Starting phenix.real_space_refine on Wed Feb 14 13:31:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fiy_31606/02_2024/7fiy_31606_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fiy_31606/02_2024/7fiy_31606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fiy_31606/02_2024/7fiy_31606.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fiy_31606/02_2024/7fiy_31606.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fiy_31606/02_2024/7fiy_31606_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fiy_31606/02_2024/7fiy_31606_neut_updated.pdb" } resolution = 3.4 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= 0.083 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5983 2.51 5 N 1638 2.21 5 O 1692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 38": "NH1" <-> "NH2" Residue "R ARG 43": "NH1" <-> "NH2" Residue "R ARG 44": "NH1" <-> "NH2" Residue "R ARG 81": "NH1" <-> "NH2" Residue "R ARG 131": "NH1" <-> "NH2" Residue "R TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 163": "NH1" <-> "NH2" Residue "R ARG 183": "NH1" <-> "NH2" Residue "R ARG 190": "NH1" <-> "NH2" Residue "R ARG 278": "NH1" <-> "NH2" Residue "R ARG 333": "NH1" <-> "NH2" Residue "R TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 336": "NH1" <-> "NH2" Residue "R ARG 341": "NH1" <-> "NH2" Residue "R ARG 366": "NH1" <-> "NH2" Residue "R ARG 413": "NH1" <-> "NH2" Residue "R ARG 414": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "G ARG 62": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9367 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2974 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 12, 'TRANS': 346} Chain breaks: 4 Chain: "P" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 233 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'AIB:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 1948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1948 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 2 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2616 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Chain: "G" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 983 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "R" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 168 Unusual residues: {'CLR': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 5.28, per 1000 atoms: 0.56 Number of scatterers: 9367 At special positions: 0 Unit cell: (79.254, 102.816, 171.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1692 8.00 N 1638 7.00 C 5983 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 70 " distance=2.03 Simple disulfide: pdb=" SG CYS R 61 " - pdb=" SG CYS R 103 " distance=2.03 Simple disulfide: pdb=" SG CYS R 84 " - pdb=" SG CYS R 118 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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: 3.32 Conformation dependent library (CDL) restraints added in 1.8 seconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 11 sheets defined 39.6% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'R' and resid 32 through 48 Processing helix chain 'R' and resid 116 through 118 No H-bonds generated for 'chain 'R' and resid 116 through 118' Processing helix chain 'R' and resid 125 through 161 removed outlier: 3.881A pdb=" N ASP R 129 " --> pdb=" O GLU R 125 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR R 142 " --> pdb=" O GLN R 138 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU R 159 " --> pdb=" O ALA R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 165 No H-bonds generated for 'chain 'R' and resid 163 through 165' Processing helix chain 'R' and resid 168 through 193 removed outlier: 3.826A pdb=" N ILE R 172 " --> pdb=" O THR R 168 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N HIS R 173 " --> pdb=" O ARG R 169 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG R 192 " --> pdb=" O LEU R 188 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU R 193 " --> pdb=" O SER R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 245 removed outlier: 3.554A pdb=" N LEU R 245 " --> pdb=" O LEU R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 257 through 280 Proline residue: R 267 - end of helix removed outlier: 3.556A pdb=" N ILE R 272 " --> pdb=" O ALA R 