Starting phenix.real_space_refine on Fri Jul 19 15:05:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxt_36712/07_2024/8jxt_36712_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxt_36712/07_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_36712/07_2024/8jxt_36712.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxt_36712/07_2024/8jxt_36712.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxt_36712/07_2024/8jxt_36712_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxt_36712/07_2024/8jxt_36712_neut.cif" } 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 5.05, per 1000 atoms: 0.61 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: 3.08 Conformation dependent library (CDL) restraints added in 1.6 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... Secondary structure from input PDB file: 25 helices and 12 sheets defined 36.7% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'B' and resid 6 through 30 Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.586A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 216 removed outlier: 3.673A pdb=" N CYS B 214 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 removed outlier: 3.808A pdb=" N GLU B 245 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 260 removed outlier: 3.912A pdb=" N THR B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 295 through 309 Processing helix chain 'B' and resid 329 through 351 removed outlier: 3.789A pdb=" N GLN B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) 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 26 Processing helix chain 'C' and resid 29 through 37 removed outlier: 4.363A pdb=" N THR C 34 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ASN C 35 " --> pdb=" O GLN C 32 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN C 36 " --> pdb=" O ILE C 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 24 removed outlier: 3.672A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.672A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 56 removed outlier: 4.359A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 43 removed outlier: 4.064A pdb=" N VAL R 36 " --> pdb=" O GLY R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 78 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 removed outlier: 3.571A pdb=" N PHE R 78 " --> pdb=" O PRO R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 118 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) removed outlier: 3.677A pdb=" N ASN R 118 " --> pdb=" O LEU R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 124 Processing helix chain 'R' and resid 130 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 171 through 181 removed outlier: 3.899A pdb=" N LEU R 175 " --> pdb=" O GLU R 171 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE R 177 " --> pdb=" O TYR R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 203 removed outlier: 4.016A pdb=" N LYS R 203 " --> pdb=" O TRP R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 329 removed outlier: 4.435A pdb=" N PHE R 312 " --> pdb=" O LEU R 308 " (cutoff:3.500A) Proline residue: R 318 - end of helix removed outlier: 4.466A pdb=" N TYR R 329 " --> pdb=" O VAL R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 337 through 349 removed outlier: 3.904A 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) Processing helix chain 'R' and resid 349 through 362 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 removed outlier: 4.162A pdb=" N HIS R 362 " --> pdb=" O TYR R 358 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 371 Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 191 removed outlier: 6.923A pdb=" N LYS B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ILE B 222 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU B 39 " --> pdb=" O CYS B 224 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N ALA B 226 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing sheet with id=AA2, 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=AA3, 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=AA4, 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=AA5, first strand: chain 'C' and resid 146 through 153 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=AA6, 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=AA7, 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: 3.896A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 277 removed outlier: 6.566A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 6.157A pdb=" N GLY E 16 " --> pdb=" O SER E 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.264A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 142 through 143 removed outlier: 3.567A pdb=" N THR E 142 " --> pdb=" O ARG E 161 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG E 161 " --> pdb=" O THR E 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.554A pdb=" N GLU E 247 " --> 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) 396 hydrogen bonds defined for protein. 