Starting phenix.real_space_refine on Sat Apr 6 01:45:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggf_40005/04_2024/8ggf_40005_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggf_40005/04_2024/8ggf_40005.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggf_40005/04_2024/8ggf_40005.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggf_40005/04_2024/8ggf_40005.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggf_40005/04_2024/8ggf_40005_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggf_40005/04_2024/8ggf_40005_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 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 3 5.49 5 S 33 5.16 5 C 4152 2.51 5 N 1187 2.21 5 O 1232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 373": "NH1" <-> "NH2" 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: 6607 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2610 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 13, 'TRANS': 345} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 374 Unresolved non-hydrogen angles: 465 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 14, 'PHE:plan': 5, 'GLU:plan': 19, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 257 Chain: "B" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2435 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 8, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 130 Chain: "G" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 360 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "R" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1155 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain breaks: 9 Unresolved non-hydrogen bonds: 504 Unresolved non-hydrogen angles: 666 Unresolved non-hydrogen dihedrals: 422 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 5, 'ASP:plan': 3, 'PHE:plan': 12, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 269 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.26, per 1000 atoms: 0.64 Number of scatterers: 6607 At special positions: 0 Unit cell: (83.2992, 137.097, 102.389, 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 33 16.00 P 3 15.00 O 1232 8.00 N 1187 7.00 C 4152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.5 seconds 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1818 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 8 sheets defined 40.5% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 13 through 37 removed outlier: 4.042A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A 37 " --> pdb=" O ASP A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.626A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 112 removed outlier: 3.724A pdb=" N GLN A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE A 95 " --> pdb=" O LYS A 91 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS A 96 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 removed outlier: 4.069A pdb=" N ASP A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR A 130 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 155 removed outlier: 4.035A pdb=" N HIS A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 153 " --> pdb=" O HIS A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 164 Processing helix chain 'A' and resid 175 through 179 Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 233 through 236 removed outlier: 3.526A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 236' Processing helix chain 'A' and resid 265 through 277 removed outlier: 3.718A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.863A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 382 removed outlier: 3.943A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 380 " --> pdb=" O PHE A 376 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.536A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'G' and resid 7 through 23 removed outlier: 3.706A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 removed outlier: 3.555A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 36 through 54 removed outlier: 3.902A pdb=" N VAL R 48 " --> pdb=" O VAL R 44 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE R 49 " --> pdb=" O LEU R 45 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 77 removed outlier: 4.183A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR R 73 " --> pdb=" O ASN R 69 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER R 74 " --> pdb=" O TYR R 70 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU R 75 " --> pdb=" O PHE R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 90 No H-bonds generated for 'chain 'R' and resid 88 through 90' Processing helix chain 'R' and resid 103 through 136 removed outlier: 4.335A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TRP R 109 " --> pdb=" O TRP R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 157 through 170 removed outlier: 3.756A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 179 through 186 Processing helix chain 'R' and resid 201 through 228 removed outlier: 4.017A