268 " (cutoff:3.500A) Proline residue: R 273 - end of helix Processing helix chain 'R' and resid 293 through 327 removed outlier: 3.928A pdb=" N ILE R 298 " --> pdb=" O ALA R 294 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE R 299 " --> pdb=" O ILE R 295 " (cutoff:3.500A) Proline residue: R 302 - end of helix removed outlier: 3.578A pdb=" N SER R 323 " --> pdb=" O GLY R 319 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 350 Proline residue: R 348 - end of helix Processing helix chain 'R' and resid 352 through 363 removed outlier: 3.604A pdb=" N PHE R 357 " --> pdb=" O GLU R 354 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA R 358 " --> pdb=" O VAL R 355 " (cutoff:3.500A) Proline residue: R 359 - end of helix Processing helix chain 'R' and resid 367 through 393 removed outlier: 3.586A pdb=" N PHE R 371 " --> pdb=" O GLY R 367 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE R 378 " --> pdb=" O LEU R 374 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE R 383 " --> pdb=" O PHE R 379 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY R 385 " --> pdb=" O SER R 381 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE R 386 " --> pdb=" O SER R 382 " (cutoff:3.500A) Processing helix chain 'R' and resid 397 through 413 Processing helix chain 'P' and resid 4 through 28 Processing helix chain 'A' and resid 10 through 39 removed outlier: 3.921A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.643A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.650A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.582A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 removed outlier: 3.696A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (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 'G' and resid 7 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'R' and resid 78 through 83 Processing sheet with id= B, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.495A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.234A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.794A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.782A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.089A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.662A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.721A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.851A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'N' and resid 122 through 124 removed outlier: 3.822A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1221 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: 2.52 Time building geometry restraints manager: 3.60 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: 3005 1.34 - 1.46: 1886 1.46 - 1.58: 4617 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 9580 Sorted by residual: bond pdb=" C GLY A 52 " pdb=" O GLY A 52 " ideal model delta sigma weight residual 1.235 1.270 -0.035 1.35e-02 5.49e+03 6.84e+00 bond pdb=" C SER A 51 " pdb=" N GLY A 52 " ideal model delta sigma weight residual 1.331 1.357 -0.027 1.46e-02 4.69e+03 3.37e+00 bond pdb=" C5 CLR R 602 " pdb=" C6 CLR R 602 " ideal model delta sigma weight residual 1.332 1.300 0.032 2.00e-02 2.50e+03 2.52e+00 bond pdb=" C5 CLR R 606 " pdb=" C6 CLR R 606 " ideal model delta sigma weight residual 1.332 1.300 0.032 2.00e-02 2.50e+03 2.49e+00 bond pdb=" C ALA R 358 " pdb=" N PRO R 359 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.20e-02 6.94e+03 2.45e+00 ... (remaining 9575 not shown) Histogram of bond angle deviations from ideal: 99.71 - 106.59: 246 106.59 - 113.46: 5244 113.46 - 120.33: 3539 120.33 - 127.21: 3875 127.21 - 134.08: 103 Bond angle restraints: 13007 Sorted by residual: angle pdb=" N GLY R 198 " pdb=" CA GLY R 198 " pdb=" C GLY R 198 " ideal model delta sigma weight residual 112.34 121.31 -8.97 2.04e+00 2.40e-01 1.93e+01 angle pdb=" C CYS R 216 " pdb=" N ARG R 217 " pdb=" CA ARG R 217 " ideal model delta sigma weight residual 120.38 126.29 -5.91 1.37e+00 5.33e-01 1.86e+01 angle pdb=" N VAL R 248 " pdb=" CA VAL R 248 " pdb=" C VAL R 248 " ideal model delta sigma weight residual 106.21 110.24 -4.03 1.07e+00 8.73e-01 1.42e+01 angle pdb=" N AIB P 2 " pdb=" CA AIB P 2 " pdb=" C AIB P 2 " ideal model delta sigma weight residual 111.00 121.27 -10.27 2.80e+00 