Starting phenix.real_space_refine on Wed Jun 26 02:16:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yuu_39583/06_2024/8yuu_39583_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yuu_39583/06_2024/8yuu_39583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yuu_39583/06_2024/8yuu_39583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yuu_39583/06_2024/8yuu_39583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yuu_39583/06_2024/8yuu_39583_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yuu_39583/06_2024/8yuu_39583_updated.pdb" } resolution = 2.7 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 5762 2.51 5 N 1537 2.21 5 O 1678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 9037 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2344 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 1 Chain: "A" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1811 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "S" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1795 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Chain: "R" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'CLR': 1, 'HSM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.18, per 1000 atoms: 0.57 Number of scatterers: 9037 At special positions: 0 Unit cell: (106.47, 121.68, 115.596, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1678 8.00 N 1537 7.00 C 5762 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 107 " - pdb=" SG CYS R 188 " distance=2.03 Simple disulfide: pdb=" SG CYS R 384 " - pdb=" SG CYS R 388 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 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: 3.75 Conformation dependent library (CDL) restraints added in 1.5 seconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 13 sheets defined 37.1% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'R' and resid 33 through 61 removed outlier: 4.587A pdb=" N ALA R 38 " --> pdb=" O ALA R 35 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR R 48 " --> pdb=" O ILE R 45 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU R 50 " --> pdb=" O ALA R 47 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY R 51 " --> pdb=" O THR R 48 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN R 52 " --> pdb=" O VAL R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 85 Processing helix chain 'R' and resid 87 through 97 Proline residue: R 93 - end of helix Processing helix chain 'R' and resid 107 through 137 removed outlier: 3.782A pdb=" N VAL R 136 " --> pdb=" O ARG R 132 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 145 Processing helix chain 'R' and resid 150 through 172 removed outlier: 3.911A pdb=" N TYR R 167 " --> pdb=" O ALA R 163 " (cutoff:3.500A) Proline residue: R 169 - end of helix Processing helix chain 'R' and resid 175 through 178 No H-bonds generated for 'chain 'R' and resid 175 through 178' Processing helix chain 'R' and resid 196 through 206 Processing helix chain 'R' and resid 208 through 234 Processing helix chain 'R' and resid 344 through 383 Proline residue: R 373 - end of helix Processing helix chain 'R' and resid 391 through 415 removed outlier: 3.648A pdb=" N LEU R 401 " --> pdb=" O SER R 397 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TRP R 402 " --> pdb=" O PHE R 398 " (cutoff:3.500A) Proline residue: R 409 - end of helix Proline residue: R 413 - end of helix Processing helix chain 'R' and resid 417 through 426 Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.839A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 231 removed outlier: 3.788A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.640A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.572A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.285A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 62 through 64 No H-bonds generated for 'chain 'S' and resid 62 through 64' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'S' and resid 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.524A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.866A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.034A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.804A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.973A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.812A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.510A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.663A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.986A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.653A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'S' and