Starting phenix.real_space_refine on Thu Jan 16 00:33:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yn9_39419/01_2025/8yn9_39419.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yn9_39419/01_2025/8yn9_39419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yn9_39419/01_2025/8yn9_39419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yn9_39419/01_2025/8yn9_39419.map" model { file = "/net/cci-nas-00/data/ceres_data/8yn9_39419/01_2025/8yn9_39419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yn9_39419/01_2025/8yn9_39419.cif" } resolution = 2.3 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= 0.014 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 58 5.16 5 C 5853 2.51 5 N 1490 2.21 5 O 1647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 9048 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1770 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 6} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1779 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 2235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2235 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 266} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 6} Unresolved non-hydrogen planarities: 24 Chain: "R" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 206 Unusual residues: {'CLR': 7, 'HSM': 1} Classifications: {'undetermined': 8, 'water': 2} Link IDs: {None: 9} Time building chain proxies: 5.47, per 1000 atoms: 0.60 Number of scatterers: 9048 At special positions: 0 Unit cell: (100.58, 118.77, 111.28, 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 58 16.00 O 1647 8.00 N 1490 7.00 C 5853 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 87 " - pdb=" SG CYS R 164 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 2.40 Conformation dependent library (CDL) restraints added in 999.6 milliseconds 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 14 sheets defined 39.1% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.539A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.374A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.746A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.625A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.525A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'R' and resid 12 through 43 removed outlier: 4.019A pdb=" N VAL R 36 " --> pdb=" O GLY R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 63 Processing helix chain 'R' and resid 67 through 78 Proline residue: R 74 - end of helix Processing helix chain 'R' and resid 83 through 118 removed outlier: 3.731A pdb=" N VAL R 88 " --> pdb=" O LYS R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 125 Processing helix chain 'R' and resid 128 through 155 removed outlier: 3.531A pdb=" N TRP R 140 " --> pdb=" O MET R 136 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN R 147 " --> pdb=" O ALA R 143 " (cutoff:3.500A) Proline residue: R 149 - end of helix Processing helix chain 'R' and resid 156 through 158 No H-bonds generated for 'chain 'R' and resid 156 through 158' Processing helix chain 'R' and resid 166 through 170 removed outlier: 3.772A pdb=" N SER R 170 " --> pdb=" O GLY R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 183 removed outlier: 3.564A pdb=" N LEU R 175 " --> pdb=" O GLU R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 200 Processing helix chain 'R' and resid 292 through 329 removed outlier: 3.518A pdb=" N PHE R 312 " --> pdb=" O LEU R 308 " (cutoff:3.500A) Proline residue: R 318 - end of helix removed outlier: 3.856A pdb=" N ILE R 324 " --> pdb=" O SER R 320 " (cutoff:3.500A) Processing helix chain 'R' and resid 337 through 358 removed outlier: 3.594A pdb=" N GLN R 347 " --> pdb=" O ALA R 343 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TRP R 348 " --> pdb=" O PHE R 344 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN R 350 " --> pdb=" O LEU R 346 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER R 351 " --> pdb=" O GLN R 347 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE R 352 " --> pdb=" O TRP R 348 " (cutoff:3.500A) Proline residue: R 355 - end of helix Processing helix chain 'R' and resid 362 through 374 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.226A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.573A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.737A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.986A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.090A 