Starting phenix.real_space_refine on Wed Mar 12 23:22:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wi9_21683/03_2025/6wi9_21683.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wi9_21683/03_2025/6wi9_21683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wi9_21683/03_2025/6wi9_21683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wi9_21683/03_2025/6wi9_21683.map" model { file = "/net/cci-nas-00/data/ceres_data/6wi9_21683/03_2025/6wi9_21683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wi9_21683/03_2025/6wi9_21683.cif" } resolution = 4.3 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= 0.004 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 53 5.16 5 C 5410 2.51 5 N 1526 2.21 5 O 1561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8550 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1646 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain breaks: 4 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 213 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "R" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2706 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 11, 'TRANS': 356} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 394 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 6, 'TRP:plan': 4, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 189 Time building chain proxies: 5.15, per 1000 atoms: 0.60 Number of scatterers: 8550 At special positions: 0 Unit cell: (78.26, 173.72, 97.18, 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 53 16.00 O 1561 8.00 N 1526 7.00 C 5410 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 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 Simple disulfide: pdb=" SG CYS R 45 " - pdb=" SG CYS R 75 " distance=2.03 Simple disulfide: pdb=" SG CYS R 89 " - pdb=" SG CYS R 123 " distance=2.03 Simple disulfide: pdb=" SG CYS R 215 " - pdb=" SG CYS R 285 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 1.1 seconds 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 40.1% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.503A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP A 33 " --> pdb=" O GLN A 29 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 removed outlier: 3.702A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.720A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.761A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 390 removed outlier: 3.685A pdb=" N ASP A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.962A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 36 removed outlier: 4.187A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 12 No H-bonds generated for 'chain 'G' and resid 10 through 12' Processing helix chain 'G' and resid 13 through 18 Processing helix chain 'G' and resid 20 through 25 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.796A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.756A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 2 through 27 Processing helix chain 'R' and resid 31 through 46 removed outlier: 4.010A pdb=" N ASP R 43 " --> pdb=" O TRP R 39 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLN R 44 " --> pdb=" O GLU R 40 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS R 45 " --> pdb=" O GLU R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 50 Processing helix chain 'R' and resid 93 through 97 Processing helix chain 'R' and resid 131 through 165 removed outlier: 3.509A pdb=" N ARG R 135 " --> pdb=" O SER R 131 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS R 136 " --> pdb=" O ASN R 132 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N SER R 137 " --> pdb=" O GLU R 133 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL R 155 " --> pdb=" O SER R 151 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU R 158 " --> pdb=" O LEU R 154 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE R 163 " --> pdb=" O VAL R 159 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU R 164 " --> pdb=" O ALA R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 200 removed outlier: 3.541A pdb=" N TYR R 176 " --> pdb=" O CYS R 172 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE R 177 " --> pdb=" O THR R 173 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N HIS R 180 " --> pdb=" O TYR R 176 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE R 193 " --> pdb=" O ALA R 189 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE R 194 " --> pdb=" O LEU R 190 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP R 196 " --> pdb=" O