pdb=" N VAL R 210 " --> pdb=" O VAL R 206 " (cutoff:3.500A) Proline residue: R 211 - end of helix removed outlier: 3.621A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN R 224 " --> pdb=" O SER R 220 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 295 removed outlier: 3.739A pdb=" N ILE R 277 " --> pdb=" O LYS R 273 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix Processing helix chain 'R' and resid 305 through 321 removed outlier: 3.985A pdb=" N ILE R 309 " --> pdb=" O LYS R 305 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU R 310 " --> pdb=" O GLU R 306 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU R 311 " --> pdb=" O VAL R 307 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY R 315 " --> pdb=" O LEU R 311 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR R 316 " --> pdb=" O ASN R 312 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 219 through 222 removed outlier: 6.917A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ALA A 243 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N LEU A 46 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE A 245 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N SER A 286 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N PHE A 246 " --> pdb=" O SER A 286 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE A 288 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL A 248 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N PHE A 290 " --> pdb=" O VAL A 248 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 79 through 83 removed outlier: 3.636A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 111 through 114 removed outlier: 3.508A pdb=" N VAL B 112 " --> pdb=" O TYR B 124 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 178 through 181 removed outlier: 3.761A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER B 160 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 220 through 222 removed outlier: 4.154A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.846A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.914A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TRP B 297 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 318 through 320 removed outlier: 3.697A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) 243 hydrogen bonds defined for protein. 714 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.70 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1382 1.33 - 1.45: 1553 1.45 - 1.57: 3738 1.57 - 1.69: 6 1.69 - 1.81: 44 Bond restraints: 6723 Sorted by residual: bond pdb=" CA ILE A 383 " pdb=" C ILE A 383 " ideal model delta sigma weight residual 1.522 1.477 0.046 1.08e-02 8.57e+03 1.80e+01 bond pdb=" N VAL R 222 " pdb=" CA VAL R 222 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.19e-02 7.06e+03 1.05e+01 bond pdb=" N ILE R 214 " pdb=" CA ILE R 214 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 8.87e+00 bond pdb=" N VAL R 216 " pdb=" CA VAL R 216 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.37e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.453 -0.056 2.00e-02 2.50e+03 7.93e+00 ... (remaining 6718 not shown) Histogram of bond angle deviations from ideal: 99.27 - 106.23: 146 106.23 - 113.20: 3691 113.20 - 120.16: 2271 120.16 - 127.12: 3016 127.12 - 134.08: 73 Bond angle restraints: 9197 Sorted by residual: angle pdb=" N GLN A 384 " pdb=" CA GLN A 384 " pdb=" C GLN A 384 " ideal model delta sigma weight residual 111.90 100.55 11.35 1.32e+00 5.74e-01 7.40e+01 angle pdb=" N ARG A 389 " pdb=" CA ARG A 389 " pdb=" C ARG A 389 " ideal model delta sigma weight residual 111.28 102.56 8.72 1.09e+00 8.42e-01 6.39e+01 angle pdb=" N ASP A 381 " pdb=" CA ASP A 381 " pdb=" C ASP A 381 " ideal model delta sigma weight residual 111.28 118.37 -7.09 1.09e+00 8.42e-01 4.23e+01 angle pdb=" N ASN A 377 " pdb=" CA ASN A 377 " pdb=" C ASN A 377 " ideal model delta sigma weight residual 113.18 105.57 7.61 1.21e+00 6.83e-01 3.95e+01 angle pdb=" N SER R 203 " pdb=" CA SER R 203 " pdb=" C SER R 203 " ideal model delta sigma weight residual 111.28 104.54 6.74 1.09e+00 8.42e-01 3.82e+01 ... (remaining 9192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.56: 3837 29.56 - 59.12: 90 59.12 - 88.68: 10 88.68 - 118.24: 1 118.24 - 147.80: 1 Dihedral angle restraints: 3939 sinusoidal: 1156 harmonic: 2783 Sorted by residual: dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -43.20 147.80 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" C4' GTP A 401 " pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual 260.87 169.92 90.95 1 2.00e+01 2.50e-03 2.44e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 163.69 16.31 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 3936 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 851 0.050 - 0.100: 178 0.100 - 0.150: 61 0.150 - 0.200: 8 0.200 - 0.250: 3 Chirality restraints: 1101 Sorted by residual: chirality pdb=" C3' GTP A 401 " pdb=" C2' GTP A 401 " pdb=" C4' GTP A 401 " pdb=" O3' GTP A 401 " both_signs