttm) REVERT: R 144 PHE cc_start: 0.8188 (t80) cc_final: 0.7962 (t80) outliers start: 6 outliers final: 6 residues processed: 114 average time/residue: 0.2111 time to fit residues: 33.1592 Evaluate side-chains 107 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 160 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN E 184 GLN R 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8487 Z= 0.174 Angle : 0.525 6.519 11574 Z= 0.278 Chirality : 0.042 0.139 1353 Planarity : 0.004 0.056 1454 Dihedral : 4.104 19.249 1178 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.77 % Allowed : 9.21 % Favored : 89.02 % 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: 0.11 (0.26), residues: 1089 helix: 1.67 (0.29), residues: 361 sheet: 0.36 (0.31), residues: 287 loop : -1.50 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 332 HIS 0.004 0.001 HIS C 225 PHE 0.014 0.001 PHE B 189 TYR 0.013 0.001 TYR E 50 ARG 0.005 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 0.898 Fit side-chains REVERT: B 33 GLU cc_start: 0.8027 (pt0) cc_final: 0.7787 (pt0) REVERT: B 346 ASN cc_start: 0.6984 (m110) cc_final: 0.6643 (m-40) REVERT: C 280 LYS cc_start: 0.7965 (tttm) cc_final: 0.7615 (tttm) REVERT: R 144 PHE cc_start: 0.8253 (t80) cc_final: 0.7981 (t80) outliers start: 15 outliers final: 10 residues processed: 115 average time/residue: 0.1978 time to fit residues: 31.5098 Evaluate side-chains 109 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain R residue 172 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 0.0570 chunk 10 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 0.4980 chunk 105 optimal weight: 5.9990 chunk 94 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 HIS B 331 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8487 Z= 0.178 Angle : 0.522 6.836 11574 Z= 0.277 Chirality : 0.042 0.140 1353 Planarity : 0.004 0.054 1454 Dihedral : 4.049 17.099 1178 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.01 % Allowed : 11.57 % Favored : 86.42 % 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: 0.14 (0.26), residues: 1089 helix: 1.65 (0.29), residues: 368 sheet: 0.33 (0.31), residues: 279 loop : -1.44 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 332 HIS 0.004 0.001 HIS E 233 PHE 0.016 0.001 PHE R 352 TYR 0.013 0.001 TYR E 50 ARG 0.003 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 0.886 Fit side-chains REVERT: B 346 ASN cc_start: 0.7035 (m110) cc_final: 0.6739 (m-40) REVERT: C 204 CYS cc_start: 0.7806 (t) cc_final: 0.7400 (t) REVERT: C 280 LYS cc_start: 0.7959 (tttm) cc_final: 0.7622 (tttm) REVERT: C 332 TRP cc_start: 0.7836 (m-10) cc_final: 0.7557 (m-10) REVERT: R 144 PHE cc_start: 0.8327 (t80) cc_final: 0.8068 (t80) outliers start: 17 outliers final: 15 residues processed: 116 average time/residue: 0.2151 time to fit residues: 34.1897 Evaluate side-chains 113 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain R residue 172 TRP Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 360 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 0 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8487 Z= 0.166 Angle : 0.505 6.575 11574 Z= 0.268 Chirality : 0.041 0.129 1353 Planarity : 0.004 0.054 1454 Dihedral : 3.981 19.614 1178 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.24 % Allowed : 12.87 % Favored : 84.89 % 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: 0.20 (0.26), residues: 1089 helix: 1.74 (0.29), residues: 370 sheet: 0.37 (0.32), residues: 279 loop : -1.46 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 332 HIS 0.004 0.001 HIS B 188 PHE 0.016 0.001 PHE R 352 TYR 0.012 0.001 TYR E 50 ARG 0.003 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 0.905 Fit side-chains REVERT: B 33 GLU cc_start: 0.7910 (pt0) cc_final: 0.7633 (pt0) REVERT: B 346 ASN cc_start: 0.7020 (m110) cc_final: 0.6729 (m-40) REVERT: C 280 LYS cc_start: 0.7877 (tttm) cc_final: 0.7523 (tttm) REVERT: C 332 TRP cc_start: 0.7607 (m-10) cc_final: 0.7206 (m-10) REVERT: