Starting phenix.real_space_refine on Tue Feb 13 18:28:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2x_30971/02_2024/7e2x_30971_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2x_30971/02_2024/7e2x_30971.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2x_30971/02_2024/7e2x_30971_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2x_30971/02_2024/7e2x_30971_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2x_30971/02_2024/7e2x_30971_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2x_30971/02_2024/7e2x_30971.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2x_30971/02_2024/7e2x_30971.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2x_30971/02_2024/7e2x_30971_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2x_30971/02_2024/7e2x_30971_neut_updated.pdb" } resolution = 3.0 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= 0.008 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 53 5.16 5 C 4708 2.51 5 N 1169 2.21 5 O 1294 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "R GLU 64": "OE1" <-> "OE2" Residue "R ARG 134": "NH1" <-> "NH2" Residue "R ARG 148": "NH1" <-> "NH2" Residue "R ARG 151": "NH1" <-> "NH2" Residue "R ARG 220": "NH1" <-> "NH2" Residue "R GLU 330": "OE1" <-> "OE2" Residue "R ARG 339": "NH1" <-> "NH2" 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: 7226 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1766 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Chain: "B" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2516 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 322} Chain: "G" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 347 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 4, 'TRANS': 40} Chain: "R" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2597 Unusual residues: {'CLR': 10, 'J40': 1, 'PLM': 3} Classifications: {'peptide': 278, 'undetermined': 14, 'water': 9} Link IDs: {'PTRANS': 11, 'TRANS': 266, None: 23} Not linked: pdbres="ILE R 415 " pdbres="J40 R 601 " Not linked: pdbres="J40 R 601 " pdbres="CLR R 602 " Not linked: pdbres="CLR R 602 " pdbres="CLR R 603 " Not linked: pdbres="CLR R 603 " pdbres="CLR R 604 " Not linked: pdbres="CLR R 604 " pdbres="CLR R 605 " ... (remaining 18 not shown) Chain breaks: 2 Time building chain proxies: 4.51, per 1000 atoms: 0.62 Number of scatterers: 7226 At special positions: 0 Unit cell: (79.092, 113.568, 112.554, 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 53 16.00 P 2 15.00 O 1294 8.00 N 1169 7.00 C 4708 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " 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: 2.70 Conformation dependent library (CDL) restraints added in 1.2 seconds 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1642 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 8 sheets defined 43.1% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 46 through 54 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 242 through 254 Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'B' and resid 14 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 19 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 'R' and resid 36 through 63 Processing helix chain 'R' and resid 65 through 67 No H-bonds generated for 'chain 'R' and resid 65 through 67' Processing helix chain 'R' and resid 70 through 99 removed outlier: 4.232A pdb=" N LEU R 90 " --> pdb=" O SER R 86 " (cutoff:3.500A) Proline residue: R 91 - end of helix Processing helix chain 'R' and resid 106 through 139 Processing helix chain 'R' and resid 141 through 146 Processing helix chain 'R' and resid 150 through 173 Proline residue: R 170 - end of helix Processing helix chain 'R' and resid 193 through 203 Processing helix chain 'R' and resid 205 through 227 Processing helix chain 'R' and