Starting phenix.real_space_refine (version: dev) on Sun Dec 11 20:29:06 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2x_30971/12_2022/7e2x_30971_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2x_30971/12_2022/7e2x_30971.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2x_30971/12_2022/7e2x_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_30971/12_2022/7e2x_30971_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2x_30971/12_2022/7e2x_30971_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2x_30971/12_2022/7e2x_30971.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2x_30971/12_2022/7e2x_30971.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2x_30971/12_2022/7e2x_30971_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2x_30971/12_2022/7e2x_30971_neut_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4807/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: 4.83, per 1000 atoms: 0.67 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: 3.14 Conformation dependent library (CDL) restraints added in 1.1 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: 0.73 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: 1.97 Time building geometry restraints manager: 3.23 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=" C24 J40 R 601 " pdb=" C25 J40 R 601 " ideal model delta sigma weight residual 1.331 1.528 -0.197 2.00e-02 2.50e+03 9.71e+01 bond pdb=" C21 J40 R 601 " pdb=" C22 J40 R 601 " ideal model delta sigma weight residual 1.331 1.528 -0.197 2.00e-02 2.50e+03 9.69e+01 bond pdb=" C15 J40 R 601 " pdb=" C16 J40 R 601 " ideal model delta sigma weight residual 1.338 1.527 -0.189 2.00e-02 2.50e+03 8.91e+01 bond pdb=" C18 J40 R 601 " pdb=" C19 J40 R 601 " ideal model delta sigma weight residual 1.339 1.526 -0.187 2.00e-02 2.50e+03 8.78e+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 152.64 112.55 40.09 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 152.64 113.09 39.55 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 152.64 113.19 39.45 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 152.65 113.67 38.98 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 - 27.09: 4190 27.09 - 54.19: 103 54.19 - 81.28: 16 81.28 - 108.37: 2 108.37 - 135.46: 2 Dihedral angle restraints: 4313 sinusoidal: 1782 harmonic: 2531 Sorted by residual: 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=" C21 J40 R 601 " pdb=" C22 J40 R 601 " pdb=" C23 J40 R 601 " pdb=" C24 J40 R 601 " ideal model delta sinusoidal sigma weight residual 228.05 92.59 135.46 1 3.00e+01 1.11e-03 1.83e+01 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 153.12 37.78 115.34 1 3.00e+01 1.11e-03 1.52e+01 ... (remaining 4310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.011: 1170 1.011 - 2.022: 0 2.022 - 3.033: 0 3.033 - 4.044: 0 4.044 - 5.055: 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 -2.53 2.53 -5.05 2.00e-01 2.50e+01 6.39e+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 -2.52 2.51 -5.04 2.00e-01 2.50e+01 6.34e+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 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. 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: 0.350 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: 2.420 Check model and map are aligned: 0.110 Convert atoms to be neutral: 0.060 Process input model: 22.590 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.070 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5960 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 0.197 7377 Z= 0.512 Angle : 1.071 40.094 10024 Z= 0.412 Chirality : 0.214 5.055 1172 Planarity : 0.010 0.235 1192 Dihedral : 12.335 135.463 2665 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer Outliers : 0.00 % 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 *********************** 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 : 0.790 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 145 average time/residue: 0.9995 time to fit residues: 154.3737 Evaluate side-chains 94 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.847 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1092 time to fit residues: 1.2714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6174 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 7377 Z= 0.273 Angle : 0.631 9.828 10024 Z= 0.302 Chirality : 0.046 0.585 1172 Planarity : 0.004 0.052 1192 Dihedral : 8.915 99.967 1094 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 3.37 % 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: 1.94 (0.30), residues: 854 helix: 3.19 (0.27), residues: 384 sheet: 0.90 (0.40), residues: 162 loop : -1.10 (0.35), residues: 308 *********************** 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 134 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 109 time to evaluate : 0.802 Fit side-chains outliers start: 25 outliers final: 11 residues processed: 121 average time/residue: 0.8204 time to fit residues: 107.1569 Evaluate side-chains 108 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 0.824 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 0.7185 time to fit residues: 4.2401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 