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: 6.261A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.651A 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: 6.784A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.514A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.604A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 5.936A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.352A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.499A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.015A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) 474 hydrogen bonds defined for protein. 1314 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: 2.83 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2829 1.34 - 1.46: 2014 1.46 - 1.58: 4341 1.58 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 9268 Sorted by residual: bond pdb=" CG HSM R 701 " pdb=" ND1 HSM R 701 " ideal model delta sigma weight residual 1.383 1.336 0.047 2.00e-02 2.50e+03 5.63e+00 bond pdb=" C5 CLR R 703 " pdb=" C6 CLR R 703 " ideal model delta sigma weight residual 1.332 1.297 0.035 2.00e-02 2.50e+03 3.08e+00 bond pdb=" C5 CLR R 704 " pdb=" C6 CLR R 704 " ideal model delta sigma weight residual 1.332 1.298 0.034 2.00e-02 2.50e+03 2.93e+00 bond pdb=" C5 CLR R 705 " pdb=" C6 CLR R 705 " ideal model delta sigma weight residual 1.332 1.298 0.034 2.00e-02 2.50e+03 2.85e+00 bond pdb=" C5 CLR R 707 " pdb=" C6 CLR R 707 " ideal model delta sigma weight residual 1.332 1.298 0.034 2.00e-02 2.50e+03 2.82e+00 ... (remaining 9263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 12320 1.78 - 3.57: 220 3.57 - 5.35: 54 5.35 - 7.13: 13 7.13 - 8.92: 4 Bond angle restraints: 12611 Sorted by residual: angle pdb=" C13 CLR R 702 " pdb=" C17 CLR R 702 " pdb=" C20 CLR R 702 " ideal model delta sigma weight residual 119.60 110.68 8.92 3.00e+00 1.11e-01 8.84e+00 angle pdb=" C13 CLR R 707 " pdb=" C17 CLR R 707 " pdb=" C20 CLR R 707 " ideal model delta sigma weight residual 119.60 111.81 7.79 3.00e+00 1.11e-01 6.74e+00 angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 126.49 -4.95 1.91e+00 2.74e-01 6.71e+00 angle pdb=" C13 CLR R 705 " pdb=" C17 CLR R 705 " pdb=" C20 CLR R 705 " ideal model delta sigma weight residual 119.60 111.90 7.70 3.00e+00 1.11e-01 6.59e+00 angle pdb=" C13 CLR R 703 " pdb=" C17 CLR R 703 " pdb=" C20 CLR R 703 " ideal model delta sigma weight residual 119.60 112.03 7.57 3.00e+00 1.11e-01 6.36e+00 ... (remaining 12606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 5479 16.92 - 33.85: 210 33.85 - 50.77: 63 50.77 - 67.70: 15 67.70 - 84.62: 3 Dihedral angle restraints: 5770 sinusoidal: 2485 harmonic: 3285 Sorted by residual: dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 158.36 21.64 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA TRP B 339 " pdb=" C TRP B 339 " pdb=" N ASN B 340 " pdb=" CA ASN B 340 " ideal model delta harmonic sigma weight residual 180.00 160.74 19.26 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 161.18 18.82 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 5767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1340 0.098 - 0.195: 82 0.195 - 0.293: 7 0.293 - 0.390: 7 0.390 - 0.487: 7 Chirality restraints: 1443 Sorted by residual: chirality pdb=" C14 CLR R 702 " pdb=" C13 CLR R 702 " pdb=" C15 CLR R 702 " pdb=" C8 CLR R 702 " both_signs ideal model delta sigma weight residual False -2.32 -2.80 0.49 2.00e-01 2.50e+01 5.94e+00 chirality pdb=" C14 CLR R 705 " pdb=" C13 CLR R 705 " pdb=" C15 CLR R 705 " pdb=" C8 CLR R 705 " both_signs ideal model delta sigma weight residual False -2.32 -2.78 0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" C14 CLR R 707 " pdb=" C13 CLR R 707 " pdb=" C15 CLR R 707 " pdb=" C8 CLR R 707 " both_signs ideal model delta sigma weight residual False -2.32 -2.78 0.46 2.00e-01 2.50e+01 5.39e+00 ... (remaining 1440 not shown) Planarity restraints: 1543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.030 5.00e-02 4.00e+02 4.46e-02 3.19e+00 pdb=" N PRO B 236 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.32e+00 pdb=" N PRO B 194 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 106 " -0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO B 107 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 107 