Starting phenix.real_space_refine on Sat Dec 28 18:09:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yn9_39419/12_2024/8yn9_39419.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yn9_39419/12_2024/8yn9_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_39419/12_2024/8yn9_39419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yn9_39419/12_2024/8yn9_39419.map" model { file = "/net/cci-nas-00/data/ceres_data/8yn9_39419/12_2024/8yn9_39419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yn9_39419/12_2024/8yn9_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-5532/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: 5.25, per 1000 atoms: 0.58 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: 2.57 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: 1.11 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: 2.61 Time building geometry restraints manager: 2.73 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: 0.310 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.480 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:10.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.240 ------------------------------------------------------------------------------- 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 : 1.021 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: 1.4209 time to fit residues: 254.7110 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 : 1.094 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 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 : 0.937 Fit side-chains REVERT: A 35 LYS cc_start: 0.8404 (mttt) cc_final: 0.8005 (mppt) REVERT: A 275 GLU cc_start: 0.7633 (pt0) cc_final: 0.7305 (pp20) REVERT: A 276 GLU cc_start: 0.8398 (mt-10) cc_final: 0.7936 (mt-10) REVERT: A 328 ASP cc_start: 0.7413 (m-30) cc_final: 0.7070 (m-30) REVERT: B 23 LYS cc_start: 0.8456 (ttmm) cc_final: 0.7790 (tptt) REVERT: C 21 MET cc_start: 0.8122 (mmm) cc_final: 0.7142 (ttp) REVERT: C 42 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: R 20 PHE cc_start: 0.8300 (t80) cc_final: 0.8011 (t80) REVERT: R 50 SER cc_start: 0.8818 (m) cc_final: 0.8462 (p) REVERT: R 342 ILE cc_start: 0.8720 (mm) cc_final: 0.8471 (mm) REVERT: R 347 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8472 (tt0) outliers start: 24 outliers final: 11 residues processed: 148 average time/residue: 1.4055 time to fit residues: 220.5890 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 : 0.945 ------------------------------------------------------------------------------- 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 56 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 0.1980 chunk 99 optimal weight: 0.4980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1497 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= 0.206 Angle : 0.524 5.543 12611 Z= 0.283 Chirality : 0.042 0.174 1443 Planarity : 0.004 0.045 1543 Dihedral : 6.767 56.886 1679 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.46 % Allowed : 10.25 % Favored : 88.28 % 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: 1.48 (0.25), residues: 1114 helix: 2.28 (0.25), residues: 412 sheet: 0.68 (0.29), residues: 287 loop : -0.05 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.004 0.001 HIS B 62 PHE 0.014 0.002 PHE B 151 TYR 0.013 0.001 TYR R 358 ARG 0.007 0.000 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 146 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 1.015 Fit side-chains REVERT: A 35 LYS cc_start: 0.8383 (mttt) cc_final: 0.8034 (mppt) REVERT: A 275 GLU cc_start: 0.7647 (pt0) cc_final: 0.7264 (pp20) REVERT: A 276 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7881 (mt-10) REVERT: A 328 ASP cc_start: 0.7404 (m-30) cc_final: 0.7079 (m-30) REVERT: B 23 LYS cc_start: 0.8441 (ttmm) cc_final: 0.7773 (tptt) REVERT: C 21 MET cc_start: 0.8091 (mmm) cc_final: 0.7137 (ttp) REVERT: C 42 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6943 (mp0) REVERT: E 18 ARG cc_start: 0.7925 (tpt-90) cc_final: 0.7630 (tpt170) REVERT: R 50 SER cc_start: 0.8804 (m) cc_final: 0.8462 (p) REVERT: R 93 THR cc_start: 0.8940 (t) cc_final: 0.8549 (p) REVERT: R 342 ILE cc_start: 0.8706 (mm) cc_final: 0.8473 (mm) outliers start: 14 outliers final: 11 residues processed: 141 average time/residue: 1.4197 time to fit residues: 212.2589 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 : 1.011 ------------------------------------------------------------------------------- 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 227 SER Chi-restraints excluded: chain C residue 42 GLU 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 75 optimal weight: 5.9990 chunk 52 optimal weight: 0.0870 chunk 11 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 101 optimal weight: 0.0040 chunk 107 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 60 optimal weight: 0.0670 overall best weight: 0.3910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 91 HIS B 259 GLN E 186 GLN R 362 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1900 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= 0.124 Angle : 0.459 5.579 12611 Z= 0.248 Chirality : 0.040 0.169 1443 Planarity : 0.003 0.044 1543 Dihedral : 6.356 58.808 1678 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.57 % Allowed : 10.98 % Favored : 87.45 % 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: 1.64 (0.25), residues: 1114 helix: 2.53 (0.25), residues: 413 sheet: 0.63 (0.29), residues: 274 loop : 0.01 (0.30), residues: 427 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 0.009 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 162 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8314 (mttt) cc_final: 0.7982 (mppt) REVERT: A 275 GLU cc_start: 0.7777 (pt0) cc_final: 0.7436 (pp20) REVERT: A 276 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7941 (mt-10) REVERT: A 328 ASP cc_start: 0.7413 (m-30) cc_final: 0.7089 (m-30) REVERT: B 23 LYS cc_start: 0.8388 (ttmm) cc_final: 0.7736 (tptt) REVERT: B 137 ARG cc_start: 0.7996 (mmt-90) cc_final: 0.7730 (tpt90) REVERT: C 21 MET cc_start: 0.8075 (mmm) cc_final: 0.7161 (ttp) REVERT: E 160 ARG cc_start: 0.8108 (mtm-85) cc_final: 0.7825 (ttp-110) REVERT: E 194 ASN cc_start: 0.8917 (m-40) cc_final: 0.8506 (m110) REVERT: R 24 LEU cc_start: 0.8825 (tp) cc_final: 0.8409 (mm) REVERT: R 50 SER cc_start: 0.8762 (m) cc_final: 0.8491 (p) REVERT: R 93 THR cc_start: 0.8818 (t) cc_final: 0.8543 (p) REVERT: R 165 GLU cc_start: 0.8363 (pt0) cc_final: 0.7563 (pp20) REVERT: R 296 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7726 (tt) REVERT: R 342 ILE cc_start: 0.8658 (mm) cc_final: 0.8441 (mm) outliers start: 15 outliers final: 7 residues processed: 153 average time/residue: 1.4529 time to fit residues: 235.1167 Evaluate side-chains 142 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 214 ARG Chi-restraints excluded: chain B residue 227 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 296 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 155 ASN B 259 GLN E 171 ASN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9268 Z= 0.245 Angle : 0.529 5.699 12611 Z= 0.285 Chirality : 0.042 0.176 1443 Planarity : 0.004 0.046 1543 Dihedral : 6.505 58.727 1678 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.88 % Allowed : 12.03 % 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: 1.56 (0.25), residues: 1114 helix: 2.47 (0.25), residues: 413 sheet: 0.54 (0.28), residues: 293 loop : -0.01 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.005 0.001 HIS E 35 PHE 0.015 0.002 PHE A 215 TYR 0.015 0.001 TYR R 358 ARG 0.008 0.001 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 147 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 1.065 Fit side-chains REVERT: A 35 LYS cc_start: 0.8395 (mttt) cc_final: 0.8035 (mppt) REVERT: A 275 GLU cc_start: 0.7786 (pt0) cc_final: 0.7417 (pp20) REVERT: A 276 