ideal model delta sigma weight residual False -2.47 -2.72 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA LEU A 393 " pdb=" N LEU A 393 " pdb=" C LEU A 393 " pdb=" CB LEU A 393 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ILE R 201 " pdb=" N ILE R 201 " pdb=" C ILE R 201 " pdb=" CB ILE R 201 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1098 not shown) Planarity restraints: 1188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 384 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C GLN A 384 " 0.059 2.00e-02 2.50e+03 pdb=" O GLN A 384 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG A 385 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 373 " 0.234 9.50e-02 1.11e+02 1.05e-01 6.74e+00 pdb=" NE ARG A 373 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 373 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 373 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 373 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 365 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.25e+00 pdb=" C CYS A 365 " 0.031 2.00e-02 2.50e+03 pdb=" O CYS A 365 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA A 366 " -0.011 2.00e-02 2.50e+03 ... (remaining 1185 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 202 2.70 - 3.25: 6561 3.25 - 3.80: 9457 3.80 - 4.35: 11592 4.35 - 4.90: 19290 Nonbonded interactions: 47102 Sorted by model distance: nonbonded pdb=" O ARG A 385 " pdb=" CG MET A 386 " model vdw 2.147 3.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.227 2.440 nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.294 2.440 nonbonded pdb=" N SER A 51 " pdb=" O2B GTP A 401 " model vdw 2.316 2.520 nonbonded pdb=" O SER A 352 " pdb=" OG SER A 352 " model vdw 2.323 2.440 ... (remaining 47097 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 group one per residue 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: 1.500 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: 7.790 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 22.420 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 0.056 6723 Z= 0.323 Angle : 0.795 11.354 9197 Z= 0.504 Chirality : 0.048 0.250 1101 Planarity : 0.004 0.105 1188 Dihedral : 13.583 147.797 2121 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.27), residues: 924 helix: 1.48 (0.29), residues: 334 sheet: -0.86 (0.42), residues: 156 loop : -0.90 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.004 0.001 HIS B 142 PHE 0.022 0.001 PHE A 146 TYR 0.006 0.001 TYR A 360 ARG 0.002 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 101 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7850 (tm-30) REVERT: G 48 ASP cc_start: 0.8506 (t70) cc_final: 0.8117 (t0) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1688 time to fit residues: 19.6852 Evaluate side-chains 62 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 28 optimal weight: 0.0000 chunk 44 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN A 387 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6723 Z= 0.372 Angle : 0.592 9.061 9197 Z= 0.321 Chirality : 0.044 0.191 1101 Planarity : 0.004 0.034 1188 Dihedral : 7.622 136.796 1030 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.50 % Allowed : 10.88 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.27), residues: 924 helix: 1.29 (0.27), residues: 348 sheet: -1.10 (0.41), residues: 159 loop : -1.14 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.009 0.002 HIS B 142 PHE 0.014 0.002 PHE B 235 TYR 0.013 0.001 TYR B 111 ARG 0.007 0.001 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.734 Fit side-chains REVERT: A 101 GLU cc_start: 0.8337 (tm-30) cc_final: 0.8017 (tm-30) REVERT: G 48 ASP cc_start: 0.8528 (t70) cc_final: 0.8137 (t0) outliers start: 8 outliers final: 8 residues processed: 67 average time/residue: 0.1387 time to fit residues: 13.8382 Evaluate side-chains 65 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain R residue 41 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 57 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 84 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 75 optimal weight: 0.3980 chunk 83 optimal weight: 0.2980 chunk 28 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6723 Z= 0.136 Angle : 0.450 5.876 9197 Z= 0.242 Chirality : 0.040 0.131 1101 Planarity : 0.003 0.031 1188 Dihedral : 6.588 122.271 1030 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.75 % Allowed : 13.70 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.28), residues: 924 helix: 1.76 (0.28), residues: 347 sheet: -0.95 (0.40), residues: 169 loop : -0.98 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 154 HIS 0.005 0.001 HIS B 225 PHE 0.019 0.001 PHE A 146 TYR 0.005 0.001 TYR B 124 ARG 0.004 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.712 Fit side-chains REVERT: A 101 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8076 (tm-30) REVERT: G 48 ASP cc_start: 0.8524 (t70) cc_final: 0.8156 (t0) REVERT: R 140 LYS cc_start: 0.7871 (ptpt) cc_final: 