1.28e-01 1.35e+01 angle pdb=" CA GLN R 364 " pdb=" CB GLN R 364 " pdb=" CG GLN R 364 " ideal model delta sigma weight residual 114.10 121.38 -7.28 2.00e+00 2.50e-01 1.33e+01 ... (remaining 13002 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.81: 5698 14.81 - 29.62: 212 29.62 - 44.43: 58 44.43 - 59.24: 1 59.24 - 74.04: 1 Dihedral angle restraints: 5970 sinusoidal: 2630 harmonic: 3340 Sorted by residual: dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 159.68 20.32 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA TYR N 60 " pdb=" C TYR N 60 " pdb=" N THR N 61 " pdb=" CA THR N 61 " ideal model delta harmonic sigma weight residual 180.00 161.54 18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ASP B 291 " pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta harmonic sigma weight residual 180.00 161.72 18.28 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 5967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1278 0.082 - 0.163: 134 0.163 - 0.245: 21 0.245 - 0.326: 6 0.326 - 0.408: 7 Chirality restraints: 1446 Sorted by residual: chirality pdb=" C14 CLR R 605 " pdb=" C13 CLR R 605 " pdb=" C15 CLR R 605 " pdb=" C8 CLR R 605 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" C14 CLR R 604 " pdb=" C13 CLR R 604 " pdb=" C15 CLR R 604 " pdb=" C8 CLR R 604 " both_signs ideal model delta sigma weight residual False -2.32 -2.72 0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" C14 CLR R 601 " pdb=" C13 CLR R 601 " pdb=" C15 CLR R 601 " pdb=" C8 CLR R 601 " both_signs ideal model delta sigma weight residual False -2.32 -2.71 0.40 2.00e-01 2.50e+01 3.93e+00 ... (remaining 1443 not shown) Planarity restraints: 1628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 198 " -0.049 5.00e-02 4.00e+02 7.32e-02 8.57e+00 pdb=" N PRO R 199 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO R 199 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO R 199 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 360 " -0.042 5.00e-02 4.00e+02 6.36e-02 6.46e+00 pdb=" N PRO A 361 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 361 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 361 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.38e+00 pdb=" N PRO A 332 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " 0.035 5.00e-02 4.00e+02 ... (remaining 1625 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2192 2.80 - 3.33: 8221 3.33 - 3.85: 14602 3.85 - 4.38: 16726 4.38 - 4.90: 29958 Nonbonded interactions: 71699 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.275 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.306 2.440 nonbonded pdb=" OG SER R 342 " pdb=" O LEU A 393 " model vdw 2.314 2.440 nonbonded pdb=" OD1 ASN A 292 " pdb=" OG1 THR A 364 " model vdw 2.334 2.440 nonbonded pdb=" OE2 GLU R 282 " pdb=" OG1 THR R 284 " model vdw 2.334 2.440 ... (remaining 71694 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 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: 4.050 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.330 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 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 : 0.004 0.050 9580 Z= 0.270 Angle : 0.820 10.274 13007 Z= 0.449 Chirality : 0.062 0.408 1446 Planarity : 0.006 0.073 1628 Dihedral : 8.340 74.045 3799 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % 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: -1.10 (0.22), residues: 1123 helix: -0.08 (0.20), residues: 434 sheet: -0.95 (0.33), residues: 226 loop : -1.09 (0.25), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 281 HIS 0.014 0.002 HIS A 220 PHE 0.024 0.002 PHE R 177 TYR 0.026 0.002 TYR P 1 ARG 0.005 0.000 ARG R 278 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 67 MET cc_start: 0.6978 (mtt) cc_final: 0.6195 (mtp) REVERT: R 252 GLU cc_start: 0.5603 (pt0) cc_final: 0.5102 (tp30) REVERT: R 376 PHE cc_start: 0.7091 (t80) cc_final: 0.6592 (t80) REVERT: P 19 GLN cc_start: 0.8365 (mt0) cc_final: 0.8163 (mt0) REVERT: P 22 PHE cc_start: 0.8598 (t80) cc_final: 0.8382 (t80) REVERT: A 343 ASP cc_start: 0.7501 (t70) cc_final: 0.7249 (t70) REVERT: G 52 THR cc_start: 0.8571 (m) cc_final: 0.8224 (p) REVERT: N 67 ARG cc_start: 0.6618 (mtp180) cc_final: 0.6196 (mtp180) REVERT: N 83 MET