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7852 (mt-10) REVERT: A 328 ASP cc_start: 0.7397 (m-30) cc_final: 0.7050 (m-30) REVERT: A 330 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7645 (mtmt) REVERT: B 23 LYS cc_start: 0.8405 (ttmm) cc_final: 0.7738 (tptt) REVERT: B 137 ARG cc_start: 0.8095 (mmt-90) cc_final: 0.7772 (tpt90) REVERT: C 21 MET cc_start: 0.8082 (mmm) cc_final: 0.7042 (ttp) REVERT: E 18 ARG cc_start: 0.7986 (tpt170) cc_final: 0.7772 (tpt170) REVERT: E 160 ARG cc_start: 0.8159 (mtm-85) cc_final: 0.7824 (ttp-110) REVERT: R 50 SER cc_start: 0.8849 (m) cc_final: 0.8477 (p) REVERT: R 93 THR cc_start: 0.8901 (t) cc_final: 0.8488 (p) REVERT: R 165 GLU cc_start: 0.8386 (pt0) cc_final: 0.7577 (pp20) REVERT: R 342 ILE cc_start: 0.8719 (mm) cc_final: 0.8501 (mm) outliers start: 18 outliers final: 11 residues processed: 139 average time/residue: 1.5825 time to fit residues: 234.3993 Evaluate side-chains 135 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 38 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 227 SER 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 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 62 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 0.0470 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 overall best weight: 1.2084 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1803 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= 0.192 Angle : 0.505 5.591 12611 Z= 0.272 Chirality : 0.042 0.175 1443 Planarity : 0.004 0.045 1543 Dihedral : 6.460 59.651 1678 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.09 % Allowed : 11.92 % Favored : 85.98 % 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: 2.50 (0.25), residues: 413 sheet: 0.57 (0.28), residues: 283 loop : -0.09 (0.31), residues: 418 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 0.013 0.001 PHE B 151 TYR 0.014 0.001 TYR R 173 ARG 0.009 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 144 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.950 Fit side-chains REVERT: A 35 LYS cc_start: 0.8387 (mttt) cc_final: 0.8030 (mppt) REVERT: A 275 GLU cc_start: 0.7792 (pt0) cc_final: 0.7430 (pp20) REVERT: A 276 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7828 (mt-10) REVERT: A 328 ASP cc_start: 0.7390 (m-30) cc_final: 0.7054 (m-30) REVERT: A 330 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7632 (mtmt) REVERT: B 23 LYS cc_start: 0.8414 (ttmm) cc_final: 0.7764 (tptt) REVERT: C 21 MET cc_start: 0.8089 (mmm) cc_final: 0.7047 (ttp) REVERT: E 160 ARG cc_start: 0.8154 (mtm-85) cc_final: 0.7822 (ttp-110) REVERT: R 50 SER cc_start: 0.8858 (m) cc_final: 0.8482 (p) REVERT: R 165 GLU cc_start: 0.8388 (pt0) cc_final: 0.7599 (pp20) REVERT: R 342 ILE cc_start: 0.8708 (mm) cc_final: 0.8497 (mm) outliers start: 20 outliers final: 13 residues processed: 137 average time/residue: 1.5233 time to fit residues: 220.5839 Evaluate side-chains 136 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 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 227 SER Chi-restraints excluded: chain E residue 6 GLU 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 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 320 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.5980 chunk 60 optimal weight: 0.0870 chunk 90 optimal weight: 0.3980 chunk 59 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2038 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= 0.128 Angle : 0.459 5.602 12611 Z= 0.247 Chirality : 0.040 0.171 1443 Planarity : 0.003 0.043 1543 Dihedral : 6.124 57.321 1678 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.46 % Allowed : 12.66 % 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: 1.65 (0.25), residues: 1114 helix: 2.64 (0.25), residues: 414 sheet: 0.59 (0.29), residues: 270 loop : -0.06 (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 B 62 PHE 0.011 0.001 PHE R 328 TYR 0.014 0.001 TYR R 173 ARG 0.009 