resid 155 through 160 Processing sheet with id= M, first strand: chain 'S' and resid 226 through 231 removed outlier: 5.990A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1146 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2068 1.33 - 1.45: 2075 1.45 - 1.57: 5004 1.57 - 1.69: 5 1.69 - 1.82: 85 Bond restraints: 9237 Sorted by residual: bond pdb=" CA TYR A 296 " pdb=" C TYR A 296 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.30e-02 5.92e+03 9.62e+00 bond pdb=" C23 CLR R 502 " pdb=" C24 CLR R 502 " ideal model delta sigma weight residual 1.525 1.578 -0.053 2.00e-02 2.50e+03 6.98e+00 bond pdb=" C16 CLR R 502 " pdb=" C17 CLR R 502 " ideal model delta sigma weight residual 1.554 1.607 -0.053 2.00e-02 2.50e+03 6.90e+00 bond pdb=" CA ALA R 53 " pdb=" C ALA R 53 " ideal model delta sigma weight residual 1.524 1.492 0.032 1.27e-02 6.20e+03 6.29e+00 bond pdb=" C GLN S 13 " pdb=" N PRO S 14 " ideal model delta sigma weight residual 1.332 1.364 -0.032 1.30e-02 5.92e+03 6.06e+00 ... (remaining 9232 not shown) Histogram of bond angle deviations from ideal: 96.83 - 104.27: 103 104.27 - 111.72: 4301 111.72 - 119.16: 3157 119.16 - 126.60: 4814 126.60 - 134.05: 145 Bond angle restraints: 12520 Sorted by residual: angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" C ASP B 76 " ideal model delta sigma weight residual 112.92 102.38 10.54 1.23e+00 6.61e-01 7.34e+01 angle pdb=" N GLY S 114 " pdb=" CA GLY S 114 " pdb=" C GLY S 114 " ideal model delta sigma weight residual 112.18 122.53 -10.35 1.34e+00 5.57e-01 5.97e+01 angle pdb=" N LEU R 172 " pdb=" CA LEU R 172 " pdb=" C LEU R 172 " ideal model delta sigma weight residual 111.07 117.03 -5.96 1.07e+00 8.73e-01 3.10e+01 angle pdb=" N GLY B 282 " pdb=" CA GLY B 282 " pdb=" C GLY B 282 " ideal model delta sigma weight residual 115.27 107.68 7.59 1.41e+00 5.03e-01 2.90e+01 angle pdb=" N LYS B 78 " pdb=" CA LYS B 78 " pdb=" C LYS B 78 " ideal model delta sigma weight residual 109.50 117.94 -8.44 1.58e+00 4.01e-01 2.85e+01 ... (remaining 12515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5237 17.99 - 35.97: 229 35.97 - 53.96: 22 53.96 - 71.94: 5 71.94 - 89.93: 6 Dihedral angle restraints: 5499 sinusoidal: 2176 harmonic: 3323 Sorted by residual: dihedral pdb=" N SER S 193 " pdb=" C SER S 193 " pdb=" CA SER S 193 " pdb=" CB SER S 193 " ideal model delta harmonic sigma weight residual 122.80 131.92 -9.12 0 2.50e+00 1.60e-01 1.33e+01 dihedral pdb=" CA SER S 208 " pdb=" C SER S 208 " pdb=" N GLY S 209 " pdb=" CA GLY S 209 " ideal model delta harmonic sigma weight residual 180.00 162.52 17.48 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" C SER S 193 " pdb=" N SER S 193 " pdb=" CA SER S 193 " pdb=" CB SER S 193 " ideal model delta harmonic sigma weight residual -122.60 -131.11 8.51 0 2.50e+00 1.60e-01 1.16e+01 ... (remaining 5496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1187 0.075 - 0.150: 184 0.150 - 0.225: 24 0.225 - 0.300: 11 0.300 - 0.375: 2 Chirality restraints: 1408 Sorted by residual: chirality pdb=" CA SER S 193 " pdb=" N SER S 193 " pdb=" C SER S 193 " pdb=" CB SER S 193 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" C13 CLR R 502 " pdb=" C12 CLR R 502 " pdb=" C14 CLR R 502 " pdb=" C17 CLR R 502 " both_signs ideal model delta sigma weight residual False -2.93 -3.24 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C17 CLR R 502 " pdb=" C13 CLR R 502 " pdb=" C16 CLR R 502 " pdb=" C20 CLR R 502 " both_signs ideal model delta sigma weight residual False 2.55 2.85 -0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 1405 not shown) Planarity restraints: 1577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 75 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C GLN B 75 " -0.062 2.00e-02 2.50e+03 pdb=" O GLN B 75 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP B 76 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS S 35 " -0.012 2.00e-02 2.50e+03 2.45e-02 5.98e+00 pdb=" C HIS S 35 " 0.042 2.00e-02 2.50e+03 pdb=" O HIS S 35 " -0.016 2.00e-02 2.50e+03 pdb=" N TRP S 36 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR S 190 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.76e+00 pdb=" C TYR S 190 " -0.042 2.00e-02 2.50e+03 pdb=" O TYR S 190 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG S 191 " 0.014 2.00e-02 2.50e+03 ... (remaining 1574 