Starting phenix.real_space_refine on Wed Feb 12 21:58:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wi9_21683/02_2025/6wi9_21683.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wi9_21683/02_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_21683/02_2025/6wi9_21683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wi9_21683/02_2025/6wi9_21683.map" model { file = "/net/cci-nas-00/data/ceres_data/6wi9_21683/02_2025/6wi9_21683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wi9_21683/02_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-5592/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: 4.90, per 1000 atoms: 0.57 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: 2.03 Conformation dependent library (CDL) restraints added in 988.8 milliseconds 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: 0.91 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: 2.57 Time building geometry restraints manager: 2.37 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 21.180 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.200 ------------------------------------------------------------------------------- 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 : 1.205 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: 0.2430 time to fit residues: 102.3012 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 : 1.179 ------------------------------------------------------------------------------- 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 = 0.3677 r_free = 0.3677 target = 0.108727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.085686 restraints weight = 23710.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.088169 restraints weight = 14275.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.089853 restraints weight = 10096.213| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 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 : 0.940 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 318 TYR cc_start: 0.7936 (t80) cc_final: 0.7211 (t80) REVERT: A 374 ARG cc_start: 0.7987 (mtt90) cc_final: 0.7467 (ttt180) REVERT: B 9 GLN cc_start: 0.8934 (tp40) cc_final: 0.8647 (mm110) REVERT: B 78 LYS cc_start: 0.8836 (mmmt) cc_final: 0.8494 (mmmt) REVERT: B 188 MET cc_start: 0.8216 (tpt) cc_final: 0.7852 (mmm) REVERT: B 217 MET cc_start: 0.8712 (ppp) cc_final: 0.8166 (ppp) REVERT: B 339 TRP cc_start: 0.8840 (m100) cc_final: 0.8587 (m100) REVERT: G 41 CYS cc_start: 0.8714 (m) cc_final: 0.8508 (m) REVERT: G 59 ASN cc_start: 0.7247 (t0) cc_final: 0.6940 (t0) REVERT: N 68 PHE cc_start: 0.8232 (m-10) cc_final: 0.7812 (m-10) REVERT: R 175 ASN cc_start: 0.9118 (m-40) cc_final: 0.8698 (m-40) REVERT: R 179 MET cc_start: 0.8035 (mmm) cc_final: 0.7794 (mmm) REVERT: R 230 TYR cc_start: 0.8670 (m-80) cc_final: 0.8394 (m-10) REVERT: R 251 GLU cc_start: 0.7591 (pm20) cc_final: 0.7246 (pm20) REVERT: R 321 MET cc_start: 0.8119 (mtt) cc_final: 0.7858 (mmm) REVERT: R 342 ARG cc_start: 0.8162 (mtm180) cc_final: 0.7912 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.2246 time to fit residues: 79.5948 Evaluate side-chains 206 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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: 0.6980 chunk 104 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 101 optimal weight: 0.3980 chunk 94 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN 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 = 0.3643 r_free = 0.3643 target = 0.106725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.084187 restraints weight = 23717.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.086738 restraints weight = 14060.