Starting phenix.real_space_refine on Thu Feb 15 17:14:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbx_33108/02_2024/7xbx_33108_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbx_33108/02_2024/7xbx_33108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbx_33108/02_2024/7xbx_33108.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbx_33108/02_2024/7xbx_33108.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbx_33108/02_2024/7xbx_33108_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbx_33108/02_2024/7xbx_33108_trim_updated.pdb" } resolution = 3.4 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 263 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians S 45 5.16 5 C 4260 2.51 5 N 1080 2.21 5 O 1231 1.98 5 H 6022 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 33": "OE1" <-> "OE2" Residue "C GLU 216": "OE1" <-> "OE2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "D TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "R TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12638 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3128 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 109 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "D" Number of atoms: 4293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 4293 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 305} Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 119 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 4, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 112 Chain: "E" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 414 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 4, 'TRANS': 28} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "R" Number of atoms: 4803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 4803 Unusual residues: {'CLR': 2} Classifications: {'peptide': 349, 'undetermined': 2} Link IDs: {'PTRANS': 10, 'TRANS': 338, None: 2} Not linked: pdbres="TYR R 410 " pdbres="CLR R 501 " Not linked: pdbres="CLR R 501 " pdbres="CLR R 502 " Chain breaks: 2 Unresolved non-hydrogen bonds: 379 Unresolved non-hydrogen angles: 471 Unresolved non-hydrogen dihedrals: 338 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 5, 'PCA:plan-2': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 6, 'TYR:plan': 4, 'PHE:plan': 10, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 241 Time building chain proxies: 6.03, per 1000 atoms: 0.48 Number of scatterers: 12638 At special positions: 0 Unit cell: (112.86, 131.67, 74.195, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 O 1231 8.00 N 1080 7.00 C 4260 6.00 H 6022 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 8 " - pdb=" SG CYS R 34 " distance=2.03 Simple disulfide: pdb=" SG CYS R 12 " - pdb=" SG CYS R 50 " distance=2.03 Simple disulfide: pdb=" SG CYS R 35 " - pdb=" SG CYS R 278 " distance=2.03 Simple disulfide: pdb=" SG CYS R 204 " - pdb=" SG CYS R 277 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 9.57 Conformation dependent library (CDL) restraints added in 1.3 seconds 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1722 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 22 helices and 8 sheets defined 39.7% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'C' and resid 7 through 31 Processing helix chain 'C' and resid 46 through 50 Processing helix chain 'C' and resid 208 through 215 removed outlier: 3.769A pdb=" N HIS C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N CYS C 214 " --> pdb=" O LYS C 210 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE C 215 " --> pdb=" O TRP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 274 through 278 Processing helix chain 'C' and resid 296 through 310 Processing helix chain 'C' and resid 328 through 348 Processing helix chain 'D' and resid 33 through 35 No H-bonds generated for 'chain 'D' and resid 33 through 35' Processing helix chain 'E' and resid 30 through 43 Processing helix chain 'R' and resid 30 through 33 No H-bonds generated for 'chain 'R' and resid 30 through 33' Processing helix chain 'R' and resid 56 through 65 removed outlier: 3.823A pdb=" N ASP R 60 " --> pdb=" O GLN R 56 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA R 61 " --> pdb=" O TRP R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 159 removed outlier: 3.515A pdb=" N ILE R 138 " --> pdb=" O VAL R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 195 Proline residue: R 187 - end of helix removed outlier: 3.516A pdb=" N ASN R 195 " --> pdb=" O HIS R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 234 Processing helix chain 'R' and resid 236 through 242 removed outlier: 4.148A pdb=" N MET R 240 " --> pdb=" O ALA R 236 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ASN R 241 " --> pdb=" O ALA R 237 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 267 Proline residue: R 265 - end of helix Processing helix chain 'R' and