0.7557 (pptt) outliers start: 4 outliers final: 3 residues processed: 69 average time/residue: 0.1252 time to fit residues: 13.5076 Evaluate side-chains 67 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain R residue 274 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 6723 Z= 0.409 Angle : 0.580 6.773 9197 Z= 0.311 Chirality : 0.044 0.135 1101 Planarity : 0.004 0.033 1188 Dihedral : 6.867 120.665 1030 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.63 % Allowed : 13.88 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.28), residues: 924 helix: 1.60 (0.28), residues: 344 sheet: -1.19 (0.41), residues: 159 loop : -1.20 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 154 HIS 0.008 0.002 HIS B 142 PHE 0.017 0.002 PHE B 235 TYR 0.017 0.002 TYR A 360 ARG 0.002 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 59 time to evaluate : 0.732 Fit side-chains REVERT: B 117 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8676 (tt) REVERT: R 140 LYS cc_start: 0.7911 (ptpt) cc_final: 0.7588 (pptt) outliers start: 14 outliers final: 10 residues processed: 70 average time/residue: 0.1368 time to fit residues: 14.3619 Evaluate side-chains 69 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 274 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 66 optimal weight: 0.0970 chunk 37 optimal weight: 8.9990 chunk 76 optimal weight: 30.0000 chunk 62 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6723 Z= 0.174 Angle : 0.460 5.129 9197 Z= 0.248 Chirality : 0.040 0.123 1101 Planarity : 0.003 0.032 1188 Dihedral : 6.231 112.161 1030 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.00 % Allowed : 13.88 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.28), residues: 924 helix: 1.90 (0.29), residues: 344 sheet: -1.09 (0.40), residues: 166 loop : -1.11 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.003 0.001 HIS B 142 PHE 0.012 0.001 PHE B 199 TYR 0.006 0.001 TYR A 360 ARG 0.003 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 59 time to evaluate : 0.798 Fit side-chains REVERT: A 101 GLU cc_start: 0.8297 (tm-30) cc_final: 0.8078 (tm-30) REVERT: B 117 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8967 (tt) REVERT: B 142 HIS cc_start: 0.8502 (OUTLIER) cc_final: 0.7919 (t-170) REVERT: R 140 LYS cc_start: 0.7936 (ptpt) cc_final: 0.7602 (pptt) outliers start: 16 outliers final: 6 residues processed: 72 average time/residue: 0.1299 time to fit residues: 14.1663 Evaluate side-chains 68 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain R residue 308 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6723 Z= 0.268 Angle : 0.500 8.002 9197 Z= 0.266 Chirality : 0.042 0.145 1101 Planarity : 0.003 0.031 1188 Dihedral : 6.113 107.880 1030 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.94 % Allowed : 14.26 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.28), residues: 924 helix: 1.82 (0.29), residues: 346 sheet: -1.19 (0.41), residues: 161 loop : -1.18 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 154 HIS 0.005 0.001 HIS B 142 PHE 0.013 0.001 PHE B 199 TYR 0.011 0.001 TYR A 360 ARG 0.003 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 60 time to evaluate : 0.788 Fit side-chains REVERT: B 117 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8974 (tt) REVERT: B 142 HIS cc_start: 0.8620 (OUTLIER) cc_final: 0.8013 (t-170) REVERT: G 48 ASP cc_start: 0.8628 (t0) cc_final: 0.7961 (t0) REVERT: R 140 LYS cc_start: 0.7926 (ptpt) cc_final: 0.7592 (pptt) outliers start: 21 outliers final: 13 residues processed: 77 average time/residue: 0.1299 time to fit residues: 15.0854 Evaluate side-chains 75 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 60 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain R residue 308 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 0.0980 chunk 10 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 75 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6723 Z= 0.135 Angle : 0.445 6.525 9197 Z= 0.236 Chirality : 0.040 0.133 1101 Planarity : 0.003 0.031 1188 Dihedral : 5.616 99.996 1030 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.00 % Allowed : 15.01 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.28), residues: 924 helix: 2.02 (0.29), residues: 352 sheet: -0.90 (0.41), residues: 161 loop : -1.05 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 154 HIS 0.003 0.001 HIS B 91 PHE 0.012 0.001 PHE B 199 TYR 0.004 0.001 TYR B 59 ARG 0.004 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 65 time to evaluate : 0.843 Fit side-chains REVERT: B 117 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8932 (tt) REVERT: B 142 HIS cc_start: 0.8388 (OUTLIER) cc_final: 0.7917 (t-170) REVERT: R 140 LYS cc_start: 0.7909 (ptpt) cc_final: 0.7591 (pptt) outliers start: 16 outliers final: 9 residues processed: 78 average time/residue: 0.1308 time to fit residues: 15.4960 Evaluate side-chains 72 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain R residue 308 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 30.0000 chunk 53 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 85 optimal weight: 0.0770 overall best weight: 2.