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.088494 restraints weight = 9748.982| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8716 Z= 0.224 Angle : 0.583 6.059 11797 Z= 0.310 Chirality : 0.042 0.212 1323 Planarity : 0.004 0.038 1516 Dihedral : 4.114 15.982 1203 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % 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: -1.48 (0.25), residues: 1086 helix: -0.02 (0.26), residues: 385 sheet: -0.84 (0.35), residues: 203 loop : -1.79 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 281 HIS 0.007 0.001 HIS B 225 PHE 0.014 0.002 PHE B 234 TYR 0.018 0.002 TYR R 138 ARG 0.004 0.000 ARG B 314 *********************** 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 248 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 TRP cc_start: 0.8589 (m100) cc_final: 0.8198 (m100) REVERT: A 374 ARG cc_start: 0.7950 (mtt90) cc_final: 0.7372 (mtt180) REVERT: B 78 LYS cc_start: 0.8872 (mmmt) cc_final: 0.8365 (mmmt) REVERT: B 188 MET cc_start: 0.8316 (tpt) cc_final: 0.8013 (mmm) REVERT: B 217 MET cc_start: 0.8604 (ppp) cc_final: 0.8160 (ppp) REVERT: B 339 TRP cc_start: 0.8960 (m100) cc_final: 0.8605 (m100) REVERT: G 41 CYS cc_start: 0.8732 (m) cc_final: 0.8411 (m) REVERT: G 59 ASN cc_start: 0.7300 (t0) cc_final: 0.6988 (t0) REVERT: N 19 ARG cc_start: 0.8159 (ttp80) cc_final: 0.7826 (ttt90) REVERT: N 64 VAL cc_start: 0.7916 (m) cc_final: 0.7464 (m) REVERT: N 72 ARG cc_start: 0.6530 (ptm-80) cc_final: 0.6113 (ptt90) REVERT: R 175 ASN cc_start: 0.9093 (m-40) cc_final: 0.8665 (m-40) REVERT: R 179 MET cc_start: 0.7979 (mmm) cc_final: 0.7691 (tpp) REVERT: R 251 GLU cc_start: 0.7319 (pm20) cc_final: 0.6425 (pp20) REVERT: R 321 MET cc_start: 0.8119 (mtt) cc_final: 0.7829 (mmm) REVERT: R 342 ARG cc_start: 0.8213 (mtm180) cc_final: 0.7888 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.2094 time to fit residues: 70.2380 Evaluate side-chains 204 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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: 4.9990 chunk 100 optimal weight: 0.0060 chunk 41 optimal weight: 0.3980 chunk 74 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 52 optimal weight: 0.3980 chunk 61 optimal weight: 10.0000 overall best weight: 1.1398 ------------------------------------------------------------------------------- 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 354 HIS ** 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 = 0.3659 r_free = 0.3659 target = 0.108035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.086215 restraints weight = 23442.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.088788 restraints weight = 13663.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.090531 restraints weight = 9352.842| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8716 Z= 0.168 Angle : 0.549 6.623 11797 Z= 0.291 Chirality : 0.041 0.162 1323 Planarity : 0.004 0.040 1516 Dihedral : 4.030 16.364 1203 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % 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: -1.09 (0.25), residues: 1086 helix: 0.33 (0.26), residues: 385 sheet: -0.58 (0.36), residues: 203 loop : -1.61 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.007 0.001 HIS B 225 PHE 0.028 0.002 PHE A 340 TYR 0.017 0.001 TYR R 138 ARG 0.007 0.000 ARG N 67 *********************** 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 253 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 ARG cc_start: 0.7873 (mtt90) cc_final: 0.7329 (mtt180) REVERT: B 15 LYS cc_start: 0.9135 (mtpt) cc_final: 0.8260 (mtpt) REVERT: B 16 ASN cc_start: 0.9320 (m110) cc_final: 0.9055 (m110) REVERT: B 217 MET cc_start: 0.8594 (ppp) cc_final: 0.8178 (ppp) REVERT: B 312 ASP cc_start: 0.7718 (p0) cc_final: 0.7451 (p0) REVERT: B 339 TRP cc_start: 0.8900 (m100) cc_final: 0.8597 (m100) REVERT: G 41 CYS cc_start: 0.8683 (m) cc_final: 0.8469 (m) REVERT: G 59 ASN cc_start: 0.7245 (t0) cc_final: 0.6954 (t0) REVERT: N 64 VAL cc_start: 0.7926 (m) cc_final: 0.7593 (m) REVERT: N 72 ARG cc_start: 0.6525 (ptm-80) cc_final: 0.6101 (ptt90) REVERT: N 76 LYS cc_start: 0.9001 (mtmm) cc_final: 0.8426 (mtmm) REVERT: N 83 MET cc_start: 0.7849 (tmm) cc_final: 0.7580 (tmm) REVERT: N 84 ASN cc_start: 0.8979 (p0) cc_final: 0.8662 (p0) REVERT: N 95 TYR cc_start: 0.8590 (m-80) cc_final: 0.8150 (m-80) REVERT: R 147 THR cc_start: 0.8838 (m) cc_final: 0.8573 (m) REVERT: R 175 ASN cc_start: 0.9003 (m-40) cc_final: 0.8552 (m-40) REVERT: R 321 MET cc_start: 0.8059 (mtt) cc_final: 0.7734 (mmm) REVERT: R 342 ARG cc_start: 0.8157 (mtm180) cc_final: 0.7810 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.2336 time to fit residues: 79.8259 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 : 1.012 ------------------------------------------------------------------------------- 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: 0.9980 chunk 48 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 259 GLN R 229 ASN ** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 392 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.105876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.083439 restraints weight = 23745.