resid 283 through 299 removed outlier: 3.516A pdb=" N GLN R 286 " --> pdb=" O GLU R 283 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLU R 287 " --> pdb=" O VAL R 284 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N TRP R 289 " --> pdb=" O GLN R 286 " (cutoff:3.500A) Proline residue: R 290 - end of helix removed outlier: 3.518A pdb=" N VAL R 295 " --> pdb=" O LEU R 292 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR R 297 " --> pdb=" O ASN R 294 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE R 299 " --> pdb=" O GLU R 296 " (cutoff:3.500A) Processing helix chain 'R' and resid 303 through 323 Processing helix chain 'R' and resid 330 through 361 removed outlier: 3.558A pdb=" N ILE R 335 " --> pdb=" O ALA R 331 " (cutoff:3.500A) Proline residue: R 348 - end of helix removed outlier: 3.614A pdb=" N LEU R 360 " --> pdb=" O GLU R 356 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TYR R 361 " --> pdb=" O THR R 357 " (cutoff:3.500A) Processing helix chain 'R' and resid 367 through 398 removed outlier: 3.671A pdb=" N CYS R 389 " --> pdb=" O PHE R 385 " (cutoff:3.500A) Proline residue: R 392 - end of helix Processing helix chain 'R' and resid 401 through 409 Processing sheet with id= A, first strand: chain 'C' and resid 36 through 39 removed outlier: 6.970A pdb=" N ALA C 220 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N LEU C 39 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE C 222 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N SER C 263 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N PHE C 223 " --> pdb=" O SER C 263 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE C 265 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N VAL C 225 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE C 267 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR C 320 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU C 268 " --> pdb=" O TYR C 320 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N HIS C 322 " --> pdb=" O LEU C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 185 through 191 removed outlier: 3.574A pdb=" N VAL C 185 " --> pdb=" O ASP C 200 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET C 198 " --> pdb=" O THR C 187 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 61 through 63 removed outlier: 3.583A pdb=" N HIS D 62 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER D 72 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE D 80 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS D 91 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASP D 83 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LYS D 89 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 103 through 105 removed outlier: 5.747A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 146 through 150 removed outlier: 6.914A pdb=" N SER D 160 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N CYS D 149 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL D 158 " --> pdb=" O CYS D 149 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR D 178 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ASP D 170 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN D 176 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 262 through 265 removed outlier: 3.826A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N THR D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA D 231 " --> pdb=" O GLY D 244 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 276 through 278 removed outlier: 6.222A pdb=" N ASP D 298 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ARG D 304 " --> pdb=" O ASP D 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 327 through 330 removed outlier: 3.527A pdb=" N ARG D 49 " --> pdb=" O ILE D 338 " (cutoff:3.500A) 300 hydrogen bonds defined for protein. 867 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: 4.08 Time building geometry restraints manager: 10.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 5994 1.04 - 1.23: 180 1.23 - 1.43: 2662 1.43 - 1.63: 3884 1.63 - 1.83: 56 Bond restraints: 12776 Sorted by residual: bond pdb=" C5 CLR R 501 " pdb=" C6 CLR R 501 " ideal model delta sigma weight residual 1.332 1.463 -0.131 2.00e-02 2.50e+03 4.27e+01 bond pdb=" C5 CLR R 502 " pdb=" C6 CLR R 502 " ideal model delta sigma weight residual 1.332 1.463 -0.131 2.00e-02 2.50e+03 4.27e+01 bond pdb=" N PCA R 1 " pdb=" CD PCA R 1 " ideal model delta sigma weight residual 1.345 1.465 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" C3 CLR R 502 " pdb=" O1 CLR R 502 " ideal model delta sigma weight residual 1.413 1.300 0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" C3 CLR R 501 " pdb=" O1 CLR R 501 " ideal model delta sigma weight residual 1.413 1.300 0.113 2.00e-02 2.50e+03 3.17e+01 ... (remaining 12771 not shown) Histogram of bond angle deviations from ideal: 99.78 - 106.61: 151 106.61 - 113.45: 14670 113.45 - 120.28: 4017 120.28 - 127.12: 4007 127.12 - 133.96: 67 Bond angle restraints: 22912 Sorted by residual: angle pdb=" CA PCA R 1 " pdb=" N PCA R 1 " pdb=" CD PCA R 1 " ideal model delta sigma weight residual 114.17 103.35 10.82 3.00e+00 1.11e-01 1.30e+01 angle pdb=" N PCA R 1 " pdb=" CD PCA R 1 " pdb=" CG PCA R 1 " ideal model delta sigma weight residual 107.23 114.76 -7.53 3.00e+00 1.11e-01 6.30e+00 angle pdb=" CA CYS R 277 " pdb=" CB CYS R 277 " pdb=" SG CYS R 277 " ideal model delta sigma weight residual 114.40 120.10 -5.70 2.30e+00 1.89e-01 6.15e+00 angle pdb=" CB ARG R 293 " pdb=" CG ARG R 293 " pdb=" CD ARG R 293 " ideal model delta sigma weight residual 111.30 116.00 -4.70 2.30e+00 1.89e-01 4.18e+00 angle pdb=" CA LYS C 257 " pdb=" CB LYS C 257 " pdb=" CG LYS C 257 " ideal model delta sigma weight residual 114.10 117.97 -3.87 2.00e+00 2.50e-01 3.75e+00 ... (remaining 22907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.67: 5682 15.67 - 31.34: 407 31.34 - 47.01: 122 47.01 - 62.67: 51 62.67 - 78.34: 3 Dihedral angle restraints: 6265 sinusoidal: 3144 harmonic: 3121 Sorted by residual: dihedral pdb=" CB CYS R 204 " pdb=" SG CYS R 204 " pdb=" SG CYS R 277 " pdb=" CB CYS R 277 " ideal model delta sinusoidal sigma weight residual -86.00 -128.07 42.07 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CA CYS R 8 " pdb=" CB CYS R 8 " pdb=" SG CYS R 8 " pdb=" SG CYS R 34 " ideal model delta sinusoidal sigma weight residual -73.00 2.56 -75.56 1 2.00e+01 2.50e-03 1.80e+01 dihedral pdb=" SG CYS R 204 " pdb=" CB CYS R 277 " pdb=" SG CYS R 277 " pdb=" CA CYS R 277 " ideal model delta sinusoidal sigma weight residual -73.00 -13.85 -59.15 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 6262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 951 0.047 - 0.094: 137 0.094 - 0.141: 48 0.141 - 0.188: 3 0.188 - 0.235: 2 Chirality restraints: 1141 Sorted by residual: chirality pdb=" C14 CLR R 501 " pdb=" C13 CLR R 501 " pdb=" C15 CLR R 501 " pdb=" C8 CLR R 501 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" C14 CLR R 502 " pdb=" C13 CLR R 502 " pdb=" C15 CLR R 502 " pdb=" C8 CLR R 502 " both_signs ideal model delta sigma weight residual False -2.32 -2.53 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" C3 CLR R 502 " pdb=" C2 CLR R 502 " pdb=" C4 CLR R 502 " pdb=" O1 CLR R 502 " both_signs ideal model delta sigma weight residual False -2.46 -2.29 -0.17 2.00e-01 2.50e+01 7.03e-01 ... (remaining 1138 not shown) Planarity restraints: 2035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 287 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO C 288 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 288 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 288 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 189 " -0.004 2.00e-02 2.50e+03 6.77e-03 1.83e+00 pdb=" CG TRP R 189 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP R 189 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP R 189 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 189 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP R 189 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 189 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 189 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 189 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP R 189 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP R 189 " -0.004 2.00e-02 2.50e+03 pdb=" HE1 TRP R 189 " -0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP R 189 " 0.000 2.00e-02 2.50e+03 pdb=" HZ2 TRP R 189 " -0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP R 189 " -0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP R 189 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 293 " -0.026 9.50e-02 1.11e+02 1.24e-02 1.82e+00 pdb=" NE ARG R 293 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG R 293 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG R 293 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG R 293 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG R 293 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG R 293 " 0.002 2.00e-02 2.50e+03 pdb="HH21 ARG R 293 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG R 293 " 0.005 2.00e-02 2.50e+03 ... (remaining 2032 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 674 2.19 - 2.79: 25025 2.79 - 3.40: 34280 3.40 - 4.00: 43620 4.00 - 4.60: 67203 Nonbonded interactions: 170802 Sorted by model distance: nonbonded pdb=" O ASN D 230 " pdb="HD21 ASN D 230 " model vdw 1.588 1.850 nonbonded pdb=" O ARG D 314 " pdb=" H TRP D 332 " model vdw 1.662 1.850 nonbonded pdb=" O ILE R 288 " pdb=" H LEU R 292 " model vdw 1.670 1.850 nonbonded pdb=" O GLY D 77 " pdb=" H LEU D 95 " model vdw 1.691 1.850 nonbonded pdb=" H LEU C 36 " pdb=" O LYS C 197 " model vdw 1.691 1.850 ... (remaining 170797 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.220 