Starting phenix.real_space_refine on Thu Mar 13 12:49:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yn9_39419/03_2025/8yn9_39419.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yn9_39419/03_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_39419/03_2025/8yn9_39419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yn9_39419/03_2025/8yn9_39419.map" model { file = "/net/cci-nas-00/data/ceres_data/8yn9_39419/03_2025/8yn9_39419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yn9_39419/03_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-5624/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: 5.70, per 1000 atoms: 0.63 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: 2.54 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.08 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: 2.80 Time building geometry restraints manager: 2.91 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: 0.010 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.020 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.740 ------------------------------------------------------------------------------- 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 : 0.937 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: 1.4596 time to fit residues: 261.1587 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 : 0.965 ------------------------------------------------------------------------------- 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: 1.9990 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: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.145738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.100913 restraints weight = 9786.812| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.88 r_work: 0.3009 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9268 Z= 0.322 Angle : 0.604 6.888 12611 Z= 0.326 Chirality : 0.045 0.187 1443 Planarity : 0.004 0.045 1543 Dihedral : 7.418 59.506 1683 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.62 % Allowed : 8.16 % 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: 1.44 (0.25), residues: 1114 helix: 1.98 (0.25), residues: 419 sheet: 0.72 (0.29), residues: 297 loop : 0.14 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS C 44 PHE 0.018 0.002 PHE A 215 TYR 0.018 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 159 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.901 Fit side-chains REVERT: A 35 LYS cc_start: 0.8512 (mttt) cc_final: 0.7963 (mppt) REVERT: A 275 GLU cc_start: 0.7745 (pt0) cc_final: 0.7307 (pp20) REVERT: A 276 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8045 (mt-10) REVERT: A 328 ASP cc_start: 0.7349 (m-30) cc_final: 0.6945 (m-30) REVERT: B 23 LYS cc_start: 0.8440 (ttmm) cc_final: 0.7731 (tptt) REVERT: C 21 MET cc_start: 0.8326 (mmm) cc_final: 0.7145 (ttp) REVERT: C 42 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: R 20 PHE cc_start: 0.8210 (t80) cc_final: 0.7919 (t80) REVERT: R 50 SER cc_start: 0.8827 (m) cc_final: 0.8459 (p) REVERT: R 297 ARG cc_start: 0.7996 (ttp-110) cc_final: 0.7679 (ttp80) REVERT: R 342 ILE cc_start: 0.8628 (mm) cc_final: 0.8397 (mm) REVERT: R 347 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8465 (tt0) outliers start: 25 outliers final: 12 residues processed: 149 average time/residue: 1.3954 time to fit residues: 220.2387 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 : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 270 ILE 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: 7.9990 chunk 63 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.149588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.107653 restraints weight = 9973.011| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.76 r_work: 0.3157 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9268 Z= 0.277 Angle : 0.565 5.779 12611 Z= 0.305 Chirality : 0.044 0.177 1443 Planarity : 0.004 0.046 1543 Dihedral : 6.906 57.355 1679 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.88 % Allowed : 9.73 % Favored : 88.39 % 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: 1.40 (0.25), residues: 1114 helix: 2.16 (0.25), residues: 414 sheet: 0.63 (0.29), residues: 293 loop : -0.06 (0.31), residues: 407 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 B 151 TYR 0.017 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 148 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 1.052 Fit side-chains REVERT: A 35 LYS cc_start: 0.8527 (mttt) cc_final: 0.8119 (mppt) REVERT: A 275 GLU cc_start: 0.7727 (pt0) cc_final: 0.7262 (pp20) REVERT: A 276 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7913 (mt-10) REVERT: A 328 ASP cc_start: 0.7377 (m-30) cc_final: 0.7044 (m-30) REVERT: A 330 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7870 (mtmt) REVERT: B 23 LYS cc_start: 0.8478 (ttmm) cc_final: 0.7807 (tptt) REVERT: C 21 MET cc_start: 0.8305 (mmm) cc_final: 0.7126 (ttp) REVERT: C 42 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7336 (mp0) REVERT: R 50 SER cc_start: 0.8963 (m) cc_final: 0.8631 (p) REVERT: R 342 ILE cc_start: 0.8798 (mm) cc_final: 0.8588 (mm) outliers start: 18 outliers final: 12 residues processed: 141 average time/residue: 1.4169 time to fit residues: 211.7941 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 : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 330 LYS 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 16 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.152759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.110462 restraints weight = 9833.751| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.78 r_work: 0.3201 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1702 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= 0.149 Angle : 0.484 5.520 12611 Z= 0.262 Chirality : 0.041 0.170 1443 Planarity : 0.004 0.044 1543 Dihedral : 6.490 56.379 1679 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.09 % Allowed : 10.67 % Favored : 87.24 % 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: 1.51 (0.25), residues: 1114 helix: 2.41 (0.25), residues: 413 sheet: 0.54 (0.29), residues: 276 loop : -0.04 (0.30), residues: 425 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 R 20 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 152 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.988 Fit side-chains REVERT: A 35 LYS cc_start: 0.8478 (mttt) cc_final: 0.8134 (mppt) REVERT: A 275 GLU cc_start: 0.7855 (pt0) cc_final: 0.7436 (pp20) REVERT: A 276 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7813 (mt-10) REVERT: A 328 ASP cc_start: 0.7346 (m-30) cc_final: 0.6964 (m-30) REVERT: B 23 LYS cc_start: 0.8446 (ttmm) cc_final: 0.7741 (tptt) REVERT: B 172 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7891 (pt0) REVERT: B 197 ARG cc_start: 0.8771 (mtp85) cc_final: 0.8413 (mtp85) REVERT: B 266 HIS cc_start: 0.8237 (t-90) cc_final: 0.8019 (t-170) REVERT: C 21 MET cc_start: 0.8289 (mmm) cc_final: 0.7134 (ttp) REVERT: E 18 ARG cc_start: 0.8158 (tpt170) cc_final: 0.7941 (tpt170) REVERT: R 50 SER cc_start: 0.8779 (m) cc_final: 0.8514 (p) REVERT: R 165 GLU cc_start: 0.8655 (pt0) cc_final: 0.7839 (pp20) outliers start: 20 outliers final: 11 residues processed: 142 average time/residue: 1.5170 time to fit residues: 228.6680 Evaluate side-chains 138 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 4.9990 chunk 72 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 171 ASN 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 = 0.3845 r_free = 0.3845 target = 0.152109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.110406 restraints weight = 9864.392| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.90 r_work: 0.3179 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9268 Z= 0.187 Angle : 0.503 5.669 12611 Z= 0.270 Chirality : 0.041 0.173 1443 Planarity : 0.004 0.044 1543 Dihedral : 6.457 56.893 1678 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.20 % Allowed : 10.88 % Favored : 86.92 % 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: 2.45 (0.25), residues: 413 sheet: 0.50 (0.29), residues: 276 loop : -0.03 (0.30), residues: 425 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 0.013 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 145 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 1.403 Fit side-chains REVERT: A 35 LYS cc_start: 0.8516 (mttt) cc_final: 0.8143 (mppt) REVERT: A 275 GLU cc_start: 0.7862 (pt0) cc_final: 0.7438 (pp20) REVERT: A 276 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7870 (mt-10) REVERT: A 328 ASP cc_start: 0.7343 (m-30) cc_final: 0.6971 (m-30) REVERT: B 23 LYS cc_start: 0.8451 (ttmm) cc_final: 0.7740 (tptt) REVERT: B 172 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7888 (pt0) REVERT: B 214 ARG cc_start: 0.8440 (mpp-170) cc_final: 0.8128 (mpp80) REVERT: B 266 HIS cc_start: 0.8222 (t-90) cc_final: 0.8016 (t-90) REVERT: C 21 MET cc_start: 0.8305 (mmm) cc_final: 