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 107 " -0.015 5.00e-02 4.00e+02 ... (remaining 1540 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1622 2.77 - 3.30: 8501 3.30 - 3.83: 15452 3.83 - 4.37: 19349 4.37 - 4.90: 32359 Nonbonded interactions: 77283 Sorted by model distance: nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.237 3.040 nonbonded pdb=" OE1 GLN A 52 " pdb=" ND2 ASN A 331 " model vdw 2.257 3.120 nonbonded pdb=" OH TYR A 230 " pdb=" O SER A 281 " model vdw 2.273 3.040 nonbonded pdb=" OD1 ASN A 269 " pdb=" OG1 THR A 324 " model vdw 2.291 3.040 nonbonded pdb=" O ALA R 332 " pdb=" NZ LYS R 336 " model vdw 2.317 3.120 ... (remaining 77278 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.910 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9268 Z= 0.232 Angle : 0.627 8.918 12611 Z= 0.279 Chirality : 0.062 0.487 1443 Planarity : 0.003 0.045 1543 Dihedral : 10.628 84.622 3641 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.73 % Allowed : 3.03 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.24), residues: 1114 helix: 1.37 (0.24), residues: 415 sheet: 0.84 (0.29), residues: 293 loop : 0.17 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 339 HIS 0.003 0.001 HIS B 142 PHE 0.014 0.001 PHE B 151 TYR 0.012 0.001 TYR E 190 ARG 0.003 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 162 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8385 (mttt) cc_final: 0.8025 (mppt) REVERT: A 261 ASP cc_start: 0.7774 (m-30) cc_final: 0.7523 (m-30) REVERT: B 79 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8952 (mt) REVERT: B 137 ARG cc_start: 0.8245 (mmt-90) cc_final: 0.8012 (tpt90) REVERT: C 21 MET cc_start: 0.8182 (mmm) cc_final: 0.7739 (mpp) REVERT: R 20 PHE cc_start: 0.8190 (t80) cc_final: 0.7744 (t80) REVERT: R 24 LEU cc_start: 0.8775 (tp) cc_final: 0.8451 (mm) REVERT: R 50 SER cc_start: 0.8879 (m) cc_final: 0.8581 (p) outliers start: 7 outliers final: 2 residues processed: 169 average time/residue: 1.4082 time to fit residues: 252.4241 Evaluate side-chains 134 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 131 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 275 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 176 GLN B 259 GLN B 266 HIS E 171 ASN E 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.146026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.101437 restraints weight = 9797.295| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.86 r_work: 0.3015 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9268 Z= 0.302 Angle : 0.593 6.796 12611 Z= 0.320 Chirality : 0.045 0.187 1443 Planarity : 0.004 0.045 1543 Dihedral : 7.371 59.708 1683 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.51 % Allowed : 8.26 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.25), residues: 1114 helix: 2.00 (0.25), residues: 419 sheet: 0.72 (0.29), residues: 297 loop : 0.15 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.004 0.001 HIS C 44 PHE 0.017 0.002 PHE A 215 TYR 0.017 0.002 TYR R 358 ARG 0.007 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.959 Fit side-chains REVERT: A 35 LYS cc_start: 0.8515 (mttt) cc_final: 0.7980 (mppt) REVERT: A 275 GLU cc_start: 0.7717 (pt0) cc_final: 0.7269 (pp20) REVERT: A 276 GLU cc_start: 0.8531 (mt-10) cc_final: 0.7992 (mt-10) REVERT: A 328 ASP cc_start: 0.7353 (m-30) cc_final: 0.6951 (m-30) REVERT: B 23 LYS cc_start: 0.8407 (ttmm) cc_final: 0.7693 (tptt) REVERT: C 21 MET cc_start: 0.8331 (mmm) cc_final: 0.7163 (ttp) REVERT: C 42 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: R 20 PHE cc_start: 0.8223 (t80) cc_final: 0.7935 (t80) REVERT: R 50 SER cc_start: 0.8823 (m) cc_final: 0.8465 (p) REVERT: R 342 ILE cc_start: 0.8636 (mm) cc_final: 0.8409 (mm) REVERT: R 347 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8469 (tt0) outliers start: 24 outliers final: 11 residues processed: 148 average time/residue: 1.4351 time to fit residues: 225.2084 Evaluate side-chains 136 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain R residue 82 PHE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 320 SER Chi-restraints excluded: chain R residue 347 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 88 optimal weight: 3.9990 chunk 7 optimal weight: 0.0170 chunk 63 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 overall best weight: 2.5224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 