Extract box with map and model: 4.310 Check model and map are aligned: 0.150 Set scattering table: 0.120 Process input model: 41.420 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6093 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 0.131 6754 Z= 0.264 Angle : 0.513 10.822 9252 Z= 0.250 Chirality : 0.040 0.235 1141 Planarity : 0.002 0.042 1155 Dihedral : 12.584 78.343 2283 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.16 % Allowed : 0.00 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.30), residues: 892 helix: 2.88 (0.28), residues: 363 sheet: -0.18 (0.44), residues: 152 loop : -0.65 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 189 HIS 0.011 0.001 HIS R 2 PHE 0.015 0.001 PHE R 211 TYR 0.009 0.001 TYR R 140 ARG 0.021 0.001 ARG R 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue MET 15 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue TYR 124 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 203 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue MET 268 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 327 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue LYS 359 is missing expected H atoms. Skipping. Residue LEU 360 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LYS 371 is missing expected H atoms. Skipping. Residue SER 386 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 183 VAL cc_start: 0.7704 (t) cc_final: 0.7324 (p) REVERT: R 337 LEU cc_start: 0.7992 (mp) cc_final: 0.7780 (mp) outliers start: 1 outliers final: 0 residues processed: 170 average time/residue: 0.3148 time to fit residues: 74.3496 Evaluate side-chains 131 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.0570 chunk 68 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 overall best weight: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN D 230 ASN R 325 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6754 Z= 0.226 Angle : 0.499 4.462 9252 Z= 0.270 Chirality : 0.039 0.151 1141 Planarity : 0.003 0.036 1155 Dihedral : 3.548 19.078 1074 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.72 % Allowed : 10.61 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.29), residues: 892 helix: 2.57 (0.27), residues: 365 sheet: -0.17 (0.44), residues: 142 loop : -0.98 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 297 HIS 0.007 0.002 HIS C 322 PHE 0.021 0.002 PHE C 307 TYR 0.013 0.001 TYR D 105 ARG 0.003 0.001 ARG R 315 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue MET 15 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue TYR 124 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 203 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue MET 268 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 327 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue LYS 359 is missing expected H atoms. Skipping. Residue LEU 360 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LYS 371 is missing expected H atoms. Skipping. Residue SER 386 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 147 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 333 GLN cc_start: 0.8279 (tp40) cc_final: 0.7944 (tp40) REVERT: C 337 ASP cc_start: 0.7333 (m-30) cc_final: 0.7094 (m-30) REVERT: D 196 THR cc_start: 0.6396 (p) cc_final: 0.6177 (p) outliers start: 11 outliers final: 8 residues processed: 154 average time/residue: 0.3111 time to fit residues: 67.2304 Evaluate side-chains 135 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 127 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 295 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 0.3980 chunk 88 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 230 ASN D 295 ASN ** R 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6754 Z= 0.223 Angle : 0.475 4.693 9252 Z= 0.259 Chirality : 0.038 0.153 1141 Planarity : 0.003 0.035 1155 Dihedral : 3.593 21.515 1074 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.65 % Allowed : 13.73 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.29), residues: 892 helix: 2.56 (0.27), residues: 364 sheet: -0.57 (0.42), residues: 145 loop : -1.05 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 99 HIS 0.006 0.001 HIS C 322 PHE 0.015 0.001 PHE C 196 TYR 0.013 0.001 TYR R 313 ARG 0.002 0.000 ARG R 293 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue MET 15 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue TYR 124 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 203 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue MET 268 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 327 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue LYS 359 is missing expected H atoms. Skipping. Residue LEU 360 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LYS 371 is missing expected H atoms. Skipping. Residue SER 386 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 150 average time/residue: 