ASN R 192 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ALA R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 246 removed outlier: 3.948A pdb=" N VAL R 220 " --> pdb=" O LYS R 216 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN R 229 " --> pdb=" O CYS R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 265 removed outlier: 3.603A pdb=" N GLY R 257 " --> pdb=" O LYS R 253 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER R 265 " --> pdb=" O PHE R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 265 through 280 removed outlier: 4.095A pdb=" N ALA R 271 " --> pdb=" O ALA R 267 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS R 278 " --> pdb=" O ALA R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 325 Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 336 through 352 removed outlier: 4.617A pdb=" N ARG R 342 " --> pdb=" O LYS R 338 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU R 346 " --> pdb=" O ARG R 342 " (cutoff:3.500A) Proline residue: R 349 - end of helix Processing helix chain 'R' and resid 353 through 359 removed outlier: 3.977A pdb=" N PHE R 358 " --> pdb=" O TYR R 355 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 368 removed outlier: 5.821A pdb=" N GLU R 367 " --> pdb=" O ASP R 364 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE R 368 " --> pdb=" O ALA R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 369 through 374 removed outlier: 3.569A pdb=" N GLU R 373 " --> pdb=" O GLN R 369 " (cutoff:3.500A) Processing helix chain 'R' and resid 376 through 378 No H-bonds generated for 'chain 'R' and resid 376 through 378' Processing helix chain 'R' and resid 379 through 390 Processing helix chain 'R' and resid 393 through 408 removed outlier: 3.514A pdb=" N GLU R 398 " --> pdb=" O GLU R 394 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL R 399 " --> pdb=" O VAL R 395 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS R 401 " --> pdb=" O LEU R 397 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS R 402 " --> pdb=" O GLU R 398 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N HIS R 407 " --> pdb=" O TRP R 403 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213 removed outlier: 3.590A pdb=" N HIS A 41 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS A 220 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.066A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.183A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.991A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.414A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.794A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.666A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.789A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.807A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP N 50 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 69 through 70 removed outlier: 3.677A pdb=" N MET R 69 " --> pdb=" O TRP R 76 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TRP R 76 " --> pdb=" O MET R 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'R' and resid 85 through 87 removed outlier: 4.269A pdb=" N LEU R 103 " --> pdb=" O VAL R 87 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 1026 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2851 1.35 - 1.46: 2108 1.46 - 1.58: 3684 1.58 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 8716 Sorted by residual: bond pdb=" CA THR B 128 " pdb=" CB THR B 128 " ideal model delta sigma weight residual 1.524 1.542 -0.018 1.37e-02 5.33e+03 1.81e+00 bond pdb=" CA ILE R 246 " pdb=" CB ILE R 246 " ideal model delta sigma weight residual 1.533 1.545 -0.012 1.19e-02 7.06e+03 9.69e-01 bond pdb=" N GLY B 116 " pdb=" CA GLY B 116 " ideal model delta sigma weight residual 1.458 1.449 0.009 9.20e-03 1.18e+04 9.13e-01 bond pdb=" CA ILE N 51 " pdb=" CB ILE N 51 " ideal model delta sigma weight residual 1.550 1.541 0.009 1.03e-02 9.43e+03 7.69e-01 bond pdb=" C GLU R 67 " pdb=" N GLY R 68 " ideal model delta sigma weight residual 1.332 1.328 0.004 5.00e-03 4.00e+04 7.03e-01 ... (remaining 8711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 11468 1.31 - 2.61: 266 2.61 - 3.92: 51 3.92 - 5.22: 9 5.22 - 6.53: 3 Bond angle restraints: 11797 Sorted by residual: angle pdb=" N GLU A 309 " pdb=" CA GLU A 309 " pdb=" C GLU A 309 " ideal model delta sigma weight residual 114.56 109.65 4.91 1.27e+00 6.20e-01 1.49e+01 angle pdb=" N ILE R 73 " pdb=" CA ILE R 73 " pdb=" C ILE R 73 " ideal model delta sigma weight residual 111.62 108.73 