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 83 2.64 - 3.21: 8149 3.21 - 3.77: 13532 3.77 - 4.34: 20069 4.34 - 4.90: 33443 Nonbonded interactions: 75276 Sorted by model distance: nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.076 2.440 nonbonded pdb=" O CYS A 3 " pdb=" OG1 THR A 4 " model vdw 2.173 2.440 nonbonded pdb=" O ASP B 154 " pdb=" OD1 ASP B 154 " model vdw 2.196 3.040 nonbonded pdb=" O GLY A 352 " pdb=" N PHE A 354 " model vdw 2.258 2.520 nonbonded pdb=" OD1 ASP R 62 " pdb=" OG SER R 64 " model vdw 2.315 2.440 ... (remaining 75271 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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.620 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 26.830 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 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 : 0.005 0.053 9237 Z= 0.343 Angle : 0.834 10.537 12520 Z= 0.527 Chirality : 0.059 0.375 1408 Planarity : 0.004 0.053 1577 Dihedral : 10.474 89.929 3345 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.26), residues: 1129 helix: 2.09 (0.26), residues: 418 sheet: 1.03 (0.30), residues: 286 loop : -0.12 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 211 HIS 0.007 0.001 HIS B 91 PHE 0.017 0.002 PHE B 199 TYR 0.014 0.002 TYR S 103 ARG 0.005 0.001 ARG S 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 197 TYR cc_start: 0.6279 (m-80) cc_final: 0.6078 (m-10) REVERT: R 354 ARG cc_start: 0.6585 (ttt180) cc_final: 0.5941 (ttp-110) REVERT: A 47 ASN cc_start: 0.7235 (m-40) cc_final: 0.6777 (p0) REVERT: A 228 SER cc_start: 0.7781 (p) cc_final: 0.6761 (m) REVERT: A 306 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7758 (mp10) REVERT: B 254 ASP cc_start: 0.7427 (t70) cc_final: 0.7188 (t70) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 1.2601 time to fit residues: 251.3764 Evaluate side-chains 138 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 52 optimal weight: 8.9990 chunk 64 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 70 ASN B 220 GLN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9237 Z= 0.186 Angle : 0.520 8.978 12520 Z= 0.279 Chirality : 0.042 0.146 1408 Planarity : 0.004 0.040 1577 Dihedral : 5.516 79.989 1314 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.21 % Favored : 97.70 % Rotamer: Outliers : 2.66 % Allowed : 9.94 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.25), residues: 1129 helix: 2.40 (0.25), residues: 416 sheet: 1.01 (0.30), residues: 276 loop : -0.09 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.003 0.001 HIS B 91 PHE 0.018 0.001 PHE R 192 TYR 0.010 0.001 TYR S 175 ARG 0.012 0.000 ARG R 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 354 ARG cc_start: 0.6574 (ttt180) cc_final: 0.5942 (ttp-110) REVERT: R 376 LEU cc_start: 0.8074 (mm) cc_final: 0.7819 (mm) REVERT: A 47 ASN cc_start: 0.7173 (m-40) cc_final: 0.6704 (p0) REVERT: A 197 LYS cc_start: 0.8687 (mttt) cc_final: 0.8364 (mttm) REVERT: A 273 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8396 (mm) REVERT: A 306 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7751 (mp10) REVERT: B 44 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7398 (mt0) REVERT: B 153 ASP cc_start: 0.7102 (t0) cc_final: 0.6873 (t70) REVERT: B 217 MET cc_start: 0.7347 (ptt) cc_final: 0.7145 (ptt) REVERT: S 85 SER cc_start: 0.8858 (m) cc_final: 0.8506 (t) outliers start: 26 outliers final: 9 residues processed: 152 average time/residue: 1.3006 time to fit residues: 209.9437 Evaluate side-chains 141 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 392 TYR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 158 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 34 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN G 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9237 Z= 0.151 Angle : 0.466 5.607 12520 Z= 0.252 Chirality : 0.040 0.140 1408 Planarity : 0.003 0.036 1577 Dihedral : 5.165 70.481 1314 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.30 % Favored : 97.61 % Rotamer: Outliers : 2.25 % Allowed : 11.07 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.25), residues: 1129 helix: 2.66 (0.26), residues: 414 sheet: 1.05 (0.29), residues: 276 loop : -0.12 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.003 0.001 HIS B 91 PHE 0.017 0.001 PHE R 192 TYR 0.010 0.001 TYR R 392 ARG 0.007 0.000 ARG R 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: R 412 TYR cc_start: 0.8333 (m-80) cc_final: 0.8067 (m-80) REVERT: A 24 ARG