21 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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: 0.6167 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 7377 Z= 0.178 Angle : 0.531 8.638 10024 Z= 0.260 Chirality : 0.040 0.304 1172 Planarity : 0.003 0.038 1192 Dihedral : 8.539 95.517 1094 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 3.51 % 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: 1.82 (0.30), residues: 854 helix: 3.15 (0.27), residues: 385 sheet: 0.66 (0.40), residues: 167 loop : -1.16 (0.34), residues: 302 *********************** 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 134 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 108 time to evaluate : 0.789 Fit side-chains outliers start: 26 outliers final: 18 residues processed: 122 average time/residue: 0.9338 time to fit residues: 122.0715 Evaluate side-chains 111 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 0.796 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 12 residues processed: 7 average time/residue: 0.1295 time to fit residues: 2.4114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 79 optimal weight: 0.0980 chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 70 optimal weight: 0.5980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 175 GLN B 237 ASN B 239 ASN R 100 ASN R 409 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6189 moved from start: 0.2815 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= 0.198 Angle : 0.546 9.188 10024 Z= 0.268 Chirality : 0.040 0.233 1172 Planarity : 0.003 0.035 1192 Dihedral : 8.076 88.448 1094 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 4.05 % 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: 1.65 (0.30), residues: 854 helix: 3.08 (0.27), residues: 384 sheet: 0.63 (0.40), residues: 168 loop : -1.39 (0.34), residues: 302 *********************** 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 133 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 103 time to evaluate : 0.843 Fit side-chains outliers start: 30 outliers final: 14 residues processed: 122 average time/residue: 0.8059 time to fit residues: 106.5613 Evaluate side-chains 111 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.830 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 10 residues processed: 4 average time/residue: 0.3084 time to fit residues: 2.5724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 71 optimal weight: 0.0040 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- 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: 0.6183 moved from start: 0.2999 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= 0.172 Angle : 0.527 8.549 10024 Z= 0.260 Chirality : 0.039 0.184 1172 Planarity : 0.003 0.034 1192 Dihedral : 7.517 81.960 1094 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer Outliers : 4.72 % 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: 1.60 (0.30), residues: 854 helix: 3.03 (0.27), residues: 384 sheet: 0.64 (0.40), residues: 167 loop : -1.42 (0.34), residues: 303 *********************** 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 130 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 95 time to evaluate : 0.852 Fit side-chains outliers start: 35 outliers final: 16 residues processed: 117 average time/residue: 0.9056 time to fit residues: 113.9604 Evaluate side-chains 104 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 0.827 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.0623 time to fit residues: 1.2964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 R 392 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6234 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 7377 Z= 0.266 Angle : 0.590 11.899 10024 Z= 0.290 Chirality : 0.041 0.199 1172 Planarity : 0.003 0.036 1192 Dihedral : 7.434 77.266 1094 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 4.59 % 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: 1.33 (0.30), residues: 854 helix: 2.78 (0.27), residues: 385 sheet: 0.49 (0.40), residues: 168 loop : -1.52 (0.33), residues: 301 *********************** 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 135 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 101 time to evaluate : 0.836 Fit side-chains outliers start: 34 outliers final: 23 residues processed: 123 average time/residue: 0.8850 time to fit residues: 117.1966 Evaluate side-chains 121 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 0.810 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 15 residues processed: 8 average time/residue: 0.1430 time to fit residues: 2.7230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 61 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 83 optimal weight: 0.0170 chunk 52 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 moved from start: 0.3464 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= 0.171 Angle : 0.567 11.040 10024 Z= 0.275 Chirality : 0.039 0.194 1172 Planarity : 0.003 0.036 1192 Dihedral : 7.017 72.776 1094 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer Outliers : 3.37 % 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: 1.42 (0.30), residues: 