resid 325 through 370 removed outlier: 3.809A pdb=" N PHE R 354 " --> pdb=" O ILE R 350 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N CYS R 357 " --> pdb=" O THR R 353 " (cutoff:3.500A) Proline residue: R 360 - end of helix Proline residue: R 369 - end of helix Processing helix chain 'R' and resid 379 through 400 removed outlier: 3.908A pdb=" N GLY R 389 " --> pdb=" O ILE R 385 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR R 390 " --> pdb=" O ASN R 386 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER R 393 " --> pdb=" O GLY R 389 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU R 394 " --> pdb=" O TYR R 390 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU R 395 " --> pdb=" O SER R 391 " (cutoff:3.500A) Proline residue: R 397 - end of helix Processing helix chain 'R' and resid 405 through 414 Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.578A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.630A 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: 6.906A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 102 through 105 removed outlier: 4.167A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU B 139 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.257A 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: 6.704A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 190 through 192 removed outlier: 3.868A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.765A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.135A 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: 6.688A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.982A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) 338 hydrogen bonds defined for protein. 996 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: 2.20 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1129 1.31 - 1.43: 1876 1.43 - 1.56: 4237 1.56 - 1.69: 61 1.69 - 1.81: 74 Bond restraints: 7377 Sorted by residual: bond pdb=" C18 J40 R 601 " pdb=" C19 J40 R 601 " ideal model delta sigma weight residual 1.333 1.526 -0.193 2.00e-02 2.50e+03 9.35e+01 bond pdb=" C21 J40 R 601 " pdb=" C22 J40 R 601 " ideal model delta sigma weight residual 1.340 1.528 -0.188 2.00e-02 2.50e+03 8.83e+01 bond pdb=" C24 J40 R 601 " pdb=" C25 J40 R 601 " ideal model delta sigma weight residual 1.341 1.528 -0.187 2.00e-02 2.50e+03 8.75e+01 bond pdb=" C15 J40 R 601 " pdb=" C16 J40 R 601 " ideal model delta sigma weight residual 1.349 1.527 -0.178 2.00e-02 2.50e+03 7.90e+01 bond pdb=" C5 CLR R 605 " pdb=" C6 CLR R 605 " ideal model delta sigma weight residual 1.332 1.469 -0.137 2.00e-02 2.50e+03 4.68e+01 ... (remaining 7372 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.07: 204 107.07 - 113.80: 4329 113.80 - 120.54: 2887 120.54 - 127.27: 2533 127.27 - 134.00: 71 Bond angle restraints: 10024 Sorted by residual: angle pdb=" C18 J40 R 601 " pdb=" C19 J40 R 601 " pdb=" C20 J40 R 601 " ideal model delta sigma weight residual 152.67 112.55 40.12 3.00e+00 1.11e-01 1.79e+02 angle pdb=" C24 J40 R 601 " pdb=" C25 J40 R 601 " pdb=" C26 J40 R 601 " ideal model delta sigma weight residual 152.63 113.09 39.54 3.00e+00 1.11e-01 1.74e+02 angle pdb=" C15 J40 R 601 " pdb=" C16 J40 R 601 " pdb=" C17 J40 R 601 " ideal model delta sigma weight residual 152.66 113.19 39.47 3.00e+00 1.11e-01 1.73e+02 angle pdb=" C21 J40 R 601 " pdb=" C22 J40 R 601 " pdb=" C23 J40 R 601 " ideal model delta sigma weight residual 152.66 113.67 38.99 3.00e+00 1.11e-01 1.69e+02 angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.47 109.60 3.87 1.01e+00 9.80e-01 1.47e+01 ... (remaining 10019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.99: 4826 34.99 - 69.98: 47 69.98 - 104.97: 7 104.97 - 139.96: 0 139.96 - 174.95: 1 Dihedral angle restraints: 4881 sinusoidal: 2350 