0.3090 time to fit residues: 65.2208 Evaluate side-chains 141 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 131 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 238 ASN Chi-restraints excluded: chain R residue 241 ASN Chi-restraints excluded: chain R residue 357 THR Chi-restraints excluded: chain R residue 367 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.0270 chunk 42 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 GLN D 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6754 Z= 0.210 Angle : 0.464 4.297 9252 Z= 0.252 Chirality : 0.037 0.155 1141 Planarity : 0.003 0.035 1155 Dihedral : 3.564 22.386 1074 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.03 % Allowed : 15.44 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.29), residues: 892 helix: 2.61 (0.27), residues: 364 sheet: -0.65 (0.41), residues: 149 loop : -1.06 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 99 HIS 0.005 0.001 HIS D 54 PHE 0.012 0.001 PHE C 196 TYR 0.012 0.001 TYR R 313 ARG 0.001 0.000 ARG D 304 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue MET 15 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue TYR 124 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 203 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue MET 268 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 327 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue LYS 359 is missing expected H atoms. Skipping. Residue LEU 360 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LYS 371 is missing expected H atoms. Skipping. Residue SER 386 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 146 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 297 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7925 (mp0) REVERT: D 105 TYR cc_start: 0.7506 (t80) cc_final: 0.6264 (t80) outliers start: 13 outliers final: 10 residues processed: 155 average time/residue: 0.3396 time to fit residues: 73.9336 Evaluate side-chains 140 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 212 PHE Chi-restraints excluded: chain R residue 238 ASN Chi-restraints excluded: chain R residue 357 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN D 230 ASN ** R 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6754 Z= 0.166 Angle : 0.446 4.560 9252 Z= 0.241 Chirality : 0.037 0.154 1141 Planarity : 0.003 0.035 1155 Dihedral : 3.375 20.208 1074 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.50 % Allowed : 17.63 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.29), residues: 892 helix: 2.63 (0.27), residues: 369 sheet: -0.56 (0.42), residues: 149 loop : -1.03 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 99 HIS 0.005 0.001 HIS C 322 PHE 0.011 0.001 PHE C 196 TYR 0.011 0.001 TYR R 313 ARG 0.001 0.000 ARG D 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue MET 15 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue TYR 124 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 203 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue MET 268 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 327 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue LYS 359 is missing expected H atoms. Skipping. Residue LEU 360 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LYS 371 is missing expected H atoms. Skipping. Residue SER 386 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 140 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 33 GLU cc_start: 0.7412 (tt0) cc_final: 0.7171 (tt0) REVERT: C 297 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7922 (mp0) REVERT: D 105 TYR cc_start: 0.7501 (t80) cc_final: 0.6326 (t80) REVERT: D 314 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6736 (ttp80) outliers start: 16 outliers final: 11 residues processed: 151 average time/residue: 0.3056 time to fit residues: 64.9861 Evaluate side-chains 147 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 212 PHE Chi-restraints excluded: chain R residue 238 ASN Chi-restraints excluded: chain R residue 357 THR Chi-restraints excluded: chain R residue 367 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.0970 chunk 21 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 230 ASN D 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6754 Z= 0.208 Angle : 0.465 4.195 9252 Z= 0.253 Chirality : 0.037 0.156 1141 Planarity : 0.003 0.035 1155 Dihedral : 3.619 23.958 1074 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.81 % Allowed : 18.72 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.29), residues: 892 helix: 2.49 (0.27), residues: 368 sheet: -0.85 (0.40), residues: 149 loop : -1.15 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 99 HIS 0.004 0.001 HIS C 322 PHE 0.010 0.001 PHE R 210 TYR 0.011 0.001 TYR R 313 ARG 0.001 0.000 ARG D 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue MET 15 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue TYR 124 