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 149 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8302 (mttt) cc_final: 0.7980 (mppt) REVERT: A 275 GLU cc_start: 0.7812 (pt0) cc_final: 0.7446 (pp20) REVERT: A 276 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7843 (mt-10) REVERT: B 23 LYS cc_start: 0.8372 (ttmm) cc_final: 0.7734 (tptt) REVERT: B 137 ARG cc_start: 0.7899 (mmt-90) cc_final: 0.7625 (tpt90) REVERT: B 219 ARG cc_start: 0.7857 (mtt-85) cc_final: 0.7534 (mmt-90) REVERT: C 21 MET cc_start: 0.8078 (mmm) cc_final: 0.7061 (ttp) REVERT: E 160 ARG cc_start: 0.8119 (mtm-85) cc_final: 0.7808 (ttp-110) REVERT: E 194 ASN cc_start: 0.8902 (m-40) cc_final: 0.8463 (m110) REVERT: R 50 SER cc_start: 0.8773 (m) cc_final: 0.8488 (p) REVERT: R 165 GLU cc_start: 0.8373 (pt0) cc_final: 0.7534 (pp20) outliers start: 14 outliers final: 10 residues processed: 144 average time/residue: 1.4576 time to fit residues: 222.1114 Evaluate side-chains 137 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 227 SER Chi-restraints excluded: chain E residue 6 GLU 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 R residue 82 PHE Chi-restraints excluded: chain R residue 187 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 0.0470 overall best weight: 0.9884 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1977 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= 0.169 Angle : 0.487 5.701 12611 Z= 0.262 Chirality : 0.041 0.174 1443 Planarity : 0.004 0.044 1543 Dihedral : 6.135 56.571 1678 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.57 % Allowed : 13.60 % Favored : 84.83 % 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: 1.62 (0.25), residues: 1114 helix: 2.60 (0.25), residues: 414 sheet: 0.58 (0.29), residues: 270 loop : -0.06 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 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 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 143 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8373 (mttt) cc_final: 0.8023 (mppt) REVERT: A 275 GLU cc_start: 0.7821 (pt0) cc_final: 0.7420 (pp20) REVERT: A 276 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7792 (mt-10) REVERT: B 23 LYS cc_start: 0.8398 (ttmm) cc_final: 0.7744 (tptt) REVERT: B 137 ARG cc_start: 0.7981 (mmt-90) cc_final: 0.7711 (tpt90) REVERT: B 219 ARG cc_start: 0.7839 (mtt-85) cc_final: 0.7466 (mmt-90) REVERT: C 21 MET cc_start: 0.7994 (mmm) cc_final: 0.7007 (ttp) REVERT: E 160 ARG cc_start: 0.8146 (mtm-85) cc_final: 0.7822 (ttp-110) REVERT: E 194 ASN cc_start: 0.8923 (m-40) cc_final: 0.8488 (m110) REVERT: R 50 SER cc_start: 0.8809 (m) cc_final: 0.8459 (p) REVERT: R 165 GLU cc_start: 0.8414 (pt0) cc_final: 0.7499 (pp20) outliers start: 15 outliers final: 10 residues processed: 137 average time/residue: 1.4565 time to fit residues: 211.1069 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 : 0.962 ------------------------------------------------------------------------------- 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 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 R residue 82 PHE Chi-restraints excluded: chain R residue 187 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN E 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9268 Z= 0.159 Angle : 0.483 5.605 12611 Z= 0.259 Chirality : 0.041 0.174 1443 Planarity : 0.003 0.043 1543 Dihedral : 6.020 56.730 1678 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.46 % Allowed : 13.60 % Favored : 84.94 % 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: 1.64 (0.25), residues: 1114 helix: 2.62 (0.25), residues: 414 sheet: 0.57 (0.29), residues: 270 loop : -0.05 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS C 44 PHE 0.012 0.001 PHE B 151 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 144 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8354 (mttt) cc_final: 0.8023 (mppt) REVERT: A 275 GLU cc_start: 0.7850 (pt0) cc_final: 0.7403 (pp20) REVERT: A 