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.085966 restraints weight = 13977.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.087728 restraints weight = 9598.595| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8716 Z= 0.233 Angle : 0.592 7.741 11797 Z= 0.312 Chirality : 0.042 0.146 1323 Planarity : 0.004 0.052 1516 Dihedral : 4.229 17.593 1203 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % 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: -0.89 (0.26), residues: 1086 helix: 0.46 (0.27), residues: 389 sheet: -0.32 (0.36), residues: 199 loop : -1.54 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.008 0.001 HIS R 241 PHE 0.021 0.002 PHE A 340 TYR 0.027 0.002 TYR G 40 ARG 0.004 0.000 ARG G 13 *********************** 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 242 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 TYR cc_start: 0.7587 (t80) cc_final: 0.7369 (t80) REVERT: A 360 TYR cc_start: 0.8893 (m-80) cc_final: 0.8532 (m-80) REVERT: A 374 ARG cc_start: 0.7887 (mtt90) cc_final: 0.7356 (mtt180) REVERT: B 9 GLN cc_start: 0.8871 (tp40) cc_final: 0.8409 (mp10) REVERT: B 82 TRP cc_start: 0.8688 (m100) cc_final: 0.8445 (m100) REVERT: B 217 MET cc_start: 0.8588 (ppp) cc_final: 0.8158 (ppp) REVERT: B 222 PHE cc_start: 0.8508 (m-80) cc_final: 0.8286 (m-10) REVERT: B 312 ASP cc_start: 0.7956 (p0) cc_final: 0.7476 (p0) REVERT: B 339 TRP cc_start: 0.8978 (m100) cc_final: 0.8626 (m100) REVERT: G 59 ASN cc_start: 0.7299 (t0) cc_final: 0.6925 (t0) REVERT: N 64 VAL cc_start: 0.8021 (m) cc_final: 0.7722 (m) REVERT: N 72 ARG cc_start: 0.6413 (ptm-80) cc_final: 0.5994 (ptt90) REVERT: N 73 ASP cc_start: 0.7729 (t70) cc_final: 0.7515 (t70) REVERT: N 76 LYS cc_start: 0.9060 (mtmm) cc_final: 0.8521 (mtmm) REVERT: N 78 THR cc_start: 0.7599 (p) cc_final: 0.7366 (p) REVERT: R 147 THR cc_start: 0.8836 (m) cc_final: 0.8615 (m) REVERT: R 164 LEU cc_start: 0.8867 (mt) cc_final: 0.8442 (mt) REVERT: R 175 ASN cc_start: 0.8997 (m-40) cc_final: 0.7975 (m-40) REVERT: R 179 MET cc_start: 0.8856 (mmp) cc_final: 0.8562 (tpp) REVERT: R 282 ASP cc_start: 0.8280 (t70) cc_final: 0.8057 (t0) REVERT: R 321 MET cc_start: 0.8133 (mtt) cc_final: 0.7792 (mmm) REVERT: R 342 ARG cc_start: 0.8263 (mtm180) cc_final: 0.7868 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.2092 time to fit residues: 68.8361 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 : 0.909 ------------------------------------------------------------------------------- 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: 0.0970 chunk 67 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN B 17 GLN ** R 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 229 ASN ** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 392 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.105347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.083211 restraints weight = 23633.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.085652 restraints weight = 14189.