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 203 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue MET 268 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 327 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue LYS 359 is missing expected H atoms. Skipping. Residue LEU 360 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LYS 371 is missing expected H atoms. Skipping. Residue SER 386 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 33 GLU cc_start: 0.7513 (tt0) cc_final: 0.7270 (tt0) REVERT: D 314 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6833 (ttp80) outliers start: 18 outliers final: 13 residues processed: 152 average time/residue: 0.3039 time to fit residues: 65.1868 Evaluate side-chains 149 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 135 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 233 CYS Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 212 PHE Chi-restraints excluded: chain R residue 238 ASN Chi-restraints excluded: chain R residue 240 MET Chi-restraints excluded: chain R residue 357 THR Chi-restraints excluded: chain R residue 367 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 230 ASN ** R 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6754 Z= 0.182 Angle : 0.461 6.580 9252 Z= 0.249 Chirality : 0.037 0.140 1141 Planarity : 0.003 0.035 1155 Dihedral : 3.526 23.282 1074 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.96 % Allowed : 19.19 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.29), residues: 892 helix: 2.56 (0.27), residues: 368 sheet: -0.95 (0.40), residues: 166 loop : -0.97 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 99 HIS 0.004 0.001 HIS C 322 PHE 0.010 0.001 PHE R 342 TYR 0.011 0.001 TYR R 313 ARG 0.001 0.000 ARG D 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue MET 15 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue TYR 124 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 203 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue MET 268 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 327 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue LYS 359 is missing expected H atoms. Skipping. Residue LEU 360 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LYS 371 is missing expected H atoms. Skipping. Residue SER 386 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 33 GLU cc_start: 0.7534 (tt0) cc_final: 0.7272 (tt0) REVERT: D 314 ARG cc_start: 0.7084 (OUTLIER) cc_final: 0.6789 (ttp80) outliers start: 19 outliers final: 15 residues processed: 157 average time/residue: 0.3158 time to fit residues: 69.8302 Evaluate side-chains 152 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 136 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 35 CYS Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 212 PHE Chi-restraints excluded: chain R residue 238 ASN Chi-restraints excluded: chain R residue 240 MET Chi-restraints excluded: chain R residue 357 THR Chi-restraints excluded: chain R residue 367 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 55 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6754 Z= 0.253 Angle : 0.497 5.220 9252 Z= 0.273 Chirality : 0.038 0.150 1141 Planarity : 0.003 0.034 1155 Dihedral : 3.871 29.269 1074 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.28 % Allowed : 19.19 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.29), residues: 892 helix: 2.34 (0.27), residues: 373 sheet: -0.82 (0.40), residues: 166 loop : -1.20 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 99 HIS 0.005 0.001 HIS C 322 PHE 0.010 0.001 PHE R 212 TYR 0.011 0.001 TYR D 105 ARG 0.001 0.000 ARG D 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue MET 15 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue TYR 124 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 203 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue MET 268 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 327 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue LYS 359 is missing expected H atoms. Skipping. Residue LEU 360 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LYS 371 is missing expected H atoms. Skipping. Residue SER 386 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 135 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 33 GLU cc_start: 0.7539 (tt0) cc_final: 0.7269 (tt0) REVERT: D 314 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6857 (ttp80) outliers start: 21 outliers final: 17 residues processed: 148 average time/residue: 0.3130 time to fit residues: 66.1595 Evaluate side-chains 146 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 233 CYS Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 35 CYS Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 212 PHE Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 238 ASN Chi-restraints excluded: chain R residue 357 THR Chi-restraints excluded: chain