cc_start: 0.7718 (mtm-85) cc_final: 0.7399 (ttm-80) REVERT: A 197 LYS cc_start: 0.8701 (mttt) cc_final: 0.8372 (mttm) REVERT: A 207 GLU cc_start: 0.6932 (tp30) cc_final: 0.6543 (mt-10) REVERT: A 273 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8372 (mm) REVERT: A 306 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7683 (mp10) REVERT: B 44 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7390 (mt0) REVERT: B 153 ASP cc_start: 0.7095 (t0) cc_final: 0.6840 (t70) REVERT: B 217 MET cc_start: 0.7302 (ptt) cc_final: 0.7030 (ptt) REVERT: B 259 GLN cc_start: 0.8375 (mt0) cc_final: 0.8155 (mt0) REVERT: S 85 SER cc_start: 0.8884 (m) cc_final: 0.8529 (t) outliers start: 22 outliers final: 10 residues processed: 140 average time/residue: 1.3190 time to fit residues: 196.2330 Evaluate side-chains 136 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 392 TYR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9237 Z= 0.286 Angle : 0.555 8.912 12520 Z= 0.295 Chirality : 0.043 0.165 1408 Planarity : 0.004 0.038 1577 Dihedral : 5.405 69.269 1314 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.48 % Favored : 97.43 % Rotamer: Outliers : 3.59 % Allowed : 12.19 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.25), residues: 1129 helix: 2.46 (0.25), residues: 414 sheet: 1.01 (0.29), residues: 286 loop : -0.22 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 176 HIS 0.006 0.001 HIS B 91 PHE 0.020 0.002 PHE R 192 TYR 0.018 0.002 TYR S 190 ARG 0.004 0.000 ARG R 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 128 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: R 376 LEU cc_start: 0.8281 (mm) cc_final: 0.8031 (mm) REVERT: R 412 TYR cc_start: 0.8348 (m-80) cc_final: 0.8066 (m-80) REVERT: A 24 ARG cc_start: 0.7795 (mtm-85) cc_final: 0.7451 (ttm-80) REVERT: A 197 LYS cc_start: 0.8720 (mttt) cc_final: 0.8390 (mttm) REVERT: A 306 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7788 (mp10) REVERT: B 44 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7451 (mt0) REVERT: B 219 ARG cc_start: 0.7174 (mmt90) cc_final: 0.6828 (mmt180) REVERT: S 85 SER cc_start: 0.8918 (m) cc_final: 0.8544 (t) outliers start: 35 outliers final: 17 residues processed: 146 average time/residue: 1.2491 time to fit residues: 194.0852 Evaluate side-chains 141 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 392 TYR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 54 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 416 HIS G 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9237 Z= 0.349 Angle : 0.590 8.974 12520 Z= 0.315 Chirality : 0.045 0.167 1408 Planarity : 0.005 0.054 1577 Dihedral : 5.781 74.177 1314 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.48 % Favored : 97.43 % Rotamer: Outliers : 3.69 % Allowed : 12.40 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.25), residues: 1129 helix: 2.23 (0.25), residues: 416 sheet: 0.95 (0.29), residues: 274 loop : -0.33 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 211 HIS 0.007 0.001 HIS B 91 PHE 0.015 0.002 PHE R 192 TYR 0.021 0.002 TYR S 190 ARG 0.005 0.001 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 139 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: R 162 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.6855 (mm) REVERT: R 354 ARG cc_start: 0.6646 (ttt180) cc_final: 0.5925 (ttp-110) REVERT: R 376 LEU cc_start: 0.8315 (mm) cc_final: 0.8030 (mm) REVERT: R 412 TYR cc_start: 0.8359 (m-80) cc_final: 0.8051 (m-80) REVERT: A 24 ARG cc_start: 0.7785 (mtm-85) cc_final: 0.7464 (ttm-80) REVERT: A 197 LYS cc_start: 0.8688 (mttt) cc_final: 0.8378 (mttm) REVERT: A 306 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7788 (mp10) REVERT: A 341 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7895 (t70) REVERT: B 44 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7473 (mt0) REVERT: B 219 ARG cc_start: 0.7282 (mmt90) cc_final: 0.7007 (mmp80) REVERT: G 46 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7907 (mmtt) REVERT: S 85 SER cc_start: 0.8909 (m) cc_final: 0.8582 (t) outliers start: 36 outliers final: 17 residues processed: 159 average time/residue: 1.3450 time to fit residues: 227.3933 Evaluate side-chains 155 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 134 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 392 TYR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 340 ASN G 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9237 Z= 0.157 Angle : 0.479 7.858 12520 