259 GLN B 266 HIS E 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.149474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.110578 restraints weight = 9912.834| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.88 r_work: 0.3151 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9268 Z= 0.332 Angle : 0.594 6.158 12611 Z= 0.321 Chirality : 0.045 0.187 1443 Planarity : 0.004 0.047 1543 Dihedral : 6.980 57.292 1679 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.30 % Allowed : 9.73 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.25), residues: 1114 helix: 2.07 (0.25), residues: 414 sheet: 0.63 (0.29), residues: 293 loop : -0.07 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.005 0.001 HIS C 44 PHE 0.018 0.002 PHE B 151 TYR 0.019 0.002 TYR R 358 ARG 0.007 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 1.011 Fit side-chains REVERT: A 35 LYS cc_start: 0.8562 (mttt) cc_final: 0.8167 (mppt) REVERT: A 275 GLU cc_start: 0.7684 (pt0) cc_final: 0.7246 (pp20) REVERT: A 276 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7921 (mt-10) REVERT: A 328 ASP cc_start: 0.7376 (m-30) cc_final: 0.7038 (m-30) REVERT: A 330 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7887 (mtmt) REVERT: B 23 LYS cc_start: 0.8477 (ttmm) cc_final: 0.7804 (tptt) REVERT: C 21 MET cc_start: 0.8328 (mmm) cc_final: 0.7143 (ttp) REVERT: C 42 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: C 62 ARG cc_start: 0.6683 (mtt90) cc_final: 0.6328 (mtt90) REVERT: R 50 SER cc_start: 0.8964 (m) cc_final: 0.8645 (p) REVERT: R 347 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8515 (tt0) outliers start: 22 outliers final: 15 residues processed: 142 average time/residue: 1.4540 time to fit residues: 218.6837 Evaluate side-chains 139 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain R residue 82 PHE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 320 SER Chi-restraints excluded: chain R residue 347 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 16 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 266 HIS E 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.151636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.110267 restraints weight = 9964.486| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.76 r_work: 0.3197 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9268 Z= 0.162 Angle : 0.493 5.501 12611 Z= 0.267 Chirality : 0.041 0.172 1443 Planarity : 0.004 0.045 1543 Dihedral : 6.534 55.977 1679 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.88 % Allowed : 10.77 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.25), residues: 1114 helix: 2.37 (0.25), residues: 413 sheet: 0.61 (0.29), residues: 285 loop : -0.08 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.012 0.001 PHE B 151 TYR 0.014 0.001 TYR E 190 ARG 0.008 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8477 (mttt) cc_final: 0.8127 (mppt) REVERT: A 275 GLU cc_start: 0.7872 (pt0) cc_final: 0.7461 (pp20) REVERT: A 276 GLU cc_start: 0.8420 (mt-10) cc_final: 0.7842 (mt-10) REVERT: A 328 ASP cc_start: 0.7351 (m-30) cc_final: 0.7013 (m-30) REVERT: B 23 LYS cc_start: 0.8477 (ttmm) cc_final: 0.7773 (tptt) REVERT: B 266 HIS cc_start: 0.8223 (t-90) cc_final: 0.8019 (t-170) REVERT: C 21 MET cc_start: 0.8309 (mmm) cc_final: 0.7153 (ttp) REVERT: E 18 ARG cc_start: 0.8161 (tpt170) cc_final: 0.7922 (tpt170) REVERT: R 50 SER cc_start: 0.8786 (m) cc_final: 0.8509 (p) REVERT: R 165 GLU cc_start: 0.8647 (pt0) cc_final: 0.7863 (pp20) REVERT: R 342 ILE cc_start: 0.8651 (mm) cc_final: 0.8449 (mm) outliers start: 18 outliers final: 10 residues processed: 141 average time/residue: 1.4722 time to fit residues: 219.4516 Evaluate side-chains 134 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain R residue 82 PHE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 320 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 105 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 chunk 13 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 155 ASN B 259 GLN E 186 GLN R 362 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.151723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.110220 restraints weight = 9819.896| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.75 r_work: 0.3193 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9268 Z= 0.171 Angle : 0.495 5.646 12611 