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.087288 restraints weight = 9873.466| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8716 Z= 0.241 Angle : 0.609 11.310 11797 Z= 0.318 Chirality : 0.043 0.248 1323 Planarity : 0.004 0.048 1516 Dihedral : 4.379 17.258 1203 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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: 0.42 (0.26), residues: 390 sheet: -0.44 (0.37), residues: 203 loop : -1.43 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 281 HIS 0.008 0.001 HIS R 241 PHE 0.021 0.002 PHE A 340 TYR 0.018 0.002 TYR R 138 ARG 0.006 0.000 ARG A 342 *********************** 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 240 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 TYR cc_start: 0.8908 (m-80) cc_final: 0.8686 (m-80) REVERT: B 78 LYS cc_start: 0.8934 (mmpt) cc_final: 0.8433 (mmtm) REVERT: B 82 TRP cc_start: 0.8860 (m100) cc_final: 0.8465 (m100) REVERT: B 217 MET cc_start: 0.8625 (ppp) cc_final: 0.8257 (ppp) REVERT: B 222 PHE cc_start: 0.8466 (m-80) cc_final: 0.8209 (m-10) REVERT: B 312 ASP cc_start: 0.7787 (p0) cc_final: 0.7403 (p0) REVERT: B 339 TRP cc_start: 0.9008 (m100) cc_final: 0.8660 (m100) REVERT: G 59 ASN cc_start: 0.7258 (t0) cc_final: 0.6850 (t0) REVERT: N 72 ARG cc_start: 0.6430 (ptm-80) cc_final: 0.6062 (ptt90) REVERT: N 76 LYS cc_start: 0.9004 (mtmm) cc_final: 0.8572 (mtmm) REVERT: R 147 THR cc_start: 0.8842 (m) cc_final: 0.8567 (m) REVERT: R 150 TYR cc_start: 0.8078 (m-10) cc_final: 0.7819 (m-80) REVERT: R 164 LEU cc_start: 0.8984 (mt) cc_final: 0.8586 (mt) REVERT: R 175 ASN cc_start: 0.9050 (m-40) cc_final: 0.7998 (m-40) REVERT: R 179 MET cc_start: 0.8835 (mmp) cc_final: 0.8629 (mmt) REVERT: R 342 ARG cc_start: 0.8255 (mtm180) cc_final: 0.7855 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.2080 time to fit residues: 68.5331 Evaluate side-chains 188 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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: 4.9990 chunk 103 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 392 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.106987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.083854 restraints weight = 23907.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.086420 restraints weight = 14106.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.088184 restraints weight = 9809.807| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4004 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= 0.187 Angle : 0.602 12.029 11797 Z= 0.314 Chirality : 0.042 0.212 1323 Planarity : 0.004 0.046 1516 Dihedral : 4.355 18.030 1203 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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: -0.76 (0.26), residues: 1086 helix: 0.61 (0.27), residues: 387 sheet: -0.28 (0.36), residues: 199 loop : -1.49 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 286 HIS 0.009 0.001 HIS B 225 PHE 0.032 0.002 PHE N 68 TYR 0.016 0.002 TYR R 138 ARG 0.007 0.000 ARG A 232 *********************** 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 230 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 TYR cc_start: 0.8939 (m-80) cc_final: 0.8616 (m-80) REVERT: B 78 LYS cc_start: 0.8918 (mmpt) cc_final: 0.8434 (mmtm) REVERT: B 82 TRP cc_start: 0.8866 (m100) cc_final: 0.8416 (m100) REVERT: B 217 MET cc_start: 0.8590 (ppp) cc_final: 0.8181 (ppp) REVERT: B 222 PHE cc_start: 0.8432 (m-80) cc_final: 0.8204 (m-10) REVERT: B 312 ASP cc_start: 0.8020 (p0) cc_final: 0.7678 (p0) REVERT: B 339 TRP cc_start: 0.9009 (m100) cc_final: 0.8600 (m100) REVERT: G 59 ASN cc_start: 0.7314 (t0) cc_final: 0.7028 (t0) REVERT: N 72 ARG cc_start: 0.6341 (ptm-80) cc_final: 0.5945 (ptt90) REVERT: N 76 LYS cc_start: 0.9021 (mtmm) cc_final: 0.8580 (mtmm) REVERT: R 147 THR cc_start: 0.8844 (m) cc_final: 0.8572 (m) REVERT: R 150 TYR cc_start: 0.7932 (m-10) cc_final: 0.7690 (m-80) REVERT: R 175 ASN cc_start: 0.8988 (m-40) cc_final: 0.8628 (m-40) REVERT: R 321 MET cc_start: 0.8503 (mmm) cc_final: 0.8296 (mmm) REVERT: R 342 ARG cc_start: 0.8253 (mtm180) cc_final: 0.7783 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2026 time to fit residues: 64.1683 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 : 1.013 ------------------------------------------------------------------------------- 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: 2.9990 chunk 84 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 HIS R 229 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.105703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.083155 restraints weight = 24031.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.085687 restraints weight = 14064.