Z= 0.256 Chirality : 0.040 0.145 1408 Planarity : 0.004 0.042 1577 Dihedral : 5.321 64.965 1314 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.21 % Favored : 97.70 % Rotamer: Outliers : 2.77 % Allowed : 14.14 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.25), residues: 1129 helix: 2.56 (0.26), residues: 413 sheet: 0.96 (0.29), residues: 286 loop : -0.33 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.003 0.001 HIS S 35 PHE 0.019 0.001 PHE R 192 TYR 0.013 0.001 TYR S 190 ARG 0.004 0.000 ARG R 154 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 131 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: R 412 TYR cc_start: 0.8332 (m-80) cc_final: 0.8125 (m-80) REVERT: A 24 ARG cc_start: 0.7691 (mtm-85) cc_final: 0.7445 (ttm-80) REVERT: A 197 LYS cc_start: 0.8686 (mttt) cc_final: 0.8370 (mttm) REVERT: A 306 GLN cc_start: 0.7964 (mm-40) cc_final: 0.7686 (mp10) REVERT: G 46 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7932 (mmtt) REVERT: S 85 SER cc_start: 0.8915 (m) cc_final: 0.8598 (t) outliers start: 27 outliers final: 14 residues processed: 145 average time/residue: 1.2876 time to fit residues: 198.7635 Evaluate side-chains 141 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 392 TYR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 416 HIS B 175 GLN G 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9237 Z= 0.295 Angle : 0.558 8.756 12520 Z= 0.295 Chirality : 0.043 0.153 1408 Planarity : 0.004 0.043 1577 Dihedral : 5.518 64.346 1314 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.66 % Favored : 97.25 % Rotamer: Outliers : 3.07 % Allowed : 13.73 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.25), residues: 1129 helix: 2.45 (0.25), residues: 413 sheet: 0.94 (0.29), residues: 274 loop : -0.38 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.006 0.001 HIS B 91 PHE 0.014 0.002 PHE R 192 TYR 0.021 0.002 TYR S 190 ARG 0.004 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 127 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: R 162 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.6771 (mm) REVERT: R 412 TYR cc_start: 0.8378 (m-80) cc_final: 0.8057 (m-80) REVERT: A 197 LYS cc_start: 0.8703 (mttt) cc_final: 0.8388 (mttm) REVERT: A 306 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7809 (mp10) REVERT: A 341 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7868 (t70) REVERT: G 46 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7938 (mmtt) REVERT: S 85 SER cc_start: 0.8917 (m) cc_final: 0.8600 (t) outliers start: 30 outliers final: 19 residues processed: 144 average time/residue: 1.2733 time to fit residues: 195.1981 Evaluate side-chains 149 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 392 TYR Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 chunk 97 optimal weight: 0.5980 chunk 102 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 340 ASN G 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9237 Z= 0.272 Angle : 0.545 8.927 12520 Z= 0.289 Chirality : 0.043 0.149 1408 Planarity : 0.004 0.042 1577 Dihedral : 5.486 60.086 1314 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.48 % Favored : 97.43 % Rotamer: Outliers : 2.66 % Allowed : 14.96 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.25), residues: 1129 helix: 2.43 (0.25), residues: 413 sheet: 0.94 (0.29), residues: 274 loop : -0.41 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.006 0.001 HIS B 91 PHE 0.021 0.002 PHE R 192 TYR 0.019 0.002 TYR S 190 ARG 0.003 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 123 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: R 56 MET cc_start: 0.7105 (mtp) cc_final: 0.6568 (mtm) REVERT: R 162 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.6770 (mm) REVERT: R 412 TYR cc_start: 0.8374 (m-80) cc_final: 0.8091 (m-80) REVERT: A 24 ARG cc_start: 0.7744 (ttm-80) cc_final: 0.7431 (ttm-80) REVERT: A 197 LYS cc_start: 0.8701 (mttt) cc_final: 0.8393 (mttm) REVERT: A 306 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7807 (mp10) REVERT: G 46 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7955 (mmtt) outliers start: 26 outliers final: 19 residues processed: 139 average time/residue: 1.3350 time to fit residues: 197.0565 Evaluate side-chains 144 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 392 TYR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN G 5 ASN G 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9237 Z= 0.148 Angle : 0.474 9.123 12520 Z= 0.253 