2.89 7.90e-01 1.60e+00 1.34e+01 angle pdb=" N ILE G 9 " pdb=" CA ILE G 9 " pdb=" C ILE G 9 " ideal model delta sigma weight residual 112.12 109.09 3.03 8.40e-01 1.42e+00 1.30e+01 angle pdb=" C GLU R 52 " pdb=" N GLN R 53 " pdb=" CA GLN R 53 " ideal model delta sigma weight residual 121.54 128.07 -6.53 1.91e+00 2.74e-01 1.17e+01 angle pdb=" N VAL N 64 " pdb=" CA VAL N 64 " pdb=" C VAL N 64 " ideal model delta sigma weight residual 113.20 110.06 3.14 9.60e-01 1.09e+00 1.07e+01 ... (remaining 11792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 4768 17.83 - 35.67: 347 35.67 - 53.50: 39 53.50 - 71.34: 6 71.34 - 89.17: 15 Dihedral angle restraints: 5175 sinusoidal: 1970 harmonic: 3205 Sorted by residual: dihedral pdb=" CB CYS R 215 " pdb=" SG CYS R 215 " pdb=" SG CYS R 285 " pdb=" CB CYS R 285 " ideal model delta sinusoidal sigma weight residual 93.00 42.54 50.46 1 1.00e+01 1.00e-02 3.49e+01 dihedral pdb=" CB CYS R 45 " pdb=" SG CYS R 45 " pdb=" SG CYS R 75 " pdb=" CB CYS R 75 " ideal model delta sinusoidal sigma weight residual 93.00 128.25 -35.25 1 1.00e+01 1.00e-02 1.76e+01 dihedral pdb=" CB GLU R 373 " pdb=" CG GLU R 373 " pdb=" CD GLU R 373 " pdb=" OE1 GLU R 373 " ideal model delta sinusoidal sigma weight residual 0.00 89.17 -89.17 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 5172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 940 0.035 - 0.071: 282 0.071 - 0.106: 87 0.106 - 0.142: 12 0.142 - 0.177: 2 Chirality restraints: 1323 Sorted by residual: chirality pdb=" CB ILE R 246 " pdb=" CA ILE R 246 " pdb=" CG1 ILE R 246 " pdb=" CG2 ILE R 246 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.85e-01 chirality pdb=" CB THR B 128 " pdb=" CA THR B 128 " pdb=" OG1 THR B 128 " pdb=" CG2 THR B 128 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" CA ILE R 288 " pdb=" N ILE R 288 " pdb=" C ILE R 288 " pdb=" CB ILE R 288 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.57e-01 ... (remaining 1320 not shown) Planarity restraints: 1516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.021 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO B 236 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 320 " 0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO A 321 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 300 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO R 301 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO R 301 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 301 " 0.017 5.00e-02 4.00e+02 ... (remaining 1513 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1049 2.75 - 3.29: 8547 3.29 - 3.83: 13270 3.83 - 4.36: 15713 4.36 - 4.90: 26736 Nonbonded interactions: 65315 Sorted by model distance: nonbonded pdb=" NH1 ARG B 42 " pdb=" O ILE B 43 " model vdw 2.214 3.120 nonbonded pdb=" O ASP B 76 " pdb=" OG SER B 98 " model vdw 2.236 3.040 nonbonded pdb=" O ARG R 339 " pdb=" OG SER R 343 " model vdw 2.312 3.040 nonbonded pdb=" OD1 ASN R 291 " pdb=" OG SER R 293 " model vdw 2.312 3.040 nonbonded pdb=" O GLY B 182 " pdb=" NZ LYS B 209 " model vdw 2.317 3.120 ... (remaining 65310 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.990 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 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 : 0.002 0.020 8716 Z= 0.110 Angle : 0.502 6.528 11797 Z= 0.312 Chirality : 0.038 0.177 1323 Planarity : 0.002 0.033 1516 Dihedral : 12.848 89.170 3086 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % 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: -3.72 (0.21), residues: 1086 helix: -2.77 (0.18), residues: 377 sheet: -1.64 (0.32), residues: 208 loop : -2.50 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 234 HIS 0.001 0.000 HIS R 241 PHE 0.013 0.001 PHE A 315 TYR 0.004 0.001 TYR B 124 ARG 0.004 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 VAL cc_start: 0.8933 (t) cc_final: 0.8615 (t) REVERT: A 374 ARG cc_start: 0.7832 (mtt90) cc_final: 0.7522 (ttt180) REVERT: B 16 ASN cc_start: 0.9351 (m110) cc_final: 0.8821 (m110) REVERT: B 45 MET cc_start: 0.7078 (mmm) cc_final: 0.6780 (tpp) REVERT: B 78 LYS cc_start: 0.8884 (mmmt) cc_final: 0.8541 (mmmt) REVERT: B 145 TYR cc_start: 0.8584 (p90) cc_final: 0.8363 (p90) REVERT: B 165 THR cc_start: 0.7995 (p) cc_final: 0.7711 (t) REVERT: B 188 MET cc_start: 0.7775 (tpt) cc_final: 0.7508 (mmm) REVERT: B 339 TRP cc_start: 0.8630 (m100) cc_final: 0.8350 (m100) REVERT: G 41 CYS cc_start: 0.8871 (m) cc_final: 0.8592 (m) REVERT: G 59 ASN cc_start: 0.7332 (t0) cc_final: 0.6484 (p0) REVERT: N 61 THR cc_start: 0.8397 (p) cc_final: 0.8140 (t) REVERT: N 83 MET cc_start: 0.8048 (pmm) cc_final: 0.7716 (pmm) REVERT: P 3 ASP cc_start: 0.8242 (t0) cc_final: 0.7914 (t0) REVERT: R 132 ASN cc_start: 0.8938 (p0) cc_final: 0.8731 (p0) REVERT: R 175 ASN cc_start: 0.9107 (m-40) cc_final: 0.8702 (m-40) REVERT: R 179 MET cc_start: 0.8074 (mmm) cc_final: 0.7814 (tpp) REVERT: R 230 TYR cc_start: 0.8606 (m-80) cc_final: 0.8047 (m-10) REVERT: R 256 GLN cc_start: 0.7622 (mt0) cc_final: 0.6522 (tm-30) REVERT: R 261 PHE cc_start: 0.9038 (t80) cc_final: 0.8828 (t80) REVERT: R 282 ASP cc_start: 0.7871 (t0) cc_final: 0.7609 (t0) REVERT: R 321 MET cc_start: 0.8108 (mtt) cc_final: 0.7812 (mmm) REVERT: R 354 HIS cc_start: 0.9050 (p-80) cc_final: 0.8655 (p-80) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.2429 time to fit residues: 103.7932 Evaluate side-chains 211 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 218 ASN B 17 GLN B 91 HIS B 220 GLN N 3 GLN R 180 HIS R 223 GLN R 229 ASN R 354 HIS R 392 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.108808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.085775 restraints weight = 23715.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.088273 restraints weight = 14319.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.089981 restraints weight = 10109.179| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8716 Z= 0.222 Angle : 0.593 6.039 11797 Z= 0.319 Chirality : 0.043 0.227 1323 Planarity : 0.004 0.038 1516 Dihedral : 3.868 16.952 1203 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % 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: -2.05 (0.24), residues: 1086 helix: -0.52 (0.25), residues: 375 sheet: -1.15 (0.34), residues: 203 loop : -2.07 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 295 HIS 0.007 0.001 HIS R 241 PHE 0.025 0.002 PHE R 358 TYR 0.017 0.002 TYR R 138 ARG 0.007 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 TYR cc_start: 0.7930 (t80) cc_final: 0.7203 (t80) REVERT: A 374 ARG cc_start: 0.7988 (mtt90) cc_final: 0.7468 (ttt180) REVERT: B 9 GLN cc_start: 0.8922 (tp40) cc_final: 0.8647 (mm110) REVERT: B 78 LYS cc_start: 0.8835 (mmmt) cc_final: 0.8492 (mmmt) REVERT: B 188 MET cc_start: 0.8212 (tpt) cc_final: 0.7850 (mmm) REVERT: B 217 MET cc_start: 0.8711 (ppp) cc_final: 0.8168 (ppp) REVERT: B 339 TRP cc_start: 0.8839 (m100) cc_final: 0.8588 (m100) REVERT: G 59 ASN cc_start: 0.7244 (t0) cc_final: 0.6941 (t0) REVERT: N 68 PHE cc_start: 0.8209 (m-10) cc_final: 0.7804 (m-10) REVERT: R 175 ASN cc_start: 0.9118 (m-40) cc_final: 0.8698 (m-40) REVERT: R 179 MET cc_start: 0.8034 (mmm) cc_final: 0.7796 (mmm) REVERT: R 230 TYR cc_start: 0.8665 (m-80) cc_final: 0.8387 (m-10) REVERT: R 251 GLU cc_start: 0.7598 (pm20) cc_final: 0.7253 (pm20) REVERT: R 321 MET cc_start: 0.8116 (mtt) cc_final: 0.7857 (mmm) REVERT: R 342 ARG cc_start: 0.8158 (mtm180) cc_final: 0.7914 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.2075 time to fit residues: 74.0149 Evaluate side-chains 205 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 89 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS B 239 ASN G 24 ASN N 53 GLN R 229 ASN R 332 ASN ** R 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.103503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.080605 restraints weight = 24172.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.083044 restraints weight = 14454.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.084702 restraints weight = 10121.758| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8716 Z= 0.330 Angle : 0.668 6.414 11797 Z= 0.354 Chirality : 0.044 0.199 1323 Planarity : 0.005 0.041 1516 Dihedral : 4.544 18.358 1203 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % 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: -1.59 (0.25), residues: 1086 helix: -0.13 (0.25), residues: 378 sheet: -0.89 (0.35), residues: 203 loop : -1.82 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 281 HIS 0.010 0.002 HIS R 241 PHE 0.014 0.002 PHE A 315 TYR 0.020 0.002 TYR R 138 ARG 0.007 0.001 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 ARG cc_start: 0.7984 (mtt90) cc_final: 0.7370 (mtt180) REVERT: B 78 LYS cc_start: 0.9011 (mmmt) cc_final: 0.8538 (mmmt) REVERT: B 145 TYR cc_start: 0.8840 (p90) cc_final: 0.8201 (p90) REVERT: B 188 MET cc_start: 0.8312 (tpt) cc_final: 0.7887 (tpt) REVERT: B 217 MET cc_start: 0.8602 (ppp) cc_final: 0.8140 (ppp) REVERT: B 312 ASP cc_start: 0.7794 (p0) cc_final: 0.7285 (p0) REVERT: B 339 TRP cc_start: 0.9033 (m100) cc_final: 0.8643 (m100) REVERT: G 14 LYS cc_start: 0.8641 (mmtt) cc_final: 0.8170 (mtmm) REVERT: G 41 CYS cc_start: 0.8779 (m) cc_final: 0.8467 (m) REVERT: G 59 ASN cc_start: 0.7431 (t0) cc_final: 0.6922 (t0) REVERT: N 19 ARG cc_start: 0.8225 (ttp80) cc_final: 0.8014 (ttt90) REVERT: N 64 VAL cc_start: 0.8018 (m) cc_final: 0.7527 (m) REVERT: R 175 ASN cc_start: 0.9160 (m-40) cc_final: 0.8773 (m-40) REVERT: R 251 GLU cc_start: 0.7335 (pm20) cc_final: 0.7051 (pp20) REVERT: R 282 ASP cc_start: 0.8357 (t70) cc_final: 0.8136 (t0) REVERT: R 321 MET cc_start: 0.8237 (mtt) cc_final: 0.7906 (mmm) REVERT: R 342 ARG cc_start: 0.8256 (mtm180) cc_final: 0.7866 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.2151 time to fit residues: 69.2183 Evaluate side-chains 195 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 6 optimal weight: 0.7980 chunk 100 optimal weight: 0.0270 chunk 41 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN R 229 ASN ** R 392 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 = 0.3647 r_free = 0.3647 target = 0.107057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.084333 restraints weight = 23694.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.086879 restraints weight = 13994.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.088628 restraints weight = 9689.404| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8716 Z= 0.172 Angle : 0.562 6.351 11797 Z= 0.298 Chirality : 0.042 0.153 1323 Planarity : 0.004 0.041 1516 Dihedral : 4.305 17.234 1203 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % 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: -1.18 (0.25), residues: 1086 helix: 0.18 (0.26), residues: 383 sheet: -0.59 (0.36), residues: 201 loop : -1.61 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 211 HIS 0.006 0.001 HIS R 241 PHE 0.021 0.002 PHE N 68 TYR 0.023 0.002 TYR N 80 ARG 0.003 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 LYS cc_start: 0.8991 (mmmt) cc_final: 0.8397 (mmmt) REVERT: B 188 MET cc_start: 0.8366 (tpt) cc_final: 0.8031 (tpp) REVERT: B 217 MET cc_start: 0.8561 (ppp) cc_final: 0.8198 (ppp) REVERT: B 339 TRP cc_start: 0.8979 (m100) cc_final: 0.8602 (m100) REVERT: G 21 MET cc_start: 0.8133 (mmm) cc_final: 0.7059 (mmm) REVERT: G 41 CYS cc_start: 0.8708 (m) cc_final: 0.8448 (m) REVERT: G 59 ASN cc_start: 0.7419 (t0) cc_final: 0.7079 (t0) REVERT: N 64 VAL cc_start: 0.7969 (m) cc_final: 0.7726 (m) REVERT: N 72 ARG cc_start: 0.6463 (ptm-80) cc_final: 0.6001 (ptt90) REVERT: N 76 LYS cc_start: 0.8977 (mtmm) cc_final: 0.8470 (mtmm) REVERT: N 84 ASN cc_start: 0.8930 (p0) cc_final: 0.8508 (p0) REVERT: N 95 TYR cc_start: 0.8638 (m-80) cc_final: 0.8156 (m-80) REVERT: R 147 THR cc_start: 0.8861 (m) cc_final: 0.8622 (m) REVERT: R 175 ASN cc_start: 0.9028 (m-40) cc_final: 0.8615 (m-40) REVERT: R 251 GLU cc_start: 0.7318 (pm20) cc_final: 0.6496 (pp20) REVERT: R 342 ARG cc_start: 0.8244 (mtm180) cc_final: 0.7841 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.2148 time to fit residues: 71.3305 Evaluate side-chains 196 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 17 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN R 229 ASN ** R 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.103636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.080622 restraints weight = 24100.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.083083 restraints weight = 14388.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.084796 restraints weight = 10005.615| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8716 Z= 0.307 Angle : 0.655 9.705 11797 Z= 0.345 Chirality : 0.044 0.233 1323 Planarity : 0.004 0.047 1516 Dihedral : 4.652 18.670 1203 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % 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: -1.26 (0.25), residues: 1086 helix: 0.07 (0.26), residues: 383 sheet: -0.60 (0.36), residues: 203 loop : -1.62 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 286 HIS 0.010 0.002 HIS R 241 PHE 0.017 0.002 PHE N 27 TYR 0.027 0.002 TYR G 40 ARG 0.006 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 ARG cc_start: 0.7947 (mtt90) cc_final: 0.7571 (mtt180) REVERT: B 82 TRP cc_start: 0.8878 (m100) cc_final: 0.8458 (m100) REVERT: B 188 MET cc_start: 0.8452 (tpt) cc_final: 0.8090 (tpp) REVERT: B 217 MET cc_start: 0.8649 (ppp) cc_final: 0.8167 (ppp) REVERT: B 222 PHE cc_start: 0.8461 (m-80) cc_final: 0.8222 (m-10) REVERT: B 339 TRP cc_start: 0.9067 (m100) cc_final: 0.8705 (m100) REVERT: G 59 ASN cc_start: 0.7343 (t0) cc_final: 0.6931 (t0) REVERT: N 72 