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.087414 restraints weight = 9726.996| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8716 Z= 0.232 Angle : 0.632 13.285 11797 Z= 0.327 Chirality : 0.043 0.197 1323 Planarity : 0.004 0.048 1516 Dihedral : 4.461 17.732 1203 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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: -0.76 (0.26), residues: 1086 helix: 0.54 (0.26), residues: 386 sheet: -0.27 (0.37), residues: 201 loop : -1.43 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 286 HIS 0.008 0.001 HIS R 241 PHE 0.028 0.002 PHE N 68 TYR 0.017 0.002 TYR R 138 ARG 0.006 0.000 ARG A 232 *********************** 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 233 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 TYR cc_start: 0.8961 (m-80) cc_final: 0.8648 (m-80) REVERT: B 82 TRP cc_start: 0.8985 (m100) cc_final: 0.8419 (m100) REVERT: B 217 MET cc_start: 0.8629 (ppp) cc_final: 0.8184 (ppp) REVERT: B 222 PHE cc_start: 0.8398 (m-80) cc_final: 0.8179 (m-10) REVERT: B 339 TRP cc_start: 0.8992 (m100) cc_final: 0.8610 (m100) REVERT: G 59 ASN cc_start: 0.7409 (t0) cc_final: 0.6990 (t0) REVERT: N 76 LYS cc_start: 0.9034 (mtmm) cc_final: 0.8539 (mtmm) REVERT: R 147 THR cc_start: 0.8838 (m) cc_final: 0.8609 (m) REVERT: R 150 TYR cc_start: 0.7929 (m-10) cc_final: 0.7614 (m-80) REVERT: R 175 ASN cc_start: 0.8879 (m-40) cc_final: 0.8303 (m-40) REVERT: R 221 LEU cc_start: 0.9303 (tp) cc_final: 0.9092 (pp) REVERT: R 321 MET cc_start: 0.8468 (mmm) cc_final: 0.8246 (mmm) REVERT: R 342 ARG cc_start: 0.8282 (mtm180) cc_final: 0.7779 (tmt-80) REVERT: R 406 TRP cc_start: 0.7566 (t60) cc_final: 0.6378 (m100) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.1922 time to fit residues: 62.0000 Evaluate side-chains 188 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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: 3.9990 chunk 8 optimal weight: 1.9990 chunk 67 optimal weight: 0.0670 chunk 12 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 overall best weight: 0.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN N 53 GLN ** R 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 354 HIS ** 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 = 0.3667 r_free = 0.3667 target = 0.108371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.085275 restraints weight = 24053.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.087958 restraints weight = 13936.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.089778 restraints weight = 9549.117| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8716 Z= 0.170 Angle : 0.628 10.686 11797 Z= 0.321 Chirality : 0.043 0.236 1323 Planarity : 0.004 0.048 1516 Dihedral : 4.311 18.822 1203 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.11 % Allowed : 0.57 % 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: -0.72 (0.26), residues: 1086 helix: 0.54 (0.26), residues: 393 sheet: -0.23 (0.37), residues: 202 loop : -1.41 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 211 HIS 0.004 0.001 HIS G 44 PHE 0.038 0.002 PHE N 68 TYR 0.015 0.001 TYR R 138 ARG 0.006 0.000 ARG A 232 *********************** 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: 1 poor density : 241 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 TYR cc_start: 0.8966 (m-80) cc_final: 0.8658 (m-80) REVERT: A 374 ARG cc_start: 0.7751 (mtt90) cc_final: 0.7466 (mtt180) REVERT: B 9 GLN cc_start: 0.8867 (tp40) cc_final: 0.8426 (mp10) REVERT: B 15 LYS cc_start: 0.9292 (mtmt) cc_final: 0.8352 (mtpt) REVERT: B 16 ASN cc_start: 0.9336 (m110) cc_final: 0.9098 (m110) REVERT: B 78 LYS cc_start: 0.8966 (mmpt) cc_final: 0.8612 (mmmt) REVERT: B 82 TRP cc_start: 0.8920 (m100) cc_final: 0.8424 (m100) REVERT: B 217 MET cc_start: 0.8402 (ppp) cc_final: 0.8155 (ppp) REVERT: B 222 PHE cc_start: 0.8397 (m-80) cc_final: 0.8192 (m-10) REVERT: B 339 TRP cc_start: 0.8931 (m100) cc_final: 0.8613 (m100) REVERT: G 59 ASN cc_start: 0.7207 (t0) cc_final: 0.6970 (t0) REVERT: N 76 LYS cc_start: 0.8958 (mtmm) cc_final: 0.8518 (mtmm) REVERT: N 81 LEU cc_start: 0.7585 (tt) cc_final: 0.7216 (tp) REVERT: R 150 TYR cc_start: 0.7798 (m-10) cc_final: 0.7519 (m-80) REVERT: R 175 ASN cc_start: 0.8818 (m-40) cc_final: 0.8539 (m-40) REVERT: R 342 ARG cc_start: 0.8149 (mtm180) cc_final: 0.7721 (tmt-80) REVERT: R 406 TRP cc_start: 0.7510 (t60) cc_final: 0.6317 (m100) outliers start: 1 outliers final: 0 residues processed: 242 average time/residue: 0.2036 time to fit residues: 67.3651 Evaluate side-chains 190 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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: 1.9990 chunk 42 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 57 optimal weight: 0.2980 chunk 51 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.106800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.083779 restraints weight = 24018.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.086205 restraints weight = 14333.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.087888 restraints weight = 10042.650| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8716 Z= 0.249 Angle : 0.673 11.194 11797 Z= 0.348 Chirality : 0.044 0.185 1323 Planarity : 0.004 0.071 1516 Dihedral : 4.519 20.814 1203 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.88 (0.26), residues: 1086 helix: 0.40 (0.26), residues: 393 sheet: -0.22 (0.37), residues: 199 loop : -1.54 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.008 0.001 HIS R 241 PHE 0.033 0.002 PHE N 68 TYR 0.018 0.002 TYR R 230 ARG 0.007 0.000 ARG B 314 ********************** 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 221 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 TYR cc_start: 0.9015 (m-80) cc_final: 0.8762 (m-80) REVERT: A 374 ARG cc_start: 0.7872 (mtt90) cc_final: 0.7585 (mtt180) REVERT: B 78 LYS cc_start: 0.8950 (mmpt) cc_final: 0.8164 (mmmt) REVERT: B 82 TRP cc_start: 0.9020 (m100) cc_final: 0.8480 (m100) REVERT: B 217 MET cc_start: 0.8619 (ppp) cc_final: 0.8265 (ppp) REVERT: B 339 TRP cc_start: 0.8981 (m100) cc_final: 0.8645 (m100) REVERT: G 59 ASN cc_start: 0.7362 (t0) cc_final: 0.6994 (t0) REVERT: N 76 LYS cc_start: 0.9033 (mtmm) cc_final: 0.8581 (mtmm) REVERT: N 80 TYR cc_start: 0.7307 (m-80) cc_final: 0.7099 (m-80) REVERT: N 81 LEU cc_start: 0.7080 (tt) cc_final: 0.6862 (tp) REVERT: R 147 THR cc_start: 0.8817 (m) cc_final: 0.8607 (m) REVERT: R 150 TYR cc_start: 0.7922 (m-10) cc_final: 0.7686 (m-80) REVERT: R 175 ASN cc_start: 0.8938 (m-40) cc_final: 0.8635 (m-40) REVERT: R 251 GLU cc_start: 0.7428 (pm20) cc_final: 0.6400 (pp20) REVERT: R 342 ARG cc_start: 0.8247 (mtm180) cc_final: 0.7723 (tmt-80) REVERT: R 406 TRP cc_start: 0.7537 (t60) cc_final: 0.6306 (m100) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.2033 time to fit residues: 61.8578 Evaluate side-chains 180 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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: 0.3980 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 0.2980 chunk 51 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 chunk 84 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS ** R 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 354 HIS ** 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 = 0.3669 r_free = 0.3669 target = 0.108953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.085672 restraints weight = 24244.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.088184 restraints weight = 14657.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.089865 restraints weight = 10293.160| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8716 Z= 0.188 Angle : 0.623 9.365 11797 Z= 0.320 Chirality : 0.042 0.179 1323 Planarity : 0.004 0.061 1516 Dihedral : 4.425 19.851 1203 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.11 % Allowed : 0.69 % Favored : 99.20 % 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: -0.79 (0.26), residues: 1086 helix: 0.56 (0.26), residues: 393 sheet: -0.24 (0.36), residues: 199 loop : -1.53 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 281 HIS 0.005 0.001 HIS R 241 PHE 0.039 0.002 PHE N 68 TYR 0.014 0.001 TYR R 138 ARG 0.006 0.000 ARG A 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2957.71 seconds wall clock time: 53 minutes 47.14 seconds (3227.14 seconds total)