cc_start: 0.7568 (mtp) cc_final: 0.7289 (mtp) REVERT: N 109 ASP cc_start: 0.6532 (p0) cc_final: 0.6307 (p0) REVERT: N 125 THR cc_start: 0.8495 (m) cc_final: 0.8293 (t) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.2905 time to fit residues: 101.1790 Evaluate side-chains 159 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 0.2980 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 101 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: R 173 HIS R 230 ASN ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 HIS B 75 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 156 GLN B 259 GLN B 266 HIS B 268 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9580 Z= 0.217 Angle : 0.561 6.304 13007 Z= 0.294 Chirality : 0.041 0.142 1446 Planarity : 0.004 0.057 1628 Dihedral : 5.174 34.378 1664 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.44 % Allowed : 10.49 % Favored : 87.07 % 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: 0.40 (0.24), residues: 1123 helix: 1.80 (0.22), residues: 449 sheet: -0.78 (0.33), residues: 231 loop : -0.68 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 39 HIS 0.008 0.001 HIS A 220 PHE 0.019 0.001 PHE R 379 TYR 0.029 0.002 TYR R 141 ARG 0.008 0.001 ARG R 370 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 179 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 39 TRP cc_start: 0.8324 (t60) cc_final: 0.7941 (t60) REVERT: R 67 MET cc_start: 0.7095 (mtt) cc_final: 0.6293 (mtp) REVERT: R 252 GLU cc_start: 0.5771 (pt0) cc_final: 0.5454 (tp30) REVERT: R 300 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.6742 (ttp80) REVERT: R 315 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.8818 (pt) REVERT: R 376 PHE cc_start: 0.7630 (t80) cc_final: 0.6955 (t80) REVERT: R 387 LEU cc_start: 0.8389 (mt) cc_final: 0.8110 (mt) REVERT: P 9 ASP cc_start: 0.8006 (t0) cc_final: 0.7777 (t0) REVERT: P 24 GLN cc_start: 0.8376 (mm-40) cc_final: 0.8130 (mm-40) REVERT: G 52 THR cc_start: 0.8604 (m) cc_final: 0.8282 (p) REVERT: N 46 GLU cc_start: 0.7509 (pt0) cc_final: 0.7296 (pt0) REVERT: N 109 ASP cc_start: 0.6646 (p0) cc_final: 0.6336 (p0) outliers start: 24 outliers final: 12 residues processed: 193 average time/residue: 0.2419 time to fit residues: 62.5882 Evaluate side-chains 167 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 153 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 300 ARG Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 398 GLU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 110 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 138 GLN ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9580 Z= 0.196 Angle : 0.507 5.434 13007 Z= 0.265 Chirality : 0.039 0.143 1446 Planarity : 0.004 0.055 1628 Dihedral : 4.846 33.278 1664 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.36 % Allowed : 11.20 % Favored : 85.44 % 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: 0.94 (0.24), residues: 1123 helix: 2.42 (0.23), residues: 448 sheet: -0.75 (0.31), residues: 248 loop : -0.40 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 233 HIS 0.009 0.001 HIS A 220 PHE 0.013 0.001 PHE R 379 TYR 0.026 0.002 TYR R 141 ARG 0.004 0.000 ARG R 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 157 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 67 MET cc_start: 0.7089 (mtt) cc_final: 0.6542 (mtp) REVERT: R 252 GLU cc_start: 0.5951 (pt0) cc_final: 0.5567 (tp30) REVERT: R 253 GLU cc_start: 0.5427 (tp30) cc_final: 0.4996 (tt0) REVERT: R 304 LEU cc_start: 0.8631 (mt) cc_final: 0.8318 (mt) REVERT: R 376 PHE cc_start: 0.7735 (t80) cc_final: 0.6920 (t80) REVERT: R 387 LEU cc_start: 0.8410 (mt) cc_final: 0.8136 (mt) REVERT: P 9 ASP cc_start: 0.7919 (t0) cc_final: 0.7674 (t0) REVERT: P 24 GLN cc_start: 0.8336 (mm-40) cc_final: 0.8129 (mm-40) REVERT: G 52 THR cc_start: 0.8559 (m) cc_final: 0.8215 (p) REVERT: G 62 ARG cc_start: 0.8085 (pmt-80) cc_final: 0.7788 (pmt-80) REVERT: N 109 ASP cc_start: 0.6505 (p0) cc_final: 0.6265 (p0) outliers start: 33 outliers final: 20 residues processed: 177 average time/residue: 0.2307 time to fit residues: 55.5722 Evaluate side-chains 167 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 380 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 102 optimal weight: 0.0870 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 29 optimal weight: 0.3980 chunk 90 optimal weight: 4.