1116 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: 2.30 Time building geometry restraints manager: 3.37 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: 1403 2.76 - 3.30: 7407 3.30 - 3.83: 12744 3.83 - 4.37: 13796 4.37 - 4.90: 25240 Nonbonded interactions: 60590 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 60585 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 24.550 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.980 ------------------------------------------------------------------------------- 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= 0.301 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 : 0.858 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: 0.2092 time to fit residues: 42.5469 Evaluate side-chains 109 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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: 0.9980 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN C 268 ASN E 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8487 Z= 0.239 Angle : 0.597 7.758 11574 Z= 0.320 Chirality : 0.044 0.154 1353 Planarity : 0.005 0.063 1454 Dihedral : 4.465 18.508 1178 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.94 % Allowed : 7.91 % Favored : 91.15 % 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: -0.27 (0.26), residues: 1089 helix: 1.28 (0.28), residues: 370 sheet: 0.15 (0.31), residues: 292 loop : -1.75 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 82 HIS 0.006 0.001 HIS E 233 PHE 0.019 0.002 PHE R 144 TYR 0.016 0.002 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 118 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: C 262 MET cc_start: 0.7725 (mmt) cc_final: 0.7264 (mmt) REVERT: C 280 LYS cc_start: 0.7950 (tttm) cc_final: 0.7736 (tttm) outliers start: 8 outliers final: 8 residues processed: 113 average time/residue: 0.2007 time to fit residues: 31.8654 Evaluate side-chains 106 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 263 THR Chi-restraints excluded: chain E residue 7 SER 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: 6.9990 chunk 30 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 27 optimal weight: 0.0870 chunk 99 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 79 optimal weight: 10.0000 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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: 0.6647 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8487 Z= 0.163 Angle : 0.518 6.572 11574 Z= 0.276 Chirality : 0.041 0.148 1353 Planarity : 0.004 0.056 1454 Dihedral : 4.139 18.051 1178 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.42 % Allowed : 9.56 % 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: 0.10 (0.26), residues: 1089 helix: 1.60 (0.29), residues: 372 sheet: 0.42 (0.31), residues: 284 loop : -1.59 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE B 189 TYR 0.019 0.001 TYR E 191 ARG 0.003 0.000 ARG C 304 *********************** 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 121 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 109 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: B 315 ASP cc_start: 0.6479 (p0) cc_final: 0.6244 (p0) REVERT: B 346 ASN cc_start: 0.6996 (m110) cc_final: 0.6711 (m-40) REVERT: C 280 LYS cc_start: 0.7923 (tttm) cc_final: 0.7614 (tttm) REVERT: R 144 PHE cc_start: 0.8171 (t80) cc_final: 0.7915 (t80) outliers start: 12 outliers final: 8 residues processed: 114 average time/residue: 0.1989 time to fit residues: 31.1537 Evaluate side-chains 106 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain C residue 228 ASP 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 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: 0.3980 chunk 74 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 0.0030 chunk 47 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 99 optimal weight: 0.4980 chunk 105 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 0.0270 overall best weight: 0.3248 ------------------------------------------------------------------------------- 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 E 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.2171 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= 0.124 Angle : 0.480 6.313 11574 Z= 0.256 Chirality : 0.040 0.143 1353 Planarity : 0.004 0.054 1454 Dihedral : 3.895 17.057 1178 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.83 % Allowed : 11.57 % Favored : 87.60 % 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: 0.30 (0.26), residues: 1089 helix: 1.86 (0.29), residues: 370 sheet: 0.32 (0.32), residues: 278 loop : -1.37 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 332 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE B 189 TYR 0.010 0.001 TYR E 50 ARG 0.008 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 118 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 111 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: B 33 GLU cc_start: 0.7744 (pt0) cc_final: 0.7495 (pt0) REVERT: B 315 ASP cc_start: 0.6241 (p0) cc_final: 0.5988 (p0) REVERT: B 346 ASN cc_start: 0.6901 (m110) cc_final: 0.6603 (m-40) REVERT: C 280 LYS cc_start: 0.7798 (tttm) cc_final: 0.7415 (tttm) REVERT: C 332 TRP cc_start: 0.7614 (m-10) cc_final: 0.7239 (m-10) REVERT: E 38 ARG cc_start: 0.6189 (ptm160) cc_final: 0.5852 (ttp-170) REVERT: R 144 PHE cc_start: 0.8264 (t80) cc_final: 0.8008 (t80) REVERT: R 195 MET cc_start: 0.5914 (mmp) cc_final: 0.5193 (ttm) outliers start: 7 outliers final: 7 residues processed: 114 average