Chirality : 0.040 0.139 1408 Planarity : 0.004 0.044 1577 Dihedral : 5.042 52.354 1314 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.39 % Favored : 97.52 % Rotamer: Outliers : 1.74 % Allowed : 15.78 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.25), residues: 1129 helix: 2.65 (0.26), residues: 412 sheet: 0.98 (0.29), residues: 275 loop : -0.39 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.000 HIS S 35 PHE 0.012 0.001 PHE A 189 TYR 0.011 0.001 TYR S 190 ARG 0.003 0.000 ARG R 154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: R 162 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6749 (mm) REVERT: R 412 TYR cc_start: 0.8354 (m-80) cc_final: 0.8077 (m-80) REVERT: A 197 LYS cc_start: 0.8690 (mttt) cc_final: 0.8372 (mttm) REVERT: A 306 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7691 (mp10) REVERT: G 46 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7968 (mmtt) REVERT: S 85 SER cc_start: 0.8929 (m) cc_final: 0.8616 (t) outliers start: 17 outliers final: 14 residues processed: 136 average time/residue: 1.4007 time to fit residues: 202.4594 Evaluate side-chains 139 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 392 TYR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 5.9990 chunk 73 optimal weight: 0.2980 chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 0.0470 chunk 69 optimal weight: 0.0870 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 0.0970 overall best weight: 0.3054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 340 ASN G 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9237 Z= 0.115 Angle : 0.460 9.238 12520 Z= 0.243 Chirality : 0.039 0.136 1408 Planarity : 0.003 0.044 1577 Dihedral : 4.601 41.875 1314 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.13 % Favored : 97.79 % Rotamer: Outliers : 1.33 % Allowed : 16.70 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.25), residues: 1129 helix: 2.77 (0.26), residues: 409 sheet: 1.00 (0.29), residues: 275 loop : -0.30 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 211 HIS 0.002 0.000 HIS S 35 PHE 0.011 0.001 PHE R 81 TYR 0.009 0.001 TYR R 189 ARG 0.008 0.000 ARG A 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 137 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: R 62 ASP cc_start: 0.6572 (t0) cc_final: 0.6190 (t0) REVERT: R 162 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6744 (mm) REVERT: R 412 TYR cc_start: 0.8311 (m-80) cc_final: 0.8036 (m-80) REVERT: A 197 LYS cc_start: 0.8679 (mttt) cc_final: 0.8355 (mttm) REVERT: A 207 GLU cc_start: 0.7138 (tp30) cc_final: 0.6713 (mt-10) REVERT: A 248 LYS cc_start: 0.8061 (mtmm) cc_final: 0.7824 (mtpt) REVERT: A 306 GLN cc_start: 0.7825 (mm-40) cc_final: 0.7617 (mp10) REVERT: B 217 MET cc_start: 0.7775 (pmt) cc_final: 0.6484 (pmt) REVERT: B 219 ARG cc_start: 0.7059 (mmt90) cc_final: 0.6854 (tpt90) REVERT: G 46 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7944 (mmtt) REVERT: S 85 SER cc_start: 0.8926 (m) cc_final: 0.8609 (t) outliers start: 13 outliers final: 9 residues processed: 143 average time/residue: 1.2915 time to fit residues: 196.6053 Evaluate side-chains 142 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 131 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 392 TYR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain S residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.4980 chunk 13 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 36 optimal weight: 0.0970 chunk 90 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN G 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.174957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.114517 restraints weight = 9414.754| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.00 r_work: 0.3113 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9237 Z= 0.157 Angle : 0.489 9.000 12520 Z= 0.257 Chirality : 0.040 0.140 1408 Planarity : 0.004 0.043 1577 Dihedral : 4.538 37.147 1314 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.21 % Favored : 97.70 % Rotamer: Outliers : 1.64 % Allowed : 16.70 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.25), residues: 1129 helix: 2.73 (0.26), residues: 411 sheet: 0.94 (0.29), residues: 280 loop : -0.30 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.014 0.001 PHE R 81 TYR 0.012 0.001 TYR S 190 ARG 0.005 0.000 ARG A 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3981.95 seconds wall clock time: 69 minutes 59.36 seconds (4199.36 seconds total)