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 92 HIS ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9580 Z= 0.185 Angle : 0.513 8.088 13007 Z= 0.263 Chirality : 0.039 0.158 1446 Planarity : 0.003 0.054 1628 Dihedral : 4.695 30.954 1664 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.85 % Allowed : 12.63 % Favored : 84.52 % 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: 1.13 (0.25), residues: 1123 helix: 2.59 (0.23), residues: 449 sheet: -0.62 (0.32), residues: 242 loop : -0.35 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 39 HIS 0.008 0.001 HIS A 220 PHE 0.014 0.001 PHE P 22 TYR 0.022 0.001 TYR R 141 ARG 0.003 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 157 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 67 MET cc_start: 0.7143 (mtt) cc_final: 0.6715 (mtp) REVERT: R 387 LEU cc_start: 0.8415 (mt) cc_final: 0.8120 (mt) REVERT: P 9 ASP cc_start: 0.7829 (t0) cc_final: 0.7577 (t0) REVERT: G 52 THR cc_start: 0.8572 (m) cc_final: 0.8252 (p) REVERT: G 63 GLU cc_start: 0.6578 (mt-10) cc_final: 0.5515 (pt0) REVERT: N 87 LYS cc_start: 0.7902 (mtpt) cc_final: 0.7684 (mtpt) REVERT: N 91 THR cc_start: 0.8884 (OUTLIER) cc_final: 0.8647 (t) REVERT: N 109 ASP cc_start: 0.6663 (p0) cc_final: 0.6391 (p0) outliers start: 28 outliers final: 22 residues processed: 171 average time/residue: 0.2309 time to fit residues: 53.6497 Evaluate side-chains 162 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 139 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 380 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 0.1980 chunk 44 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 74 optimal weight: 0.0170 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 92 HIS P 24 GLN ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9580 Z= 0.179 Angle : 0.508 8.627 13007 Z= 0.261 Chirality : 0.039 0.215 1446 Planarity : 0.003 0.051 1628 Dihedral : 4.630 38.300 1664 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.95 % Allowed : 12.93 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 1.32 (0.25), residues: 1123 helix: 2.84 (0.23), residues: 442 sheet: -0.60 (0.32), residues: 242 loop : -0.26 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 39 HIS 0.009 0.001 HIS A 220 PHE 0.016 0.001 PHE P 22 TYR 0.021 0.001 TYR R 141 ARG 0.006 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 147 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 35 LEU cc_start: 0.8900 (mt) cc_final: 0.8646 (mt) REVERT: R 39 TRP cc_start: 0.8203 (t60) cc_final: 0.7888 (t60) REVERT: R 67 MET cc_start: 0.7086 (mtt) cc_final: 0.6567 (mtp) REVERT: R 188 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7895 (mm) REVERT: R 387 LEU cc_start: 0.8407 (mt) cc_final: 0.8109 (mt) REVERT: P 9 ASP cc_start: 0.7892 (t0) cc_final: 0.7630 (t0) REVERT: A 339 TYR cc_start: 0.8171 (m-80) cc_final: 0.7862 (m-80) REVERT: G 52 THR cc_start: 0.8570 (m) cc_final: 0.8205 (p) REVERT: N 87 LYS cc_start: 0.7962 (mtpt) cc_final: 0.7754 (mtpt) REVERT: N 91 THR cc_start: 0.8877 (OUTLIER) cc_final: 0.8645 (t) REVERT: N 109 ASP cc_start: 0.6616 (p0) cc_final: 0.6270 (p0) outliers start: 29 outliers final: 21 residues processed: 164 average time/residue: 0.2307 time to fit residues: 52.0957 Evaluate side-chains 164 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 380 LEU Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 8.9990 chunk 26 optimal weight: 0.5980 chunk 108 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 92 HIS R 138 GLN ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9580 Z= 0.248 Angle : 0.538 8.387 13007 Z= 0.277 Chirality : 0.040 0.196 1446 Planarity : 0.003 0.051 1628 Dihedral : 4.699 37.840 1664 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.85 % Allowed : 13.65 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 1.26 (0.25), residues: 1123 helix: 2.90 (0.23), residues: 444 sheet: -0.74 (0.31), residues: 242 loop : -0.36 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 47 HIS 0.010 0.001 HIS A 220 PHE 0.018 0.001 PHE P 22 TYR 0.019 0.002 TYR R 141 ARG 0.004 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 143 time to evaluate : 1.137 Fit