ARG cc_start: 0.6426 (ptm-80) cc_final: 0.6099 (ptt90) REVERT: N 73 ASP cc_start: 0.7860 (t70) cc_final: 0.7626 (t70) REVERT: N 76 LYS cc_start: 0.9014 (mtmm) cc_final: 0.8567 (mtmm) REVERT: N 84 ASN cc_start: 0.8831 (p0) cc_final: 0.8493 (p0) REVERT: R 175 ASN cc_start: 0.9110 (m-40) cc_final: 0.8777 (m-40) REVERT: R 321 MET cc_start: 0.8377 (mmm) cc_final: 0.7848 (mmm) REVERT: R 342 ARG cc_start: 0.8307 (mtm180) cc_final: 0.7809 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.2115 time to fit residues: 65.7851 Evaluate side-chains 189 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 102 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 32 optimal weight: 0.1980 chunk 81 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 103 optimal weight: 0.0970 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 57 optimal weight: 20.0000 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 53 GLN R 192 ASN R 229 ASN ** R 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.105869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.083506 restraints weight = 23529.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.086049 restraints weight = 13912.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.087768 restraints weight = 9612.773| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8716 Z= 0.191 Angle : 0.584 8.083 11797 Z= 0.306 Chirality : 0.042 0.182 1323 Planarity : 0.004 0.044 1516 Dihedral : 4.462 17.693 1203 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % 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: -1.03 (0.26), residues: 1086 helix: 0.27 (0.26), residues: 382 sheet: -0.48 (0.37), residues: 203 loop : -1.49 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 281 HIS 0.006 0.001 HIS R 241 PHE 0.017 0.001 PHE N 27 TYR 0.020 0.002 TYR G 40 ARG 0.008 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 ARG cc_start: 0.7898 (mtt90) cc_final: 0.7569 (mtt180) REVERT: B 78 LYS cc_start: 0.8451 (mmtm) cc_final: 0.8152 (mmtm) REVERT: B 82 TRP cc_start: 0.8960 (m100) cc_final: 0.8389 (m100) REVERT: B 188 MET cc_start: 0.8497 (tpt) cc_final: 0.8262 (tpt) REVERT: B 217 MET cc_start: 0.8631 (ppp) cc_final: 0.8279 (ppp) REVERT: B 222 PHE cc_start: 0.8432 (m-80) cc_final: 0.8222 (m-10) REVERT: B 339 TRP cc_start: 0.9005 (m100) cc_final: 0.8629 (m100) REVERT: G 21 MET cc_start: 0.8189 (mmm) cc_final: 0.7257 (mmm) REVERT: G 59 ASN cc_start: 0.7406 (t0) cc_final: 0.7118 (t0) REVERT: N 20 LEU cc_start: 0.9097 (mm) cc_final: 0.8834 (mm) REVERT: N 68 PHE cc_start: 0.8264 (m-10) cc_final: 0.7317 (m-10) REVERT: N 72 ARG cc_start: 0.6209 (ptm-80) cc_final: 0.5946 (ptt90) REVERT: N 76 LYS cc_start: 0.9012 (mtmm) cc_final: 0.8557 (mtmm) REVERT: R 147 THR cc_start: 0.8845 (m) cc_final: 0.8621 (m) REVERT: R 150 TYR cc_start: 0.7992 (m-10) cc_final: 0.7744 (m-80) REVERT: R 175 ASN cc_start: 0.9076 (m-40) cc_final: 0.8746 (m-40) REVERT: R 221 LEU cc_start: 0.9353 (tp) cc_final: 0.9101 (pp) REVERT: R 230 TYR cc_start: 0.8568 (m-10) cc_final: 0.8338 (m-10) REVERT: R 321 MET cc_start: 0.8275 (mmm) cc_final: 0.7749 (mmm) REVERT: R 342 ARG cc_start: 0.8277 (mtm180) cc_final: 0.7789 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.2064 time to fit residues: 67.1610 Evaluate side-chains 192 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 50 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN N 53 GLN R 229 ASN R 392 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.107648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.084421 restraints weight = 23858.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.087113 restraints weight = 13825.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.088937 restraints weight = 9467.306| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8716 Z= 0.170 Angle : 0.592 7.598 11797 Z= 0.311 Chirality : 0.042 0.172 1323 Planarity : 0.003 0.042 1516 Dihedral : 4.377 17.262 1203 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % 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: -0.78 (0.26), residues: 1086 helix: 0.50 (0.26), residues: 387 sheet: -0.04 (0.38), residues: 197 loop : -1.53 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 286 HIS 0.005 0.001 HIS R 354 PHE 0.029 0.002 PHE N 27 TYR 0.023 0.002 TYR A 360 ARG 0.004 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 CYS cc_start: 0.8277 (p) cc_final: 0.7974 (p) REVERT: B 16 ASN cc_start: 0.9319 (m110) cc_final: 0.9053 (m110) REVERT: B 138 GLU cc_start: 0.7376 (tm-30) cc_final: 0.6835 (tm-30) REVERT: B 217 MET cc_start: 