0.7132 (ttp) REVERT: E 160 ARG cc_start: 0.8332 (mtm-85) cc_final: 0.8006 (ttp-110) REVERT: R 50 SER cc_start: 0.8815 (m) cc_final: 0.8524 (p) REVERT: R 165 GLU cc_start: 0.8661 (pt0) cc_final: 0.7854 (pp20) outliers start: 21 outliers final: 13 residues processed: 136 average time/residue: 1.5589 time to fit residues: 223.8777 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 : 1.083 ------------------------------------------------------------------------------- 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 146 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 43 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.152651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.109979 restraints weight = 9760.551| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.79 r_work: 0.3199 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9268 Z= 0.166 Angle : 0.491 5.589 12611 Z= 0.264 Chirality : 0.041 0.173 1443 Planarity : 0.004 0.044 1543 Dihedral : 6.410 58.564 1678 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.99 % Allowed : 11.72 % Favored : 86.30 % 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: 1.55 (0.25), residues: 1114 helix: 2.51 (0.25), residues: 413 sheet: 0.46 (0.29), residues: 276 loop : -0.01 (0.30), residues: 425 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 0.012 0.001 PHE B 151 TYR 0.014 0.001 TYR R 173 ARG 0.008 0.000 ARG B 19 *********************** 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 143 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 1.044 Fit side-chains REVERT: A 35 LYS cc_start: 0.8493 (mttt) cc_final: 0.8130 (mppt) REVERT: A 275 GLU cc_start: 0.7866 (pt0) cc_final: 0.7437 (pp20) REVERT: A 276 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7863 (mt-10) REVERT: A 328 ASP cc_start: 0.7376 (m-30) cc_final: 0.7007 (m-30) REVERT: A 330 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7882 (mtmt) REVERT: B 23 LYS cc_start: 0.8427 (ttmm) cc_final: 0.7736 (tptt) REVERT: B 172 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7932 (tp30) REVERT: B 214 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8024 (mpp80) REVERT: B 266 HIS cc_start: 0.8186 (t-90) cc_final: 0.7974 (t-170) REVERT: C 21 MET cc_start: 0.8296 (mmm) cc_final: 0.7130 (ttp) REVERT: E 18 ARG cc_start: 0.8105 (tpt-90) cc_final: 0.7890 (tpt170) REVERT: E 160 ARG cc_start: 0.8291 (mtm-85) cc_final: 0.7972 (ttp-110) REVERT: R 50 SER cc_start: 0.8799 (m) cc_final: 0.8522 (p) REVERT: R 165 GLU cc_start: 0.8641 (pt0) cc_final: 0.7836 (pp20) outliers start: 19 outliers final: 14 residues processed: 135 average time/residue: 1.4649 time to fit residues: 209.2819 Evaluate side-chains 138 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 214 ARG 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 107 optimal weight: 0.0060 chunk 61 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 6 optimal weight: 0.0770 chunk 47 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.5554 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.153940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.111511 restraints weight = 9890.087| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.81 r_work: 0.3219 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1932 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= 0.133 Angle : 0.468 5.650 12611 Z= 0.252 Chirality : 0.040 0.171 1443 Planarity : 0.004 0.043 1543 Dihedral : 6.280 59.679 1678 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.78 % Allowed : 11.92 % Favored : 86.30 % 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: 2.58 (0.25), residues: 414 sheet: 0.50 (0.29), residues: 274 loop : -0.01 (0.30), residues: 426 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 B 151 TYR 0.014 0.001 TYR E 190 ARG 0.008 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: 17 poor density : 131 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8466 (mttt) cc_final: 0.8113 (mppt) REVERT: A 275 GLU cc_start: 0.7874 (pt0) cc_final: 0.7453 (pp20) REVERT: A 276 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7879 (mt-10) REVERT: B 23 LYS cc_start: 0.8467 (ttmm) cc_final: 0.7813 (tptt) REVERT: B 172 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7852 (tp30) REVERT: B 219 ARG cc_start: 0.8232 (mtt-85) cc_final: 0.7910 (mmt-90) REVERT: B 266 HIS cc_start: 0.8199 (t-90) cc_final: 0.7988 (t-170) REVERT: C 21 MET cc_start: 0.8311 (mmm) cc_final: 0.7156 (ttp) REVERT: E 160 ARG