harmonic: 2531 Sorted by residual: dihedral pdb=" C19 J40 R 601 " pdb=" C20 J40 R 601 " pdb=" C21 J40 R 601 " pdb=" C22 J40 R 601 " ideal model delta sinusoidal sigma weight residual -137.17 37.78 -174.95 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 130.24 -37.24 1 1.00e+01 1.00e-02 1.96e+01 dihedral pdb=" CA ASP A 337 " pdb=" CB ASP A 337 " pdb=" CG ASP A 337 " pdb=" OD1 ASP A 337 " ideal model delta sinusoidal sigma weight residual -30.00 -88.07 58.07 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 4878 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.008: 1170 1.008 - 2.016: 0 2.016 - 3.025: 0 3.025 - 4.033: 0 4.033 - 5.041: 2 Chirality restraints: 1172 Sorted by residual: chirality pdb=" C1 J40 R 601 " pdb=" C2 J40 R 601 " pdb=" C6 J40 R 601 " pdb=" O1 J40 R 601 " both_signs ideal model delta sigma weight residual False -2.51 2.53 -5.04 2.00e-01 2.50e+01 6.35e+02 chirality pdb=" C4 J40 R 601 " pdb=" C3 J40 R 601 " pdb=" C5 J40 R 601 " pdb=" O4 J40 R 601 " both_signs ideal model delta sigma weight residual False -2.50 2.51 -5.01 2.00e-01 2.50e+01 6.28e+02 chirality pdb=" C14 CLR R 605 " pdb=" C13 CLR R 605 " pdb=" C15 CLR R 605 " pdb=" C8 CLR R 605 " both_signs ideal model delta sigma weight residual False -2.32 -2.56 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1169 not shown) Planarity restraints: 1192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 J40 R 601 " 0.137 2.00e-02 2.50e+03 2.35e-01 5.53e+02 pdb=" C21 J40 R 601 " -0.304 2.00e-02 2.50e+03 pdb=" C22 J40 R 601 " 0.303 2.00e-02 2.50e+03 pdb=" C23 J40 R 601 " -0.135 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 J40 R 601 " -0.136 2.00e-02 2.50e+03 2.30e-01 5.28e+02 pdb=" C24 J40 R 601 " 0.295 2.00e-02 2.50e+03 pdb=" C25 J40 R 601 " -0.295 2.00e-02 2.50e+03 pdb=" C26 J40 R 601 " 0.136 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 J40 R 601 " -0.133 2.00e-02 2.50e+03 1.33e-01 1.78e+02 pdb=" C18 J40 R 601 " 0.134 2.00e-02 2.50e+03 pdb=" C19 J40 R 601 " 0.133 2.00e-02 2.50e+03 pdb=" C20 J40 R 601 " -0.133 2.00e-02 2.50e+03 ... (remaining 1189 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 55 2.59 - 3.16: 5928 3.16 - 3.74: 10367 3.74 - 4.32: 14218 4.32 - 4.90: 23975 Nonbonded interactions: 54543 Sorted by model distance: nonbonded pdb=" O ARG B 314 " pdb=" OG SER B 331 " model vdw 2.008 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.023 2.440 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.094 2.440 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.183 2.440 nonbonded pdb=" NZ LYS A 271 " pdb=" O THR A 324 " model vdw 2.202 2.520 ... (remaining 54538 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: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 1.940 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 23.150 Find NCS groups from input model: 0.230 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:11.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5703 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 : 0.010 0.193 7377 Z= 0.525 Angle : 1.071 40.124 10024 Z= 0.413 Chirality : 0.213 5.041 1172 Planarity : 0.010 0.235 1192 Dihedral : 11.846 174.954 3233 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.48 (0.31), residues: 854 helix: 3.90 (0.27), residues: 378 sheet: 1.14 (0.42), residues: 151 loop : -1.02 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 297 HIS 0.004 0.000 HIS R 126 PHE 0.019 0.001 PHE R 411 TYR 0.011 0.001 TYR B 59 ARG 0.003 0.000 ARG R 220 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.927 Fit side-chains REVERT: A 29 LYS cc_start: 0.6209 (tmtt) cc_final: 0.5588 (ttmt) REVERT: A 188 HIS cc_start: 0.8327 (m-70) cc_final: 0.8086 (m90) REVERT: A 242 ARG cc_start: 0.8405 (mtt180) cc_final: 0.8153 (ptp-110) REVERT: A 257 LYS cc_start: 0.7780 (ptmm) cc_final: 0.7301 (tppt) REVERT: A 269 ASN cc_start: 0.8706 (m-40) cc_final: 0.8468 (m-40) REVERT: A 282 PRO cc_start: 0.7589 (Cg_endo) cc_final: 0.7340 (Cg_exo) REVERT: A 324 THR cc_start: 0.7294 (m) cc_final: 0.6857 (m) REVERT: A 331 ASN cc_start: 0.8076 (m110) cc_final: 0.7801 (m110) REVERT: B 58 ILE cc_start: 0.7645 (pt) cc_final: 0.7365 (pp) REVERT: B 153 ASP cc_start: 0.7541 (m-30) cc_final: 0.6963 (p0) REVERT: B 214 ARG cc_start: 0.7935 (ttt-90) cc_final: 0.7540 (tmt170) REVERT: B 237 ASN cc_start: 0.8312 (t0) cc_final: 0.8037 (t0) REVERT: B 316 SER cc_start: 0.7517 (p) cc_final: 0.7261 (p) REVERT: B 322 ASP cc_start: 0.8370 (t70) cc_final: 0.8164 (t70) REVERT: G 38 MET cc_start: 0.7476 (ttm) cc_final: 0.7275 (tpt) outliers start: 0 outliers final: 1 residues processed: 145 average time/residue: 1.0845 time to fit residues: 166.8995 Evaluate side-chains 108 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 198 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 256 ASN A 331 ASN B 62 HIS B 75 GLN B 175 GLN R 100 ASN R 126 HIS R 409 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5922 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7377 Z= 0.261 Angle : 0.645 10.825 10024 Z= 0.304 Chirality : 0.050 0.769 1172 Planarity : 0.003 0.034 1192 Dihedral : 9.040 135.313 1664 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.83 % Allowed : 10.66 % Favored : 86.50 % 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: 1.91 (0.30), residues: 854 helix: 3.11 (0.27), residues: 384 sheet: 0.91 (0.40), residues: 160 loop : -1.03 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 297 HIS 0.004 0.001 HIS B 142 PHE 0.016 0.002 PHE R 354 TYR 0.015 0.002 TYR A 296 ARG 0.006 0.001 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 114 time to evaluate : 0.777 Fit side-chains REVERT: A 29 LYS cc_start: 0.6233 (tmtt) cc_final: 0.5644 (ttmt) REVERT: A 188 HIS cc_start: 0.8305 (m90) cc_final: 0.8079 (m90) REVERT: A 242 ARG cc_start: 0.8611 (mtt180) cc_final: 0.8229 (mtp85) REVERT: A 257 LYS cc_start: 0.8098 (ptmm) cc_final: 0.7615 (tppt) REVERT: A 282 PRO cc_start: 0.7556 (Cg_endo) cc_final: 0.7219 (Cg_exo) REVERT: A 308 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7736 (mt-10) REVERT: B 153 ASP cc_start: 0.7544 (m-30) cc_final: 0.7040 (p0) REVERT: B 214 ARG cc_start: 0.7997 (ttt-90) cc_final: 0.7680 (tmt170) REVERT: B 322 ASP cc_start: 0.8601 (t70) cc_final: 0.8273 (t0) REVERT: R 100 ASN cc_start: 0.6892 (t160) cc_final: 0.6690 (t0) outliers start: 21 outliers final: 13 residues processed: 124 average time/residue: 1.0148 time to fit residues: 134.3075 Evaluate side-chains 112 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain R residue 84 MET Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 349 ILE Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 407 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5909 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7377 Z= 0.175 Angle : 0.552 11.305 10024 Z= 0.263 Chirality : 0.044 0.527 1172 Planarity : 0.003 0.035 1192 Dihedral : 8.867 138.571 1662 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.37 % Allowed : 13.50 % Favored : 83.13 % 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: 1.81 (0.30), residues: 854 helix: 3.07 (0.27), residues: 385 sheet: 0.60 (0.40), residues: 167 loop : -1.02 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.007 0.001 HIS B 54 PHE 0.012 0.001 PHE A 336 TYR 0.010 0.001 TYR A 296 ARG 0.009 0.000 ARG R 227 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 0.769 Fit side-chains REVERT: A 29 LYS cc_start: 0.6225 (tmtt) cc_final: 0.5655 (ttmt) REVERT: A 188 HIS cc_start: 0.8236 (m90) cc_final: 0.7950 (m90) REVERT: A 242 ARG cc_start: 0.8591 (mtt180) cc_final: 0.8297 (mtp85) REVERT: A 