0.8556 (ppp) cc_final: 0.8105 (ppp) REVERT: B 222 PHE cc_start: 0.8380 (m-80) cc_final: 0.8180 (m-10) REVERT: B 275 SER cc_start: 0.8999 (t) cc_final: 0.8792 (p) REVERT: B 339 TRP cc_start: 0.8946 (m100) cc_final: 0.8582 (m100) REVERT: G 59 ASN cc_start: 0.7336 (t0) cc_final: 0.7121 (t0) REVERT: N 76 LYS cc_start: 0.9005 (mtmm) cc_final: 0.8543 (mtmm) REVERT: R 147 THR cc_start: 0.8801 (m) cc_final: 0.8566 (m) REVERT: R 150 TYR cc_start: 0.7794 (m-10) cc_final: 0.7489 (m-80) REVERT: R 175 ASN cc_start: 0.8969 (m-40) cc_final: 0.8627 (m-40) REVERT: R 221 LEU cc_start: 0.9338 (tp) cc_final: 0.9104 (pp) REVERT: R 251 GLU cc_start: 0.7633 (pm20) cc_final: 0.7432 (pm20) REVERT: R 253 LYS cc_start: 0.8146 (ptpp) cc_final: 0.7462 (tttt) REVERT: R 342 ARG cc_start: 0.8232 (mtm180) cc_final: 0.7727 (tmt-80) REVERT: R 406 TRP cc_start: 0.7525 (t60) cc_final: 0.6338 (m100) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.2159 time to fit residues: 74.8295 Evaluate side-chains 195 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 14 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN N 53 GLN R 229 ASN R 392 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.107031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.084490 restraints weight = 23916.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.087113 restraints weight = 14100.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.088902 restraints weight = 9670.321| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8716 Z= 0.206 Angle : 0.636 9.609 11797 Z= 0.329 Chirality : 0.043 0.276 1323 Planarity : 0.004 0.056 1516 Dihedral : 4.427 18.716 1203 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.11 % Allowed : 1.38 % Favored : 98.51 % 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: -0.85 (0.26), residues: 1086 helix: 0.40 (0.26), residues: 385 sheet: -0.07 (0.37), residues: 199 loop : -1.54 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.007 0.001 HIS B 225 PHE 0.036 0.002 PHE N 68 TYR 0.022 0.002 TYR A 360 ARG 0.008 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 CYS cc_start: 0.8342 (p) cc_final: 0.8141 (p) REVERT: A 360 TYR cc_start: 0.8681 (m-10) cc_final: 0.8315 (m-80) REVERT: A 374 ARG cc_start: 0.7889 (mtt90) cc_final: 0.7557 (mtt180) REVERT: B 78 LYS cc_start: 0.8837 (mmpt) cc_final: 0.8625 (mmmt) REVERT: B 217 MET cc_start: 0.8514 (ppp) cc_final: 0.8220 (ppp) REVERT: B 222 PHE cc_start: 0.8452 (m-80) cc_final: 0.8132 (m-10) REVERT: B 275 SER cc_start: 0.9052 (t) cc_final: 0.8832 (p) REVERT: B 339 TRP cc_start: 0.8976 (m100) cc_final: 0.8588 (m100) REVERT: G 59 ASN cc_start: 0.7390 (t0) cc_final: 0.7118 (t0) REVERT: N 76 LYS cc_start: 0.9000 (mtmm) cc_final: 0.8487 (mtmm) REVERT: N 81 LEU cc_start: 0.7865 (tt) cc_final: 0.7398 (tp) REVERT: N 82 GLN cc_start: 0.7897 (mm110) cc_final: 0.7564 (mm-40) REVERT: R 147 THR cc_start: 0.8836 (m) cc_final: 0.8582 (m) REVERT: R 150 TYR cc_start: 0.7825 (m-10) cc_final: 0.7541 (m-80) REVERT: R 175 ASN cc_start: 0.8968 (m-40) cc_final: 0.8646 (m-40) REVERT: R 342 ARG cc_start: 0.8231 (mtm180) cc_final: 0.7719 (tmt-80) REVERT: R 406 TRP cc_start: 0.7540 (t60) cc_final: 0.6365 (m100) outliers start: 1 outliers final: 0 residues processed: 242 average time/residue: 0.2038 time to fit residues: 68.1254 Evaluate side-chains 194 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 88 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 13 optimal weight: 0.0370 chunk 64 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS N 53 GLN ** R 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 392 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.108309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.084731 restraints weight = 24115.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.087454 restraints weight = 14038.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.089313 restraints weight = 9606.572| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8716 Z= 0.182 Angle : 0.628 8.356 11797 Z= 0.324 Chirality : 0.043 0.275 1323 Planarity : 0.004 0.053 1516 Dihedral : 4.387 22.016 1203 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % 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: -0.75 (0.26), residues: 1086 helix: 0.46 (0.26), residues: 389 sheet: -0.00 (0.38), residues: 199 loop : -1.48 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS B 225 PHE 0.036 0.002 PHE N 68 TYR 0.018 0.002 TYR A 360 ARG 0.006 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 CYS cc_start: 0.8372 (p) cc_final: 0.8157 (p) REVERT: A 360 TYR cc_start: 0.8672 (m-10) cc_final: 0.8379 (m-80) REVERT: A 374 ARG cc_start: 0.7844 (mtt90) cc_final: 0.7596 (mtt180) REVERT: B 78 LYS cc_start: 0.8880 (mmpt) cc_final: 0.8639 (mmmt) REVERT: B 212 ASP cc_start: 0.8627 (t70) cc_final: 0.8365 (t0) REVERT: B 217 MET cc_start: 0.8479 (ppp) cc_final: 0.8193 (ppp) REVERT: B 222 PHE cc_start: 0.8354 (m-80) cc_final: 0.8135 (m-10) REVERT: B 275 SER cc_start: 0.9046 (t) cc_final: 0.8784 (p) REVERT: B 339 TRP cc_start: 0.8983 (m100) cc_final: 0.8601 (m100) REVERT: N 64 VAL cc_start: 0.8000 (m) cc_final: 0.7652 (m) REVERT: N 76 LYS cc_start: 0.8950 (mtmm) cc_final: 0.8497 (mtmm) REVERT: N 81 LEU cc_start: 0.7414 (tt) cc_final: 0.7189 (tt) REVERT: R 147 THR cc_start: 0.8821 (m) cc_final: 0.8576 (m) REVERT: R 150 TYR cc_start: 0.7801 (m-10) cc_final: 0.7516 (m-80) REVERT: R 175 ASN cc_start: 0.8882 (m-40) cc_final: 0.8597 (m-40) REVERT: R 251 GLU cc_start: 0.7741 (pm20) cc_final: 0.7483 (pm20) REVERT: R 253 LYS cc_start: 0.8224 (ptpp) cc_final: 0.7602 (tttt) REVERT: R 342 ARG cc_start: 0.8264 (mtm180) cc_final: 0.7660 (tmt-80) REVERT: R 406 TRP cc_start: 0.7545 (t60) cc_final: 0.6300 (m100) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.1978 time to fit residues: 65.9580 Evaluate side-chains 198 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 63 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** R 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.107824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.084726 restraints weight = 24188.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.087273 restraints weight = 14652.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.089024 restraints weight = 10247.789| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8716 Z= 0.227 Angle : 0.653 8.690 11797 Z= 0.338 Chirality : 0.044 0.268 1323 Planarity : 0.004 0.048 1516 Dihedral : 4.500 18.908 1203 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.11 % Allowed : 0.00 % Favored : 99.89 % 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: -0.87 (0.26), residues: 1086 helix: 0.38 (0.26), residues: 395 sheet: -0.14 (0.37), residues: 201 loop : -1.56 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.007 0.001 HIS R 241 PHE 0.028 0.002 PHE N 68 TYR 0.019 0.002 TYR A 318 ARG 0.007 0.000 ARG B 251 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 231 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 CYS cc_start: 0.8294 (p) cc_final: 0.8056 (p) REVERT: B 16 ASN cc_start: 0.9288 (m110) cc_final: 0.9021 (m110) REVERT: B 82 TRP cc_start: 0.9105 (m100) cc_final: 0.8036 (m100) REVERT: B 217 MET cc_start: 0.8593 (ppp) cc_final: 0.8301 (ppp) REVERT: B 339 TRP cc_start: 0.8987 (m100) cc_final: 0.8664 (m100) REVERT: N 76 LYS cc_start: 0.8982 (mtmm) cc_final: 0.8553 (mtmm) REVERT: R 147 THR cc_start: 0.8855 (m) cc_final: 0.8597 (m) REVERT: R 150 TYR cc_start: 0.7911 (m-10) cc_final: 0.7681 (m-80) REVERT: R 251 GLU cc_start: 0.7759 (pm20) cc_final: 0.7286 (pm20) REVERT: R 342 ARG cc_start: 0.8203 (mtm180) cc_final: 0.7657 (tmt-80) REVERT: R 406 TRP cc_start: 0.7519 (t60) cc_final: 0.6288 (m100) outliers start: 1 outliers final: 1 residues processed: 232 average time/residue: 0.1988 time to fit residues: 63.1157 Evaluate side-chains 181 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 44 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 51 optimal weight: 7.9990 chunk 79 optimal weight: 0.4980 chunk 84 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 229 ASN ** R 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 392 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.108524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.085095 restraints weight = 24139.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.087541 restraints weight = 14621.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.089240 restraints weight = 10335.140| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8716 Z= 0.194 Angle : 0.650 10.083 11797 Z= 0.331 Chirality : 0.044 0.269 1323 Planarity : 0.004 0.057 1516 Dihedral : 4.427 18.706 1203 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: -0.87 (0.26), residues: 1086 helix: 0.41 (0.26), residues: 393 sheet: -0.30 (0.36), residues: 204 loop : -1.51 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.005 0.001 HIS R 241 PHE 0.028 0.002 PHE N 68 TYR 0.030 0.001 TYR A 318 ARG 0.003 0.000 ARG G 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2984.33 seconds wall clock time: 52 minutes 21.70 seconds (3141.70 seconds total)