854 helix: 2.89 (0.27), residues: 385 sheet: 0.49 (0.40), residues: 165 loop : -1.49 (0.33), residues: 304 *********************** 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 119 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 94 time to evaluate : 0.901 Fit side-chains outliers start: 25 outliers final: 18 residues processed: 113 average time/residue: 0.8364 time to fit residues: 102.0944 Evaluate side-chains 109 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 0.747 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.1485 time to fit residues: 1.8943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 chunk 65 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 80 optimal weight: 0.0040 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 7377 Z= 0.157 Angle : 0.564 10.387 10024 Z= 0.274 Chirality : 0.039 0.194 1172 Planarity : 0.003 0.035 1192 Dihedral : 6.730 67.612 1094 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 3.64 % 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: 1.49 (0.30), residues: 854 helix: 2.87 (0.27), residues: 389 sheet: 0.58 (0.41), residues: 165 loop : -1.45 (0.33), residues: 300 *********************** 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 117 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 90 time to evaluate : 0.830 Fit side-chains outliers start: 27 outliers final: 18 residues processed: 110 average time/residue: 0.8504 time to fit residues: 101.0746 Evaluate side-chains 109 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 0.758 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 3 average time/residue: 0.7175 time to fit residues: 3.3909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 39 optimal weight: 0.0010 chunk 57 optimal weight: 0.7980 overall best weight: 0.6788 ------------------------------------------------------------------------------- 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: 0.6183 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 7377 Z= 0.161 Angle : 0.570 10.834 10024 Z= 0.276 Chirality : 0.039 0.195 1172 Planarity : 0.003 0.036 1192 Dihedral : 6.523 62.285 1094 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 3.51 % 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: 1.56 (0.30), residues: 854 helix: 2.98 (0.27), residues: 385 sheet: 0.62 (0.41), residues: 165 loop : -1.42 (0.33), residues: 304 *********************** 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 112 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 86 time to evaluate : 0.779 Fit side-chains outliers start: 26 outliers final: 19 residues processed: 103 average time/residue: 0.8507 time to fit residues: 94.8095 Evaluate side-chains 100 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 0.833 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 15 residues processed: 4 average time/residue: 0.5088 time to fit residues: 3.4283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.2980 chunk 69 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 53 optimal weight: 0.0040 chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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: 0.6171 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 7377 Z= 0.155 Angle : 0.573 12.815 10024 Z= 0.276 Chirality : 0.039 0.195 1172 Planarity : 0.003 0.034 1192 Dihedral : 6.342 57.686 1094 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 3.10 % 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: 3.01 (0.27), residues: 386 sheet: 0.60 (0.41), residues: 165 loop : -1.36 (0.33), residues: 303 ********************** 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 106 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 83 time to evaluate : 0.839 Fit side-chains outliers start: 23 outliers final: 16 residues processed: 101 average time/residue: 0.9628 time to fit residues: 104.4891 Evaluate side-chains 96 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 0.823 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.1628 time to fit residues: 1.5845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 70 optimal weight: 0.1980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 79 optimal weight: 0.3980 chunk 46 optimal weight: 0.0270 overall best weight: 0.4638 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.175000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.132087 restraints weight = 8482.643| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 3.24 r_work: 0.3529 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6107 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 7377 Z= 0.154 Angle : 0.580 11.778 10024 Z= 0.280 Chirality : 0.039 0.194 1172 Planarity : 0.003 0.034 1192 Dihedral : 6.256 59.796 1094 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 2.70 % 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: 1.61 (0.30), residues: 854 helix: 3.13 (0.27), residues: 380 sheet: 0.57 (0.43), residues: 150 loop : -1.33 (0.32), residues: 324 =============================================================================== Job complete usr+sys time: 2524.44 seconds wall clock time: 45 minutes 44.77 seconds (2744.77 seconds total)