276 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7800 (mt-10) REVERT: B 23 LYS cc_start: 0.8398 (ttmm) cc_final: 0.7753 (tptt) REVERT: B 137 ARG cc_start: 0.7940 (mmt-90) cc_final: 0.7649 (tpt90) REVERT: B 219 ARG cc_start: 0.7868 (mtt-85) cc_final: 0.7466 (mmt-90) REVERT: B 254 ASP cc_start: 0.8388 (t70) cc_final: 0.8035 (t70) REVERT: C 21 MET cc_start: 0.8000 (mmm) cc_final: 0.7007 (ttp) REVERT: E 160 ARG cc_start: 0.8146 (mtm-85) cc_final: 0.7821 (ttp-110) REVERT: E 194 ASN cc_start: 0.8918 (m-40) cc_final: 0.8472 (m110) REVERT: R 50 SER cc_start: 0.8802 (m) cc_final: 0.8467 (p) outliers start: 14 outliers final: 9 residues processed: 141 average time/residue: 1.4767 time to fit residues: 220.2720 Evaluate side-chains 138 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 227 SER 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 R residue 82 PHE Chi-restraints excluded: chain R residue 187 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.5980 chunk 73 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 0.0000 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 0.2980 chunk 68 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2137 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= 0.133 Angle : 0.471 5.702 12611 Z= 0.253 Chirality : 0.040 0.172 1443 Planarity : 0.003 0.042 1543 Dihedral : 5.825 57.177 1678 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.36 % Allowed : 13.91 % Favored : 84.73 % 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: 2.68 (0.25), residues: 414 sheet: 0.56 (0.29), residues: 270 loop : -0.03 (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 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 144 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8313 (mttt) cc_final: 0.8003 (mppt) REVERT: A 275 GLU cc_start: 0.7851 (pt0) cc_final: 0.7398 (pp20) REVERT: A 276 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7750 (mt-10) REVERT: B 23 LYS cc_start: 0.8380 (ttmm) cc_final: 0.7720 (tptt) REVERT: B 137 ARG cc_start: 0.7902 (mmt-90) cc_final: 0.7627 (tpt90) REVERT: B 219 ARG cc_start: 0.7927 (mtt-85) cc_final: 0.7513 (mmt-90) REVERT: B 254 ASP cc_start: 0.8367 (t70) cc_final: 0.8012 (t70) REVERT: C 21 MET cc_start: 0.7994 (mmm) cc_final: 0.7015 (ttp) REVERT: C 42 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6881 (tp30) REVERT: E 160 ARG cc_start: 0.8130 (mtm-85) cc_final: 0.7817 (ttp-110) REVERT: E 194 ASN cc_start: 0.8891 (m-40) cc_final: 0.8461 (m110) REVERT: R 50 SER cc_start: 0.8776 (m) cc_final: 0.8473 (p) outliers start: 13 outliers final: 10 residues processed: 139 average time/residue: 1.5469 time to fit residues: 228.0007 Evaluate side-chains 140 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 227 SER Chi-restraints excluded: chain C residue 42 GLU 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 R residue 82 PHE Chi-restraints excluded: chain R residue 187 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 77 optimal weight: 0.3980 chunk 5 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.151703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.109470 restraints weight = 9741.852| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.90 r_work: 0.3166 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9268 Z= 0.258 Angle : 0.540 5.688 12611 Z= 0.291 Chirality : 0.043 0.179 1443 Planarity : 0.004 0.055 1543 Dihedral : 6.099 56.458 1678 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.46 % Allowed : 13.81 % Favored : 84.73 % 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: 1.54 (0.25), residues: 1114 helix: 2.50 (0.25), residues: 414 sheet: 0.47 (0.28), residues: 290 loop : -0.04 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.005 0.001 HIS E 35 PHE 0.016 0.002 PHE A 215 TYR 0.016 0.002 TYR R 358 ARG 0.011 0.001 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4133.64 seconds wall clock time: 74 minutes 38.21 seconds (4478.21 seconds total)