R residue 367 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6754 Z= 0.212 Angle : 0.479 4.320 9252 Z= 0.261 Chirality : 0.037 0.158 1141 Planarity : 0.003 0.035 1155 Dihedral : 4.121 51.192 1074 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.81 % Allowed : 20.12 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.29), residues: 892 helix: 2.37 (0.27), residues: 372 sheet: -0.79 (0.40), residues: 171 loop : -1.22 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 99 HIS 0.005 0.001 HIS C 322 PHE 0.011 0.001 PHE R 212 TYR 0.010 0.001 TYR R 313 ARG 0.001 0.000 ARG D 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue MET 15 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue TYR 124 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 203 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue MET 268 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 327 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue LYS 359 is missing expected H atoms. Skipping. Residue LEU 360 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LYS 371 is missing expected H atoms. Skipping. Residue SER 386 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 139 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 33 GLU cc_start: 0.7574 (tt0) cc_final: 0.7288 (tt0) REVERT: D 314 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6825 (ttp80) outliers start: 18 outliers final: 16 residues processed: 150 average time/residue: 0.3194 time to fit residues: 68.5996 Evaluate side-chains 149 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 233 CYS Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 35 CYS Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 212 PHE Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 238 ASN Chi-restraints excluded: chain R residue 357 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.7980 chunk 59 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 82 optimal weight: 0.4980 chunk 71 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 56 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6754 Z= 0.168 Angle : 0.459 4.151 9252 Z= 0.248 Chirality : 0.037 0.157 1141 Planarity : 0.003 0.036 1155 Dihedral : 4.014 46.460 1074 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.96 % Allowed : 20.28 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.29), residues: 892 helix: 2.56 (0.27), residues: 367 sheet: -0.88 (0.40), residues: 164 loop : -1.17 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 346 HIS 0.005 0.001 HIS C 322 PHE 0.011 0.001 PHE R 342 TYR 0.010 0.001 TYR R 313 ARG 0.001 0.000 ARG D 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue MET 15 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue TYR 124 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 203 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue MET 268 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 327 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue LYS 359 is missing expected H atoms. Skipping. Residue LEU 360 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LYS 371 is missing expected H atoms. Skipping. Residue SER 386 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 314 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6790 (ttp80) outliers start: 19 outliers final: 17 residues processed: 146 average time/residue: 0.3079 time to fit residues: 63.5584 Evaluate side-chains 155 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 137 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 233 CYS Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 35 CYS Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 212 PHE Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 238 ASN Chi-restraints excluded: chain R residue 357 THR Chi-restraints excluded: chain R residue 367 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 0.0970 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 51 optimal weight: 0.0570 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.165596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.128728 restraints weight = 25690.917| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.99 r_work: 0.3770 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6754 Z= 0.152 Angle : 0.465 4.212 9252 Z= 0.249 Chirality : 0.037 0.157 1141 Planarity : 0.003 0.036 1155 Dihedral : 3.896 50.407 1074 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.50 % Allowed : 20.75 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.29), residues: 892 helix: 2.59 (0.27), residues: 367 sheet: -1.04 (0.42), residues: 149 loop : -1.06 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 99 HIS 0.005 0.001 HIS C 322 PHE 0.010 0.001 PHE R 342 TYR 0.012 0.001 TYR R 395 ARG 0.002 0.000 ARG D 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3818.91 seconds wall clock time: 68 minutes 16.18 seconds (4096.18 seconds total)