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6723 Z= 0.354 Angle : 0.549 6.122 9197 Z= 0.291 Chirality : 0.043 0.157 1101 Planarity : 0.003 0.030 1188 Dihedral : 5.891 100.055 1030 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.00 % Allowed : 16.14 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.28), residues: 924 helix: 1.87 (0.29), residues: 347 sheet: -1.23 (0.41), residues: 161 loop : -1.19 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 286 HIS 0.006 0.001 HIS B 142 PHE 0.017 0.002 PHE A 146 TYR 0.014 0.001 TYR A 360 ARG 0.004 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 60 time to evaluate : 0.666 Fit side-chains REVERT: A 95 ILE cc_start: 0.9482 (mp) cc_final: 0.9276 (mp) REVERT: B 117 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8614 (tt) REVERT: B 142 HIS cc_start: 0.8660 (OUTLIER) cc_final: 0.8016 (t-170) REVERT: R 140 LYS cc_start: 0.7941 (ptpt) cc_final: 0.7625 (pptt) outliers start: 16 outliers final: 13 residues processed: 74 average time/residue: 0.1108 time to fit residues: 12.9506 Evaluate side-chains 76 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain R residue 308 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 75 optimal weight: 20.0000 chunk 79 optimal weight: 8.9990 chunk 54 optimal weight: 0.0470 chunk 88 optimal weight: 10.0000 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6723 Z= 0.270 Angle : 0.511 7.131 9197 Z= 0.271 Chirality : 0.042 0.143 1101 Planarity : 0.003 0.031 1188 Dihedral : 5.811 97.781 1030 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.00 % Allowed : 16.32 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.28), residues: 924 helix: 1.85 (0.29), residues: 347 sheet: -1.26 (0.40), residues: 161 loop : -1.18 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 286 HIS 0.004 0.001 HIS B 142 PHE 0.012 0.001 PHE B 199 TYR 0.010 0.001 TYR A 360 ARG 0.004 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 61 time to evaluate : 0.809 Fit side-chains REVERT: A 95 ILE cc_start: 0.9486 (mp) cc_final: 0.9279 (mp) REVERT: B 117 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8963 (tt) REVERT: B 142 HIS cc_start: 0.8619 (OUTLIER) cc_final: 0.8063 (t-170) REVERT: R 140 LYS cc_start: 0.7947 (ptpt) cc_final: 0.7630 (pptt) outliers start: 16 outliers final: 12 residues processed: 75 average time/residue: 0.1079 time to fit residues: 12.7374 Evaluate side-chains 75 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain R residue 308 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 92 optimal weight: 0.1980 chunk 85 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 56 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6723 Z= 0.144 Angle : 0.470 6.981 9197 Z= 0.246 Chirality : 0.040 0.148 1101 Planarity : 0.003 0.031 1188 Dihedral : 5.449 93.479 1030 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.44 % Allowed : 17.07 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.28), residues: 924 helix: 2.02 (0.29), residues: 354 sheet: -0.94 (0.41), residues: 161 loop : -1.06 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 154 HIS 0.004 0.001 HIS B 91 PHE 0.024 0.001 PHE A 146 TYR 0.005 0.001 TYR A 339 ARG 0.003 0.000 ARG A 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 0.807 Fit side-chains REVERT: A 95 ILE cc_start: 0.9490 (OUTLIER) cc_final: 0.9287 (mp) REVERT: B 117 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8967 (tt) REVERT: B 142 HIS cc_start: 0.8418 (OUTLIER) cc_final: 0.7954 (t-170) REVERT: R 140 LYS cc_start: 0.7928 (ptpt) cc_final: 0.7625 (pptt) outliers start: 13 outliers final: 10 residues processed: 72 average time/residue: 0.1207 time to fit residues: 13.6166 Evaluate side-chains 74 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain R residue 308 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 75 optimal weight: 0.0870 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.127134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.094691 restraints weight = 13630.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.097208 restraints weight = 7738.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.098925 restraints weight = 5521.523| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6723 Z= 0.197 Angle : 0.482 6.628 9197 Z= 0.253 Chirality : 0.041 0.142 1101 Planarity : 0.003 0.031 1188 Dihedral : 5.415 92.051 1030 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.00 % Allowed : 16.70 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.28), residues: 924 helix: 2.03 (0.29), residues: 354 sheet: -0.94 (0.41), residues: 161 loop : -1.08 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 286 HIS 0.004 0.001 HIS B 142 PHE 0.013 0.001 PHE B 292 TYR 0.007 0.001 TYR A 360 ARG 0.003 0.000 ARG A 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1516.06 seconds wall clock time: 28 minutes 9.29 seconds (1689.29 seconds total)