Z= 0.267 Chirality : 0.041 0.172 1443 Planarity : 0.004 0.045 1543 Dihedral : 6.462 57.238 1678 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.09 % Allowed : 10.88 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.25), residues: 1114 helix: 2.46 (0.25), residues: 413 sheet: 0.57 (0.29), residues: 282 loop : -0.11 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS C 44 PHE 0.013 0.001 PHE B 151 TYR 0.013 0.001 TYR E 190 ARG 0.008 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.998 Fit side-chains REVERT: A 35 LYS cc_start: 0.8491 (mttt) cc_final: 0.8131 (mppt) REVERT: A 275 GLU cc_start: 0.7861 (pt0) cc_final: 0.7425 (pp20) REVERT: A 276 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7868 (mt-10) REVERT: A 328 ASP cc_start: 0.7348 (m-30) cc_final: 0.6983 (m-30) REVERT: B 23 LYS cc_start: 0.8440 (ttmm) cc_final: 0.7735 (tptt) REVERT: B 172 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7797 (pt0) REVERT: C 21 MET cc_start: 0.8293 (mmm) cc_final: 0.7124 (ttp) REVERT: E 160 ARG cc_start: 0.8314 (mtm-85) cc_final: 0.7994 (ttp-110) REVERT: R 50 SER cc_start: 0.8822 (m) cc_final: 0.8528 (p) REVERT: R 165 GLU cc_start: 0.8655 (pt0) cc_final: 0.7827 (pp20) outliers start: 20 outliers final: 13 residues processed: 137 average time/residue: 1.5301 time to fit residues: 222.2523 Evaluate side-chains 133 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 82 PHE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 320 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 43 optimal weight: 1.9990 chunk 103 optimal weight: 0.0470 chunk 53 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 259 GLN E 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.153582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.111190 restraints weight = 9784.617| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.79 r_work: 0.3216 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9268 Z= 0.142 Angle : 0.472 5.581 12611 Z= 0.255 Chirality : 0.040 0.171 1443 Planarity : 0.003 0.044 1543 Dihedral : 6.332 59.127 1678 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.67 % Allowed : 12.24 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.25), residues: 1114 helix: 2.56 (0.25), residues: 413 sheet: 0.55 (0.29), residues: 270 loop : -0.05 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS C 44 PHE 0.011 0.001 PHE B 151 TYR 0.013 0.001 TYR E 190 ARG 0.009 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.971 Fit side-chains REVERT: A 35 LYS cc_start: 0.8472 (mttt) cc_final: 0.8125 (mppt) REVERT: A 275 GLU cc_start: 0.7871 (pt0) cc_final: 0.7443 (pp20) REVERT: A 276 GLU cc_start: 0.8410 (mt-10) cc_final: 0.7875 (mt-10) REVERT: A 328 ASP cc_start: 0.7372 (m-30) cc_final: 0.6978 (m-30) REVERT: B 23 LYS cc_start: 0.8444 (ttmm) cc_final: 0.7741 (tptt) REVERT: B 172 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7757 (tp30) REVERT: B 219 ARG cc_start: 0.8177 (mtt-85) cc_final: 0.7870 (mmt-90) REVERT: C 21 MET cc_start: 0.8306 (mmm) cc_final: 0.7139 (ttp) REVERT: E 160 ARG cc_start: 0.8279 (mtm-85) cc_final: 0.7967 (ttp-110) REVERT: E 194 ASN cc_start: 0.8859 (m-40) cc_final: 0.8501 (m110) REVERT: R 24 LEU cc_start: 0.8834 (tp) cc_final: 0.8363 (mm) REVERT: R 50 SER cc_start: 0.8770 (m) cc_final: 0.8512 (p) REVERT: R 165 GLU cc_start: 0.8611 (pt0) cc_final: 0.7827 (pp20) outliers start: 16 outliers final: 12 residues processed: 141 average time/residue: 1.4541 time to fit residues: 217.0840 Evaluate side-chains 137 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 82 PHE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 320 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 107 optimal weight: 0.0020 chunk 61 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 6 optimal weight: 0.0060 chunk 47 optimal weight: 0.4980 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 322 HIS B 259 GLN E 171 ASN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.154561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.112365 restraints weight = 9917.228| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.80 r_work: 0.3232 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9268 Z= 0.127 Angle : 0.464 5.680 12611 Z= 0.250 Chirality : 0.040 0.171 1443 Planarity : 0.003 0.042 1543 Dihedral : 6.217 59.316 1678 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.20 % Allowed : 