257 LYS cc_start: 0.8126 (ptmm) cc_final: 0.7602 (tppt) REVERT: A 308 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7654 (mt-10) REVERT: B 153 ASP cc_start: 0.7444 (m-30) cc_final: 0.6936 (p0) REVERT: B 322 ASP cc_start: 0.8685 (t70) cc_final: 0.8358 (t70) REVERT: G 32 LYS cc_start: 0.8530 (tppt) cc_final: 0.8233 (tppt) outliers start: 25 outliers final: 11 residues processed: 120 average time/residue: 1.0204 time to fit residues: 130.7894 Evaluate side-chains 108 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 349 ILE Chi-restraints excluded: chain R residue 353 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 70 optimal weight: 0.3980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN R 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5917 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7377 Z= 0.182 Angle : 0.551 11.252 10024 Z= 0.265 Chirality : 0.042 0.410 1172 Planarity : 0.003 0.049 1192 Dihedral : 8.599 135.667 1662 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.51 % Allowed : 14.44 % Favored : 82.05 % 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: 1.74 (0.30), residues: 854 helix: 3.07 (0.27), residues: 385 sheet: 0.56 (0.40), residues: 167 loop : -1.15 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.005 0.001 HIS B 54 PHE 0.013 0.001 PHE B 292 TYR 0.010 0.001 TYR R 195 ARG 0.005 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 0.737 Fit side-chains REVERT: A 29 LYS cc_start: 0.6222 (tmtt) cc_final: 0.5659 (ttmt) REVERT: A 188 HIS cc_start: 0.8283 (m90) cc_final: 0.7929 (m90) REVERT: A 242 ARG cc_start: 0.8619 (mtt180) cc_final: 0.8259 (mtp85) REVERT: A 257 LYS cc_start: 0.8176 (ptmm) cc_final: 0.7612 (tppt) REVERT: A 308 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7879 (mt-10) REVERT: B 153 ASP cc_start: 0.7462 (m-30) cc_final: 0.6948 (p0) REVERT: B 322 ASP cc_start: 0.8694 (t70) cc_final: 0.8434 (t70) outliers start: 26 outliers final: 15 residues processed: 113 average time/residue: 0.9297 time to fit residues: 112.8376 Evaluate side-chains 110 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 84 MET Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 349 ILE Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 407 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 71 optimal weight: 0.1980 chunk 58 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 chunk 75 optimal weight: 0.4980 chunk 21 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN R 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5905 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7377 Z= 0.153 Angle : 0.522 9.432 10024 Z= 0.252 Chirality : 0.039 0.253 1172 Planarity : 0.003 0.037 1192 Dihedral : 8.223 132.044 1662 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.24 % Allowed : 15.25 % Favored : 81.51 % 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: 1.69 (0.30), residues: 854 helix: 3.10 (0.27), residues: 384 sheet: 0.54 (0.42), residues: 150 loop : -1.18 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.003 0.000 HIS B 54 PHE 0.013 0.001 PHE B 292 TYR 0.008 0.001 TYR R 195 ARG 0.006 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 0.717 Fit side-chains REVERT: A 29 LYS cc_start: 0.6123 (tmtt) cc_final: 0.5578 (ttmt) REVERT: A 188 HIS cc_start: 0.8215 (m90) cc_final: 0.7926 (m-70) REVERT: A 242 ARG cc_start: 0.8615 (mtt180) cc_final: 0.8263 (mtp85) REVERT: A 257 LYS cc_start: 0.8150 (ptmm) cc_final: 0.7560 (tppt) REVERT: A 308 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7908 (mt-10) REVERT: B 37 ILE cc_start: 0.7773 (mm) cc_final: 0.7404 (tt) REVERT: B 153 ASP cc_start: 0.7411 (m-30) cc_final: 0.6804 (p0) REVERT: B 274 THR cc_start: 0.8362 (m) cc_final: 0.8071 (p) REVERT: B 322 ASP cc_start: 0.8705 (t70) cc_final: 0.8441 (t70) REVERT: G 32 LYS cc_start: 0.8652 (tppt) cc_final: 0.8407 (tppt) outliers start: 24 outliers final: 12 residues processed: 112 average time/residue: 0.9067 time to fit residues: 108.8141 Evaluate side-chains 107 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 349 ILE Chi-restraints excluded: chain R residue 351 MET Chi-restraints excluded: chain R residue 353 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 chunk 44 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN R 97 GLN R 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5931 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7377 Z= 0.191 Angle : 0.529 9.058 10024 Z= 0.260 Chirality : 0.039 0.157 1172 Planarity : 0.003 0.034 1192 Dihedral : 7.958 128.549 1662 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.91 % Allowed : 15.52 % Favored : 80.57 % 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: 1.55 (0.30), residues: 854 helix: 2.92 (0.27), residues: 389 sheet: 0.56 (0.42), residues: 150 loop : -1.27 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.000 HIS B 54 PHE 0.011 0.001 PHE B 222 TYR 0.010 0.001 TYR R 195 ARG 0.006 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 97 time to evaluate : 0.703 Fit side-chains REVERT: A 29 LYS cc_start: 0.6049 (tmtt) cc_final: 0.5541 (ttmt) REVERT: A 188 HIS cc_start: 0.8215 (m90) cc_final: 0.7868 (m90) REVERT: A 242 ARG cc_start: 0.8613 (mtt180) cc_final: 0.8410 (mtm-85) REVERT: A 257 LYS cc_start: 0.8180 (ptmm) cc_final: 0.7624 (tppt) REVERT: A 308 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7834 (mt-10) REVERT: B 153 ASP cc_start: 0.7445 (m-30) cc_final: 0.6911 (p0) REVERT: B 274 THR cc_start: 0.8329 (m) cc_final: 0.8034 (p) REVERT: B 322 ASP cc_start: 0.8763 (t70) cc_final: 0.8485 (t70) REVERT: G 32 LYS cc_start: 0.8607 (tppt) cc_final: 0.8319 (tppt) REVERT: R 84 MET cc_start: 0.5365 (ttm) cc_final: 0.5158 (ttm) outliers start: 29 outliers final: 16 residues processed: 113 average time/residue: 0.9427 time to fit residues: 114.2721 Evaluate side-chains 111 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 349 ILE Chi-restraints excluded: chain R residue 353 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 4.9990 chunk 47 optimal weight: 0.0970 chunk 61 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 75 GLN B 175 GLN R 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5954 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7377 Z= 0.227 Angle : 0.548 9.533 10024 Z= 0.273 Chirality : 0.040 0.149 1172 Planarity : 0.003 0.037 1192 Dihedral : 7.922 125.907 1662 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.78 % Allowed : 16.46 % Favored : 79.76 % 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: 1.48 (0.30), residues: 854 helix: 2.81 (0.27), residues: 389 sheet: 0.56 (0.41), residues: 165 loop : -1.34 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS B 54 PHE 0.012 0.001 PHE B 292 TYR 0.012 0.001 TYR R 195 ARG 0.009 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 94 time to evaluate : 0.760 Fit side-chains REVERT: A 29 LYS cc_start: 0.6205 (tmtt) cc_final: 0.5687 (ttmt) REVERT: A 188 HIS cc_start: 0.8241 (m90) cc_final: 0.7880 (m90) REVERT: A 257 LYS cc_start: 0.8203 (ptmm) cc_final: 0.7608 (tppt) REVERT: A 308 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7825 (mt-10) REVERT: B 68 ARG cc_start: 0.7204 (ttt180) cc_final: 0.6425 (ttt90) REVERT: B 111 TYR cc_start: 0.7592 (m-80) cc_final: 0.7344 (m-80) REVERT: B 153 ASP cc_start: 0.7501 (m-30) cc_final: 0.6975 (p0) REVERT: B 219 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.6530 (mmp80) REVERT: B 274 THR cc_start: 0.8305 (m) cc_final: 0.8005 (p) REVERT: B 322 ASP cc_start: 0.8754 (t70) cc_final: 0.8474 (t70) REVERT: G 32 LYS cc_start: 0.8651 (tppt) cc_final: 0.8375 (tppt) outliers start: 28 outliers final: 20 residues processed: 110 average time/residue: 1.0226 time to fit residues: 120.3532 Evaluate side-chains 114 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 349 ILE Chi-restraints excluded: chain R residue 351 MET Chi-restraints excluded: chain R residue 353 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 4.9990 chunk 53 optimal weight: 0.0570 chunk 57 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 7 optimal weight: 0.1980 chunk 65 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 73 optimal weight: 0.0040 chunk 78 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 overall best weight: 0.4110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 75 GLN B 175 GLN R 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5898 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7377 Z= 0.131 Angle : 0.514 10.030 10024 Z= 0.252 Chirality : 0.038 0.145 1172 Planarity : 0.003 0.032 1192 Dihedral : 7.576 120.264 1662 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.70 % Allowed : 17.54 % Favored : 79.76 % 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: 1.62 (0.30), residues: 854 helix: 2.97 (0.27), residues: 390 sheet: 0.45 (0.41), residues: 156 loop : -1.19 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.000 HIS B 62 PHE 0.011 0.001 PHE B 292 TYR 0.007 0.001 TYR A 296 ARG 0.004 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 0.767 Fit side-chains REVERT: A 29 LYS cc_start: 0.6063 (tmtt) cc_final: 0.5533 (ttmt) REVERT: A 188 HIS cc_start: 0.8224 (m90) cc_final: 0.7885 (m90) REVERT: A 257 LYS cc_start: 0.8139 (ptmm) cc_final: 0.7538 (tppt) REVERT: A 308 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7804 (mt-10) REVERT: B 68 ARG cc_start: 0.7197 (ttt180) cc_final: 0.6448 (ttt90) REVERT: B 153 ASP cc_start: 0.7431 (m-30) cc_final: 0.6832 (p0) REVERT: B 219 ARG cc_start: 0.6813 (OUTLIER) cc_final: 0.6568 (mmp80) REVERT: B 274 THR cc_start: 0.8303 (m) cc_final: 0.8045 (p) REVERT: B 297 TRP cc_start: 0.8119 (m100) cc_final: 0.7770 (m-10) REVERT: B 322 ASP cc_start: 0.8756 (t70) cc_final: 0.8464 (t70) REVERT: B 325 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7340 (mmm) REVERT: G 32 LYS cc_start: 0.8634 (tppt) cc_final: 0.8396 (tppt) outliers start: 20 outliers final: 10 residues processed: 106 average time/residue: 1.0763 time to fit residues: 121.4744 Evaluate side-chains 102 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 347 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 70 optimal weight: 0.0670 chunk 73 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 75 GLN B 175 GLN R 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5910 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7377 Z= 0.152 Angle : 0.523 10.958 10024 Z= 0.259 Chirality : 0.039 0.147 1172 Planarity : 0.003 0.032 1192 Dihedral : 7.505 117.102 1662 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.70 % Allowed : 18.49 % Favored : 78.81 % 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: 1.65 (0.30), residues: 854 helix: 3.00 (0.27), residues: 389 sheet: 0.61 (0.43), residues: 150 loop : -1.22 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.002 0.000 HIS B 54 PHE 0.012 0.001 PHE B 292 TYR 0.008 0.001 TYR R 195 ARG 0.004 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 0.785 Fit side-chains REVERT: A 29 LYS cc_start: 0.5980 (tmtt) cc_final: 0.5448 (ttmt) REVERT: A 188 HIS cc_start: 0.8278 (m90) cc_final: 0.7985 (m-70) REVERT: A 257 LYS cc_start: 0.8137 (ptmm) cc_final: 0.7538 (tppt) REVERT: A 308 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7806 (mt-10) REVERT: B 68 ARG cc_start: 0.7197 (ttt180) cc_final: 0.6450 (ttt90) REVERT: B 153 ASP cc_start: 0.7506 (m-30) cc_final: 0.6892 (p0) REVERT: B 219 ARG cc_start: 