side-chains REVERT: R 67 MET cc_start: 0.7176 (mtt) cc_final: 0.6788 (mtp) REVERT: R 269 LEU cc_start: 0.7859 (tt) cc_final: 0.7623 (tp) REVERT: P 9 ASP cc_start: 0.7951 (t0) cc_final: 0.7663 (t0) REVERT: B 234 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.7930 (t80) REVERT: G 52 THR cc_start: 0.8605 (m) cc_final: 0.8082 (p) REVERT: G 63 GLU cc_start: 0.6587 (mt-10) cc_final: 0.5677 (pt0) REVERT: N 109 ASP cc_start: 0.6553 (p0) cc_final: 0.6125 (p0) outliers start: 28 outliers final: 23 residues processed: 159 average time/residue: 0.2299 time to fit residues: 50.1020 Evaluate side-chains 156 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 380 LEU Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 60 optimal weight: 0.3980 chunk 107 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9580 Z= 0.204 Angle : 0.517 7.879 13007 Z= 0.266 Chirality : 0.039 0.198 1446 Planarity : 0.003 0.050 1628 Dihedral : 4.616 39.824 1664 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.75 % Allowed : 13.95 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 1.29 (0.25), residues: 1123 helix: 2.95 (0.24), residues: 443 sheet: -0.78 (0.31), residues: 245 loop : -0.32 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 39 HIS 0.009 0.001 HIS A 220 PHE 0.017 0.001 PHE P 22 TYR 0.019 0.001 TYR R 141 ARG 0.004 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 140 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: R 67 MET cc_start: 0.7157 (mtt) cc_final: 0.6763 (mtp) REVERT: R 318 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8507 (mm) REVERT: P 9 ASP cc_start: 0.7948 (t0) cc_final: 0.7654 (t0) REVERT: B 234 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.7981 (t80) REVERT: G 52 THR cc_start: 0.8672 (m) cc_final: 0.8163 (p) REVERT: N 91 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8644 (t) outliers start: 27 outliers final: 21 residues processed: 153 average time/residue: 0.2366 time to fit residues: 49.1560 Evaluate side-chains 156 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 281 TYR Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 380 LEU Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 0.0980 chunk 53 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 92 HIS ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9580 Z= 0.171 Angle : 0.501 7.813 13007 Z= 0.258 Chirality : 0.039 0.189 1446 Planarity : 0.003 0.051 1628 Dihedral : 4.512 46.663 1664 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.65 % Allowed : 14.66 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 1.36 (0.25), residues: 1123 helix: 2.98 (0.24), residues: 442 sheet: -0.72 (0.31), residues: 241 loop : -0.27 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 39 HIS 0.008 0.001 HIS A 220 PHE 0.026 0.001 PHE R 345 TYR 0.018 0.001 TYR R 141 ARG 0.006 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: R 39 TRP cc_start: 0.8138 (t60) cc_final: 0.7839 (t60) REVERT: R 67 MET cc_start: 0.7157 (mtt) cc_final: 0.6661 (mtp) REVERT: R 90 TRP cc_start: 0.7172 (p90) cc_final: 0.6654 (p90) REVERT: R 318 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8532 (mm) REVERT: R 387 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8076 (mt) REVERT: P 9 ASP cc_start: 0.7915 (t0) cc_final: 0.7626 (t0) REVERT: B 234 PHE cc_start: 0.9133 (OUTLIER) cc_final: 0.8157 (t80) REVERT: G 52 THR cc_start: 0.8621 (m) cc_final: 0.8125 (p) REVERT: N 91 THR cc_start: 0.8864 (OUTLIER) cc_final: 0.8627 (t) REVERT: N 109 ASP cc_start: 0.6439 (p0) cc_final: 0.6034 (p0) outliers start: 26 outliers final: 19 residues processed: 154 average time/residue: 0.2349 time to fit residues: 49.1710 Evaluate side-chains 157 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 134 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 380 LEU Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9580 Z= 0.225 Angle : 0.533 7.921 13007 Z= 0.277 Chirality : 0.039 0.200 1446 Planarity : 0.003 0.050 1628 Dihedral : 4.608 54.964 1664 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.95 % Allowed : 14.77 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 1.26 (0.25), residues: 1123 helix: 2.85 (0.24), residues: 443 sheet: -0.75 (0.32), residues: 233 loop : -0.31 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 