12.03 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.25), residues: 1114 helix: 2.62 (0.25), residues: 414 sheet: 0.54 (0.29), residues: 270 loop : -0.05 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.011 0.001 PHE R 328 TYR 0.013 0.001 TYR R 173 ARG 0.010 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8449 (mttt) cc_final: 0.8107 (mppt) REVERT: A 275 GLU cc_start: 0.7857 (pt0) cc_final: 0.7419 (pp20) REVERT: A 276 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7849 (mt-10) REVERT: A 330 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7835 (mtmt) REVERT: B 23 LYS cc_start: 0.8432 (ttmm) cc_final: 0.7741 (tptt) REVERT: B 172 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7731 (tp30) REVERT: C 21 MET cc_start: 0.8293 (mmm) cc_final: 0.7129 (ttp) REVERT: E 160 ARG cc_start: 0.8278 (mtm-85) cc_final: 0.7981 (ttp-110) REVERT: E 194 ASN cc_start: 0.8822 (m-40) cc_final: 0.8463 (m110) REVERT: R 50 SER cc_start: 0.8749 (m) cc_final: 0.8513 (p) REVERT: R 165 GLU cc_start: 0.8612 (pt0) cc_final: 0.7838 (pp20) outliers start: 21 outliers final: 12 residues processed: 139 average time/residue: 1.4694 time to fit residues: 216.0238 Evaluate side-chains 139 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 82 PHE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 320 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 48 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 322 HIS B 259 GLN E 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.151591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.110035 restraints weight = 10113.768| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.77 r_work: 0.3193 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9268 Z= 0.199 Angle : 0.504 5.652 12611 Z= 0.271 Chirality : 0.042 0.175 1443 Planarity : 0.004 0.044 1543 Dihedral : 6.271 56.730 1678 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.09 % Allowed : 12.45 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.25), residues: 1114 helix: 2.55 (0.25), residues: 414 sheet: 0.48 (0.28), residues: 277 loop : -0.01 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.001 PHE A 215 TYR 0.013 0.001 TYR R 358 ARG 0.009 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8486 (mttt) cc_final: 0.8125 (mppt) REVERT: A 275 GLU cc_start: 0.7881 (pt0) cc_final: 0.7397 (pp20) REVERT: A 276 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7797 (mt-10) REVERT: A 330 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7842 (mtmt) REVERT: B 23 LYS cc_start: 0.8403 (ttmm) cc_final: 0.7742 (tptt) REVERT: B 172 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7834 (tp30) REVERT: B 219 ARG cc_start: 0.8173 (mtt-85) cc_final: 0.7854 (mmt-90) REVERT: C 21 MET cc_start: 0.8225 (mmm) cc_final: 0.7093 (ttp) REVERT: E 160 ARG cc_start: 0.8292 (mtm-85) cc_final: 0.7972 (ttp-110) REVERT: R 50 SER cc_start: 0.8863 (m) cc_final: 0.8548 (p) REVERT: R 165 GLU cc_start: 0.8633 (pt0) cc_final: 0.7770 (pp20) outliers start: 20 outliers final: 14 residues processed: 136 average time/residue: 1.4910 time to fit residues: 214.6681 Evaluate side-chains 138 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 82 PHE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 320 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 89 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 43 optimal weight: 0.0060 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 90 optimal weight: 0.0670 chunk 23 optimal weight: 1.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 322 HIS B 259 GLN E 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.153098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.111796 restraints weight = 9868.628| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.76 r_work: 0.3214 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9268 Z= 0.150 Angle : 0.485 5.611 12611 Z= 0.260 Chirality : 0.041 0.173 1443 Planarity : 0.004 0.043 1543 Dihedral : 6.124 56.274 1678 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.88 % Allowed : 12.87 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.25), residues: 1114 helix: 2.59 (0.25), residues: 414 sheet: 0.51 (0.29), residues: 270 loop : -0.03 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS C 44 PHE 0.011 0.001 PHE R 328 TYR 0.015 0.001 TYR R 173 ARG 0.009 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8475 (mttt) cc_final: 0.8116 (mppt) REVERT: A 275 GLU cc_start: 0.7888 (pt0) cc_final: 0.7401 (pp20) REVERT: A 276 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7799 (mt-10) REVERT: A 330 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7839 (mtmt) REVERT: B 23 LYS cc_start: 0.8432 (ttmm) cc_final: 0.7749 (tptt) REVERT: B 172 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7814 (tp30) REVERT: B 219 ARG cc_start: 0.8218 (mtt-85) cc_final: 0.7896 (mmt-90) REVERT: C 21 MET cc_start: 0.8214 (mmm) cc_final: 0.7090 (ttp) REVERT: E 160 ARG cc_start: 0.8278 (mtm-85) cc_final: 0.7958 (ttp-110) REVERT: E 194 ASN cc_start: 0.8851 (m-40) cc_final: 0.8496 (m110) REVERT: R 50 SER cc_start: 0.8814 (m) cc_final: 0.8540 (p) REVERT: R 165 GLU cc_start: 0.8600 (pt0) cc_final: 0.7719 (pp20) outliers start: 18 outliers final: 12 residues processed: 141 average time/residue: 1.4481 time to fit residues: 216.4591 Evaluate side-chains 141 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 82 PHE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 320 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 29 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 74 optimal weight: 0.0970 chunk 46 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN E 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.153732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.111583 restraints weight = 9949.734| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.80 r_work: 0.3216 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9268 Z= 0.149 Angle : 0.482 5.648 12611 Z= 0.259 Chirality : 0.041 0.173 1443 Planarity : 0.003 0.043 1543 Dihedral : 5.942 56.766 1678 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.78 % Allowed : 12.97 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.25), residues: 1114 helix: 2.61 (0.25), residues: 414 sheet: 0.53 (0.29), residues: 270 loop : -0.02 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS C 44 PHE 0.011 0.001 PHE B 151 TYR 0.014 0.001 TYR R 173 ARG 0.009 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8466 (mttt) cc_final: 0.8107 (mppt) REVERT: A 275 GLU cc_start: 0.7931 (pt0) cc_final: 0.7417 (pp20) REVERT: A 276 GLU cc_start: 0.8411 (mt-10) cc_final: 0.7870 (mt-10) REVERT: A 330 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7846 (mtmt) REVERT: B 23 LYS cc_start: 0.8440 (ttmm) cc_final: 0.7755 (tptt) REVERT: B 172 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7856 (tp30) REVERT: B 219 ARG cc_start: 0.8259 (mtt-85) cc_final: 0.7914 (mmt-90) REVERT: B 254 ASP cc_start: 0.8407 (t70) cc_final: 0.8087 (t70) REVERT: B 325 MET cc_start: 0.9208 (mmt) cc_final: 0.8887 (tpp) REVERT: C 21 MET cc_start: 0.8218 (mmm) cc_final: 0.7091 (ttp) REVERT: E 160 ARG cc_start: 0.8289 (mtm-85) cc_final: 0.7971 (ttp-110) REVERT: E 194 ASN cc_start: 0.8846 (m-40) cc_final: 0.8496 (m110) REVERT: R 50 SER cc_start: 0.8787 (m) cc_final: 0.8511 (p) outliers start: 17 outliers final: 13 residues processed: 140 average time/residue: 1.4138 time to fit residues: 210.0960 Evaluate side-chains 143 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 82 PHE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 320 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 8 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 36 optimal weight: 0.1980 chunk 85 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 7 optimal weight: 0.0470 chunk 72 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 259 GLN E 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.154945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.112708 restraints weight = 9891.505| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.79 r_work: 0.3235 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9268 Z= 0.132 Angle : 0.468 5.617 12611 Z= 0.250 Chirality : 0.040 0.172 1443 Planarity : 0.003 0.042 1543 Dihedral : 5.773 57.203 1678 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.57 % Allowed : 12.87 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.25), residues: 1114 helix: 2.66 (0.25), residues: 414 sheet: 0.52 (0.29), residues: 270 loop : 0.02 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.011 0.001 PHE R 328 TYR 0.014 0.001 TYR R 173 ARG 0.009 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9229.88 seconds wall clock time: 163 minutes 0.59 seconds (9780.59 seconds total)