0.6797 (OUTLIER) cc_final: 0.6552 (mmp80) REVERT: B 262 MET cc_start: 0.7979 (pmm) cc_final: 0.7581 (pmm) REVERT: B 274 THR cc_start: 0.8294 (m) cc_final: 0.8030 (p) REVERT: B 297 TRP cc_start: 0.8163 (m100) cc_final: 0.7827 (m-10) REVERT: B 322 ASP cc_start: 0.8766 (t70) cc_final: 0.8473 (t70) REVERT: B 325 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.7338 (mmm) REVERT: G 32 LYS cc_start: 0.8627 (tppt) cc_final: 0.8408 (tppt) REVERT: R 356 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7590 (tp) outliers start: 20 outliers final: 12 residues processed: 107 average time/residue: 1.0087 time to fit residues: 115.2802 Evaluate side-chains 107 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 20.0000 chunk 79 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 54 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 75 GLN B 175 GLN R 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5924 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7377 Z= 0.170 Angle : 0.542 10.227 10024 Z= 0.266 Chirality : 0.039 0.147 1172 Planarity : 0.003 0.032 1192 Dihedral : 7.459 113.346 1662 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.97 % Allowed : 18.89 % Favored : 78.14 % 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: 1.64 (0.30), residues: 854 helix: 2.98 (0.27), residues: 389 sheet: 0.57 (0.43), residues: 152 loop : -1.20 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.002 0.000 HIS B 62 PHE 0.012 0.001 PHE B 222 TYR 0.009 0.001 TYR R 195 ARG 0.004 0.000 ARG A 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 90 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.6046 (tmtt) cc_final: 0.5537 (ttmt) REVERT: A 188 HIS cc_start: 0.8192 (m90) cc_final: 0.7911 (m-70) REVERT: A 257 LYS cc_start: 0.8160 (ptmm) cc_final: 0.7572 (tppt) REVERT: A 308 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7805 (mt-10) REVERT: B 153 ASP cc_start: 0.7576 (m-30) cc_final: 0.6994 (p0) REVERT: B 219 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.6538 (mmt90) REVERT: B 262 MET cc_start: 0.7961 (pmm) cc_final: 0.7571 (pmm) REVERT: B 274 THR cc_start: 0.8298 (m) cc_final: 0.8023 (p) REVERT: B 322 ASP cc_start: 0.8732 (t70) cc_final: 0.8446 (t70) REVERT: G 32 LYS cc_start: 0.8647 (tppt) cc_final: 0.8430 (tppt) REVERT: R 356 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7582 (tp) outliers start: 22 outliers final: 14 residues processed: 103 average time/residue: 1.0447 time to fit residues: 114.6377 Evaluate side-chains 103 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 87 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.2980 chunk 60 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 46 optimal weight: 0.0870 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 75 GLN B 175 GLN R 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.170445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.123401 restraints weight = 8311.385| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 3.52 r_work: 0.3347 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5807 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7377 Z= 0.144 Angle : 0.553 13.123 10024 Z= 0.267 Chirality : 0.038 0.145 1172 Planarity : 0.003 0.032 1192 Dihedral : 7.360 110.392 1662 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.16 % Allowed : 19.84 % Favored : 78.00 % 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: 1.69 (0.30), residues: 854 helix: 3.05 (0.27), residues: 389 sheet: 0.47 (0.42), residues: 158 loop : -1.18 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.002 0.000 HIS B 54 PHE 0.014 0.001 PHE B 222 TYR 0.010 0.001 TYR B 59 ARG 0.004 0.000 ARG A 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2699.43 seconds wall clock time: 49 minutes 39.41 seconds (2979.41 seconds total)