R 144 PHE cc_start: 0.8287 (t80) cc_final: 0.8047 (t80) outliers start: 19 outliers final: 17 residues processed: 111 average time/residue: 0.2017 time to fit residues: 31.0169 Evaluate side-chains 116 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain R residue 172 TRP Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 349 PHE Chi-restraints excluded: chain R residue 360 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 55 optimal weight: 6.9990 chunk 101 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8487 Z= 0.154 Angle : 0.496 6.317 11574 Z= 0.263 Chirality : 0.041 0.135 1353 Planarity : 0.004 0.052 1454 Dihedral : 3.906 18.208 1178 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.48 % Allowed : 13.81 % Favored : 83.71 % 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: 0.32 (0.26), residues: 1089 helix: 1.87 (0.29), residues: 367 sheet: 0.45 (0.32), residues: 274 loop : -1.39 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.016 0.001 PHE R 352 TYR 0.011 0.001 TYR E 50 ARG 0.008 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 101 time to evaluate : 0.906 Fit side-chains REVERT: B 216 GLU cc_start: 0.7327 (tt0) cc_final: 0.7107 (mt-10) REVERT: B 346 ASN cc_start: 0.6999 (m110) cc_final: 0.6693 (m-40) REVERT: C 280 LYS cc_start: 0.7828 (tttm) cc_final: 0.7484 (tttm) REVERT: C 332 TRP cc_start: 0.7700 (m-10) cc_final: 0.7318 (m-10) REVERT: R 144 PHE cc_start: 0.8236 (t80) cc_final: 0.8008 (t80) outliers start: 21 outliers final: 17 residues processed: 112 average time/residue: 0.2067 time to fit residues: 32.0296 Evaluate side-chains 116 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain R residue 172 TRP Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 349 PHE Chi-restraints excluded: chain R residue 360 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 0.0970 chunk 88 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8487 Z= 0.148 Angle : 0.491 6.149 11574 Z= 0.260 Chirality : 0.041 0.134 1353 Planarity : 0.004 0.050 1454 Dihedral : 3.842 18.699 1178 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.36 % Allowed : 13.93 % Favored : 83.71 % 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: 0.38 (0.26), residues: 1089 helix: 1.86 (0.29), residues: 368 sheet: 0.49 (0.32), residues: 274 loop : -1.31 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 82 HIS 0.004 0.001 HIS B 188 PHE 0.019 0.001 PHE R 352 TYR 0.010 0.001 TYR E 50 ARG 0.004 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 0.939 Fit side-chains REVERT: B 216 GLU cc_start: 0.7307 (tt0) cc_final: 0.7093 (mt-10) REVERT: B 346 ASN cc_start: 0.7032 (m110) cc_final: 0.6715 (m-40) REVERT: C 280 LYS cc_start: 0.7777 (tttm) cc_final: 0.7412 (tttm) REVERT: C 332 TRP cc_start: 0.7744 (m-10) cc_final: 0.7308 (m-10) REVERT: R 144 PHE cc_start: 0.8230 (t80) cc_final: 0.8026 (t80) outliers start: 20 outliers final: 17 residues processed: 115 average time/residue: 0.2186 time to fit residues: 34.6364 Evaluate side-chains 119 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain R residue 172 TRP Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 360 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 66 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 51 optimal weight: 0.0470 chunk 9 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8487 Z= 0.152 Angle : 0.496 6.307 11574 Z= 0.261 Chirality : 0.041 0.134 1353 Planarity : 0.004 0.051 1454 Dihedral : 3.823 18.135 1178 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.24 % Allowed : 14.52 % Favored : 83.23 % 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: 0.43 (0.26), residues: 1089 helix: 1.89 (0.29), residues: 367 sheet: 0.52 (0.32), residues: 273 loop : -1.25 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.021 0.001 PHE R 352 TYR 0.010 0.001 TYR E 50 ARG 0.003 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 0.908 Fit side-chains REVERT: B 33 GLU cc_start: 0.8184 (pt0) cc_final: 0.7887 (pt0) REVERT: C 280 LYS cc_start: 0.7774 (tttm) cc_final: 0.7383 (tttm) REVERT: C 332 TRP cc_start: 0.7783 (m-10) cc_final: 0.7357 (m-10) outliers start: 19 outliers final: 18 residues processed: 111 average time/residue: 0.2274 time to fit residues: 34.4225 Evaluate side-chains 116 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain R residue 172 TRP Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 360 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 58 optimal weight: 0.0170 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 88 optimal weight: 0.0270 chunk 92 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8487 Z= 0.135 Angle : 0.480 5.961 11574 Z= 0.253 Chirality : 0.040 0.137 1353 Planarity : 0.003 0.050 1454 Dihedral : 3.722 19.062 1178 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.01 % Allowed : 14.76 % Favored : 83.23 % 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: 0.61 (0.26), residues: 1089 helix: 2.11 (0.29), residues: 362 sheet: 0.57 (0.32), residues: 273 loop : -1.14 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 82 HIS 0.004 0.001 HIS E 35 PHE 0.023 0.001 PHE R 352 TYR 0.008 0.001 TYR E 50 ARG 0.007 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 0.870 Fit side-chains REVERT: C 280 LYS cc_start: 0.7719 (tttm) cc_final: 0.7377 (tttm) REVERT: C 332 TRP cc_start: 0.7666 (m-10) cc_final: 0.7294 (m-10) outliers start: 17 outliers final: 17 residues processed: 109 average time/residue: 0.2050 time to fit residues: 31.1091 Evaluate side-chains 117 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 100 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain R residue 172 TRP Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 349 PHE Chi-restraints excluded: chain R residue 360 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8487 Z= 0.219 Angle : 0.544 7.580 11574 Z= 0.288 Chirality : 0.043 0.166 1353 Planarity : 0.004 0.052 1454 Dihedral : 4.028 24.791 1178 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.13 % Allowed : 14.76 % Favored : 83.12 % 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: 0.41 (0.26), residues: 1089 helix: 1.89 (0.29), residues: 363 sheet: 0.45 (0.32), residues: 278 loop : -1.23 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 332 HIS 0.005 0.001 HIS E 233 PHE 0.033 0.002 PHE R 144 TYR 0.016 0.001 TYR E 50 ARG 0.005 0.000 ARG C 304 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 0.930 Fit side-chains REVERT: C 280 LYS cc_start: 0.7920 (tttm) cc_final: 0.7522 (tttm) REVERT: C 332 TRP cc_start: 0.7800 (m-10) cc_final: 0.7438 (m-10) outliers start: 18 outliers final: 16 residues processed: 110 average time/residue: 0.2208 time to fit residues: 32.8762 Evaluate side-chains 114 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain R residue 172 TRP Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 360 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.1980 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 76 optimal weight: 0.3980 chunk 4 optimal weight: 0.1980 chunk 62 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.200682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.154621 restraints weight = 8967.280| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 3.50 r_work: 0.3627 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8487 Z= 0.149 Angle : 0.506 8.620 11574 Z= 0.266 Chirality : 0.041 0.135 1353 Planarity : 0.003 0.050 1454 Dihedral : 3.877 25.038 1178 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.13 % Allowed : 14.76 % Favored : 83.12 % 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: 0.52 (0.26), residues: 1089 helix: 1.99 (0.29), residues: 365 sheet: 0.56 (0.32), residues: 272 loop : -1.21 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 82 HIS 0.004 0.001 HIS E 35 PHE 0.030 0.001 PHE R 352 TYR 0.009 0.001 TYR E 50 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: 1961.57 seconds wall clock time: 36 minutes 30.38 seconds (2190.38 seconds total)