39 HIS 0.009 0.001 HIS A 220 PHE 0.022 0.001 PHE R 345 TYR 0.022 0.001 TYR R 36 ARG 0.006 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: R 67 MET cc_start: 0.7217 (mtt) cc_final: 0.6820 (mtp) REVERT: R 90 TRP cc_start: 0.7202 (p90) cc_final: 0.6669 (p90) REVERT: R 160 SER cc_start: 0.6457 (m) cc_final: 0.6216 (p) REVERT: R 318 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8471 (mm) REVERT: R 387 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8136 (mt) REVERT: P 9 ASP cc_start: 0.7938 (t0) cc_final: 0.7658 (t0) REVERT: B 234 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.8179 (t80) REVERT: B 292 PHE cc_start: 0.8563 (m-80) cc_final: 0.8250 (m-10) REVERT: G 52 THR cc_start: 0.8633 (m) cc_final: 0.8117 (p) REVERT: G 63 GLU cc_start: 0.6586 (mt-10) cc_final: 0.5814 (pt0) REVERT: N 91 THR cc_start: 0.8872 (OUTLIER) cc_final: 0.8628 (t) outliers start: 29 outliers final: 25 residues processed: 154 average time/residue: 0.2298 time to fit residues: 48.1984 Evaluate side-chains 160 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 131 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 281 TYR Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 380 LEU Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.0470 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 111 optimal weight: 0.0010 chunk 102 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 70 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 overall best weight: 0.5084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9580 Z= 0.171 Angle : 0.511 7.748 13007 Z= 0.265 Chirality : 0.038 0.192 1446 Planarity : 0.003 0.051 1628 Dihedral : 4.501 58.429 1664 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.55 % Allowed : 15.17 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 1.27 (0.25), residues: 1123 helix: 2.86 (0.24), residues: 442 sheet: -0.72 (0.31), residues: 241 loop : -0.29 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 39 HIS 0.008 0.001 HIS A 220 PHE 0.022 0.001 PHE R 345 TYR 0.029 0.001 TYR R 36 ARG 0.005 0.000 ARG G 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 138 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 39 TRP cc_start: 0.8067 (t60) cc_final: 0.7730 (t60) REVERT: R 67 MET cc_start: 0.7285 (mtt) cc_final: 0.6752 (mtp) REVERT: R 90 TRP cc_start: 0.7196 (p90) cc_final: 0.6688 (p90) REVERT: R 160 SER cc_start: 0.6393 (m) cc_final: 0.6088 (p) REVERT: R 318 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8497 (mm) REVERT: P 9 ASP cc_start: 0.7927 (t0) cc_final: 0.7628 (t0) REVERT: B 234 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8205 (t80) REVERT: B 292 PHE cc_start: 0.8541 (m-80) cc_final: 0.8289 (m-10) REVERT: G 52 THR cc_start: 0.8569 (m) cc_final: 0.8203 (p) REVERT: N 91 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8616 (t) outliers start: 25 outliers final: 21 residues processed: 151 average time/residue: 0.2465 time to fit residues: 50.8029 Evaluate side-chains 158 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 281 TYR Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 380 LEU Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 16 optimal weight: 9.9990 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 0.0020 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 255 HIS ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.200257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.168231 restraints weight = 10575.550| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.26 r_work: 0.3484 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9580 Z= 0.183 Angle : 0.508 7.556 13007 Z= 0.265 Chirality : 0.039 0.193 1446 Planarity : 0.003 0.050 1628 Dihedral : 4.389 48.985 1664 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.85 % Allowed : 14.77 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 1.28 (0.25), residues: 1123 helix: 2.87 (0.24), residues: 442 sheet: -0.71 (0.31), residues: 241 loop : -0.29 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 39 HIS 0.010 0.001 HIS R 255 PHE 0.021 0.001 PHE R 345 TYR 0.028 0.001 TYR R 36 ARG 0.005 0.000 ARG G 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2201.76 seconds wall clock time: 40 minutes 31.26 seconds (2431.26 seconds total)