cc_start: 0.8290 (mtm-85) cc_final: 0.7975 (ttp-110) REVERT: E 194 ASN cc_start: 0.8849 (m-40) cc_final: 0.8509 (m110) REVERT: R 50 SER cc_start: 0.8773 (m) cc_final: 0.8520 (p) REVERT: R 165 GLU cc_start: 0.8599 (pt0) cc_final: 0.7834 (pp20) outliers start: 17 outliers final: 10 residues processed: 140 average time/residue: 1.6092 time to fit residues: 238.0586 Evaluate side-chains 135 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 48 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 155 ASN B 259 GLN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.152234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.110545 restraints weight = 9994.772| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.77 r_work: 0.3198 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9268 Z= 0.180 Angle : 0.495 5.631 12611 Z= 0.267 Chirality : 0.041 0.174 1443 Planarity : 0.004 0.044 1543 Dihedral : 6.245 56.686 1678 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.51 % Allowed : 11.61 % Favored : 85.88 % 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: 2.54 (0.25), residues: 414 sheet: 0.45 (0.29), residues: 281 loop : 0.04 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS C 44 PHE 0.013 0.001 PHE B 151 TYR 0.015 0.001 TYR R 173 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: 24 poor density : 121 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8499 (mttt) cc_final: 0.8119 (mppt) REVERT: A 275 GLU cc_start: 0.7896 (pt0) cc_final: 0.7449 (pp20) REVERT: A 276 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7780 (mt-10) REVERT: A 330 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7852 (mtmt) REVERT: B 23 LYS cc_start: 0.8441 (ttmm) cc_final: 0.7754 (tptt) REVERT: B 172 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7812 (tp30) REVERT: B 214 ARG cc_start: 0.8151 (mtm-85) cc_final: 0.7522 (mtm110) REVERT: B 219 ARG cc_start: 0.8222 (mtt-85) cc_final: 0.7903 (mmt-90) REVERT: B 266 HIS cc_start: 0.8150 (t-90) cc_final: 0.7943 (t-170) REVERT: C 21 MET cc_start: 0.8302 (mmm) cc_final: 0.7129 (ttp) REVERT: E 160 ARG cc_start: 0.8290 (mtm-85) cc_final: 0.7967 (ttp-110) REVERT: R 50 SER cc_start: 0.8839 (m) cc_final: 0.8544 (p) REVERT: R 165 GLU cc_start: 0.8630 (pt0) cc_final: 0.7855 (pp20) REVERT: R 297 ARG cc_start: 0.8077 (ttp80) cc_final: 0.7817 (ttp80) REVERT: R 347 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8482 (tt0) outliers start: 24 outliers final: 14 residues processed: 135 average time/residue: 1.4421 time to fit residues: 206.1793 Evaluate side-chains 136 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 146 LEU 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 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 Chi-restraints excluded: chain R residue 347 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 89 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 43 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 90 optimal weight: 0.0070 chunk 23 optimal weight: 1.9990 overall best weight: 0.9002 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.152890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.111374 restraints weight = 9850.084| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.76 r_work: 0.3207 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9268 Z= 0.165 Angle : 0.491 5.631 12611 Z= 0.264 Chirality : 0.041 0.174 1443 Planarity : 0.004 0.043 1543 Dihedral : 6.142 56.125 1678 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.88 % Allowed : 12.55 % 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: 1.61 (0.25), residues: 1114 helix: 2.58 (0.25), residues: 414 sheet: 0.49 (0.29), residues: 274 loop : 0.01 (0.30), residues: 426 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 0.012 0.001 PHE B 151 TYR 0.014 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 141 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8473 (mttt) cc_final: 0.8113 (mppt) REVERT: A 275 GLU cc_start: 0.7890 (pt0) cc_final: 0.7415 (pp20) REVERT: A 276 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7776 (mt-10) REVERT: A 330 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7847 (mtmt) REVERT: B 23 LYS cc_start: 0.8435 (ttmm) cc_final: 0.7778 (tptt) REVERT: B 172 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7805 (tp30) REVERT: B 219 ARG cc_start: 0.8253 (mtt-85) cc_final: 0.7902 (mmt-90) REVERT: B 266 HIS cc_start: 0.8171 (t-90) cc_final: 0.7969 (t-170) REVERT: C 21 MET cc_start: 