time/residue: 0.2108 time to fit residues: 33.7291 Evaluate side-chains 105 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 215 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.2296 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= 0.172 Angle : 0.508 6.787 11574 Z= 0.269 Chirality : 0.041 0.138 1353 Planarity : 0.004 0.055 1454 Dihedral : 3.940 19.056 1178 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.89 % Allowed : 12.99 % Favored : 85.12 % 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: 0.29 (0.26), residues: 1089 helix: 1.81 (0.29), residues: 373 sheet: 0.35 (0.32), residues: 280 loop : -1.38 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 332 HIS 0.004 0.001 HIS B 188 PHE 0.013 0.001 PHE B 189 TYR 0.015 0.001 TYR E 50 ARG 0.001 0.000 ARG E 192 *********************** 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 118 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 0.854 Fit side-chains REVERT: B 315 ASP cc_start: 0.6173 (p0) cc_final: 0.5858 (p0) REVERT: B 346 ASN cc_start: 0.6966 (m110) cc_final: 0.6686 (m-40) REVERT: C 280 LYS cc_start: 0.7881 (tttm) cc_final: 0.7490 (tttm) REVERT: C 332 TRP cc_start: 0.7740 (m-10) cc_final: 0.7513 (m-10) REVERT: R 144 PHE cc_start: 0.8238 (t80) cc_final: 0.8001 (t80) outliers start: 16 outliers final: 15 residues processed: 109 average time/residue: 0.1976 time to fit residues: 30.0809 Evaluate side-chains 115 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 76 ASP Chi-restraints excluded: chain C residue 228 ASP 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 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: 0.3980 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 105 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 20.0000 chunk 101 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.6648 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8487 Z= 0.161 Angle : 0.500 6.420 11574 Z= 0.265 Chirality : 0.041 0.136 1353 Planarity : 0.004 0.052 1454 Dihedral : 3.908 17.788 1178 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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: 0.39 (0.26), residues: 1089 helix: 1.90 (0.29), residues: 373 sheet: 0.49 (0.32), residues: 273 loop : -1.36 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 332 HIS 0.003 0.001 HIS E 35 PHE 0.026 0.001 PHE R 180 TYR 0.013 0.001 TYR E 50 ARG 0.002 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 121 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 101 time to evaluate : 0.877 Fit side-chains REVERT: B 33 GLU cc_start: 0.7827 (pt0) cc_final: 0.7541 (pt0) REVERT: B 315 ASP cc_start: 0.6130 (p0) cc_final: 0.5779 (p0) REVERT: B 346 ASN cc_start: 0.6993 (m110) cc_final: 0.6689 (m-40) REVERT: C 280 LYS cc_start: 0.7852 (tttm) cc_final: 0.7481 (tttm) REVERT: C 332 TRP cc_start: 0.7543 (m-10) cc_final: 0.7018 (m-10) REVERT: R 144 PHE cc_start: 0.8244 (t80) cc_final: 0.8036 (t80) outliers start: 20 outliers final: 15 residues processed: 111 average time/residue: 0.1984 time to fit residues: 30.5860 Evaluate side-chains 111 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 96 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 70 LEU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 329 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.7980 chunk 60 optimal weight: 0.3980 chunk 77 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 58 optimal weight: 0.0170 chunk 105 optimal weight: 0.0980 chunk 65 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- 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: 0.6618 moved from start: 0.2569 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= 0.131 Angle : 0.478 6.002 11574 Z= 0.254 Chirality : 0.040 0.137 1353 Planarity : 0.004 0.050 1454 Dihedral : 3.779 18.460 1178 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.01 % Allowed : 14.52 % Favored : 83.47 % 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: 0.50 (0.26), residues: 1089 helix: 1.97 (0.29), residues: 373 sheet: 0.54 (0.32), residues: 273 loop : -1.28 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.026 0.001 PHE R 180 TYR 0.009 0.001 TYR E 50 ARG 0.002 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 115 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 0.940 Fit side-chains REVERT: B 33 GLU cc_start: 0.7743 (pt0) cc_final: 0.7483 (pt0) REVERT: B 315 ASP cc_start: 0.6271 (p0) cc_final: 0.5946 (p0) REVERT: B 346 ASN cc_start: 0.6918 (m110) cc_final: 0.6625 (m-40) REVERT: C 280 LYS cc_start: 0.7741 (tttm) cc_final: 0.7387 (tttm) REVERT: C 332 TRP cc_start: 0.7541 (m-10) cc_final: 0.7091 (m-10) outliers start: 17 outliers final: 15 residues processed: 106 average time/residue: 0.2191 time to fit residues: 31.6046 Evaluate side-chains 110 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 76 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 7 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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: 0.6733 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8487 Z= 0.291 Angle : 0.595 9.148 11574 Z= 0.315 Chirality : 0.044 0.194 1353 Planarity : 0.004 0.053 1454 Dihedral : 4.283 24.800 1178 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.60 % Allowed : 14.40 % Favored : 83.00 % 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: 0.19 (0.26), residues: 1089 helix: 1.68 (0.28), residues: 375 sheet: 0.32 (0.32), residues: 278 loop : -1.42 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 332 HIS 0.006 0.001 HIS E 233 PHE 0.027 0.002 PHE R 180 TYR 0.024 0.002 TYR E 50 ARG 0.002 0.000 ARG E 192 *********************** 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 126 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 1.050 Fit side-chains REVERT: B 315 ASP cc_start: 0.6158 (p0) cc_final: 0.5802 (p0) REVERT: B 346 ASN cc_start: 0.7223 (m110) cc_final: 0.7009 (m-40) REVERT: C 76 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6546 (m-30) REVERT: C 280 LYS cc_start: 0.7998 (tttm) cc_final: 0.7632 (tttm) REVERT: C 332 TRP cc_start: 0.7804 (m-10) cc_final: 0.7378 (m-10) outliers start: 22 outliers final: 17 residues processed: 116 average time/residue: 0.2191 time to fit residues: 36.3508 Evaluate side-chains 115 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 70 LEU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain R residue 42 VAL 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: 2.9990 chunk 100 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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: 0.6723 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8487 Z= 0.251 Angle : 0.574 8.274 11574 Z= 0.304 Chirality : 0.043 0.167 1353 Planarity : 0.004 0.052 1454 Dihedral : 4.331 32.170 1178 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.36 % Allowed : 14.99 % Favored : 82.64 % 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: 0.18 (0.26), residues: 1089 helix: 1.72 (0.28), residues: 372 sheet: 0.35 (0.31), residues: 287 loop : -1.50 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 332 HIS 0.005 0.001 HIS E 233 PHE 0.027 0.002 PHE R 180 TYR 0.021 0.002 TYR E 50 ARG 0.003 0.000 ARG E 192 *********************** 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 118 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 0.899 Fit side-chains REVERT: B 315 ASP cc_start: 0.6242 (p0) cc_final: 0.5876 (p0) REVERT: C 280 LYS cc_start: 0.8023 (tttm) cc_final: 0.7636 (tttm) REVERT: C 332 TRP cc_start: 0.7842 (m-10) cc_final: 0.7502 (m-10) outliers start: 20 outliers final: 19 residues processed: 109 average time/residue: 0.2142 time to fit residues: 31.9313 Evaluate side-chains 116 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 70 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 64 VAL 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 353 VAL 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: 0.3980 chunk 71 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 8 optimal weight: 0.0980 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.6662 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8487 Z= 0.160 Angle : 0.521 8.148 11574 Z= 0.273 Chirality : 0.041 0.136 1353 Planarity : 0.004 0.050 1454 Dihedral : 4.074 32.994 1178 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.65 % Allowed : 15.82 % Favored : 82.53 % 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: 0.39 (0.26), residues: 1089 helix: 1.90 (0.28), residues: 377 sheet: 0.45 (0.32), residues: 272 loop : -1.35 (0.28), residues: 440 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 0.034 0.001 PHE R 144 TYR 0.012 0.001 TYR E 50 ARG 0.002 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 114 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 0.888 Fit side-chains REVERT: B 33 GLU cc_start: 0.7920 (pt0) cc_final: 0.7648 (pt0) REVERT: B 315 ASP cc_start: 0.6153 (p0) cc_final: 0.5766 (p0) REVERT: B 346 ASN cc_start: 0.6935 (m110) cc_final: 0.6659 (m-40) REVERT: C 280 LYS cc_start: 0.7861 (tttm) cc_final: 0.7408 (tttm) REVERT: C 332 TRP cc_start: 0.7835 (m-10) cc_final: 0.7484 (m-10) outliers start: 14 outliers final: 13 residues processed: 108 average time/residue: 0.2037 time to fit residues: 30.2539 Evaluate side-chains 112 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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 228 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 7 SER 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: 9.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 88 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.4322 r_free = 0.4322 target = 0.197207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.151009 restraints weight = 9007.327| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 3.82 r_work: 0.3582 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8487 Z= 0.204 Angle : 0.548 8.143 11574 Z= 0.287 Chirality : 0.042 0.135 1353 Planarity : 0.004 0.051 1454 Dihedral : 4.167 37.063 1178 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.01 % Allowed : 15.94 % Favored : 82.05 % 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: 1.82 (0.28), residues: 377 sheet: 0.40 (0.32), residues: 277 loop : -1.36 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 82 HIS 0.004 0.001 HIS E 233 PHE 0.027 0.001 PHE R 180 TYR 0.017 0.001 TYR E 50 ARG 0.002 0.000 ARG E 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2009.02 seconds wall clock time: 36 minutes 37.75 seconds (2197.75 seconds total)