0.8300 (mmm) cc_final: 0.7121 (ttp) REVERT: E 160 ARG cc_start: 0.8288 (mtm-85) cc_final: 0.7968 (ttp-110) REVERT: E 194 ASN cc_start: 0.8865 (m-40) cc_final: 0.8490 (m110) REVERT: R 50 SER cc_start: 0.8806 (m) cc_final: 0.8525 (p) REVERT: R 165 GLU cc_start: 0.8627 (pt0) cc_final: 0.7757 (pp20) REVERT: R 297 ARG cc_start: 0.8074 (ttp80) cc_final: 0.7814 (ttp80) REVERT: R 347 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8453 (tt0) outliers start: 18 outliers final: 13 residues processed: 135 average time/residue: 1.5049 time to fit residues: 215.4515 Evaluate side-chains 137 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 146 LEU 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 Chi-restraints excluded: chain R residue 347 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 29 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 90 optimal weight: 0.1980 chunk 74 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.153943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.111350 restraints weight = 9933.935| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.81 r_work: 0.3216 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9268 Z= 0.151 Angle : 0.481 5.636 12611 Z= 0.259 Chirality : 0.041 0.173 1443 Planarity : 0.003 0.043 1543 Dihedral : 5.959 56.562 1678 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.67 % Allowed : 12.66 % Favored : 85.67 % 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: 1.65 (0.25), residues: 1114 helix: 2.60 (0.25), residues: 414 sheet: 0.51 (0.29), residues: 274 loop : 0.03 (0.31), residues: 426 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: 16 poor density : 131 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8473 (mttt) cc_final: 0.8136 (mppt) REVERT: A 275 GLU cc_start: 0.7938 (pt0) cc_final: 0.7458 (pp20) REVERT: A 276 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7833 (mt-10) REVERT: A 330 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7853 (mtmt) REVERT: B 23 LYS cc_start: 0.8472 (ttmm) cc_final: 0.7805 (tptt) REVERT: B 172 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7845 (tp30) REVERT: B 219 ARG cc_start: 0.8292 (mtt-85) cc_final: 0.7947 (mmt-90) REVERT: B 325 MET cc_start: 0.9224 (mmt) cc_final: 0.8899 (tpp) REVERT: C 21 MET cc_start: 0.8230 (mmm) cc_final: 0.7121 (ttp) REVERT: E 160 ARG cc_start: 0.8302 (mtm-85) cc_final: 0.7987 (ttp-110) REVERT: E 194 ASN cc_start: 0.8853 (m-40) cc_final: 0.8501 (m110) REVERT: R 50 SER cc_start: 0.8791 (m) cc_final: 0.8535 (p) REVERT: R 165 GLU cc_start: 0.8639 (pt0) cc_final: 0.7797 (pp20) REVERT: R 297 ARG cc_start: 0.8112 (ttp80) cc_final: 0.7853 (ttp80) REVERT: R 347 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8468 (tt0) outliers start: 16 outliers final: 12 residues processed: 141 average time/residue: 1.4947 time to fit residues: 224.5034 Evaluate side-chains 142 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 1.878 ------------------------------------------------------------------------------- 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 146 LEU 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 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 Chi-restraints excluded: chain R residue 347 GLN 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: 0.8980 chunk 36 optimal weight: 0.0040 chunk 85 optimal weight: 0.2980 chunk 17 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 91 optimal weight: 0.0970 chunk 71 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.3790 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.153977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.111656 restraints weight = 9877.700| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.79 r_work: 0.3215 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 9268 Z= 0.194 Angle : 0.842 59.192 12611 Z= 0.500 Chirality : 0.043 0.603 1443 Planarity : 0.003 0.043 1543 Dihedral : 5.967 56.568 1678 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.78 % Allowed : 13.08 % Favored : 85.15 % Cbeta Deviations : 0.09 % 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: 1.64 (0.25), residues: 1114 helix: 2.61 (0.25), residues: 414 sheet: 0.50 (0.29), residues: 274 loop : 0.01 (0.30), residues: 426 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 0.013 0.001 TYR R 173 ARG 0.007 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9548.29 seconds wall clock time: 165 minutes 22.69 seconds (9922.69 seconds total)