Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 12:37:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2x_30971/04_2023/7e2x_30971_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2x_30971/04_2023/7e2x_30971.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2x_30971/04_2023/7e2x_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_30971/04_2023/7e2x_30971_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2x_30971/04_2023/7e2x_30971_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2x_30971/04_2023/7e2x_30971.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2x_30971/04_2023/7e2x_30971.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2x_30971/04_2023/7e2x_30971_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2x_30971/04_2023/7e2x_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 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-1.21rc1-4938/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: 4.40, per 1000 atoms: 0.61 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: 2.86 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: 0.61 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: 2.13 Time building geometry restraints manager: 3.10 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: 4263 34.99 - 69.98: 42 69.98 - 104.97: 7 104.97 - 139.96: 0 139.96 - 174.95: 1 Dihedral angle restraints: 4313 sinusoidal: 1782 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 4310 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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.230 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 22.990 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.420 ------------------------------------------------------------------------------- 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 : 12.339 174.954 2665 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 % 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 : 0.845 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 145 average time/residue: 1.0842 time to fit residues: 166.8930 Evaluate side-chains 94 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.803 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1200 time to fit residues: 1.3147 ------------------------------------------------------------------------------- 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: 0.6980 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 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: 0.5912 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 7377 Z= 0.262 Angle : 0.621 9.915 10024 Z= 0.299 Chirality : 0.044 0.482 1172 Planarity : 0.004 0.048 1192 Dihedral : 9.114 135.728 1094 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 3.24 % 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: 1.89 (0.30), residues: 854 helix: 3.14 (0.27), residues: 384 sheet: 0.88 (0.41), 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 132 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 0.897 Fit side-chains outliers start: 24 outliers final: 12 residues processed: 120 average time/residue: 0.9853 time to fit residues: 126.6502 Evaluate side-chains 107 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.842 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 5 average time/residue: 0.7385 time to fit residues: 5.1861 ------------------------------------------------------------------------------- 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: 0.9990 chunk 24 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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: 0.5898 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 7377 Z= 0.168 Angle : 0.524 8.765 10024 Z= 0.258 Chirality : 0.040 0.320 1172 Planarity : 0.003 0.037 1192 Dihedral : 9.014 139.668 1094 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 3.24 % 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: 3.17 (0.27), residues: 385 sheet: 0.59 (0.40), residues: 169 loop : -1.16 (0.35), residues: 300 *********************** 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 128 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 104 time to evaluate : 0.772 Fit side-chains outliers start: 24 outliers final: 15 residues processed: 117 average time/residue: 1.0502 time to fit residues: 130.9275 Evaluate side-chains 105 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 0.747 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 11 residues processed: 5 average time/residue: 0.1348 time to fit residues: 2.0857 ------------------------------------------------------------------------------- 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: 0.8980 chunk 59 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 70 optimal weight: 0.0870 overall best weight: 0.9362 ------------------------------------------------------------------------------- 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: 0.5907 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 7377 Z= 0.177 Angle : 0.519 8.685 10024 Z= 0.258 Chirality : 0.039 0.261 1172 Planarity : 0.003 0.034 1192 Dihedral : 8.776 136.014 1094 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 3.91 % 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: 3.15 (0.27), residues: 384 sheet: 0.63 (0.40), residues: 167 loop : -1.30 (0.34), residues: 303 *********************** 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 129 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 100 time to evaluate : 0.858 Fit side-chains outliers start: 29 outliers final: 12 residues processed: 118 average time/residue: 0.9233 time to fit residues: 116.9485 Evaluate side-chains 105 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.797 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.0860 time to fit residues: 1.4022 ------------------------------------------------------------------------------- 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: 0.9990 chunk 1 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 71 optimal weight: 0.0870 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.9762 ------------------------------------------------------------------------------- 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: 0.5918 moved from start: 0.2923 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= 0.180 Angle : 0.528 8.722 10024 Z= 0.261 Chirality : 0.039 0.213 1172 Planarity : 0.003 0.035 1192 Dihedral : 8.586 132.930 1094 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 4.45 % 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: 1.63 (0.30), residues: 854 helix: 3.06 (0.27), residues: 384 sheet: 0.63 (0.40), residues: 167 loop : -1.39 (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 135 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 102 time to evaluate : 0.841 Fit side-chains outliers start: 33 outliers final: 16 residues processed: 121 average time/residue: 0.9085 time to fit residues: 118.5111 Evaluate side-chains 109 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 0.788 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 10 residues processed: 6 average time/residue: 0.2782 time to fit residues: 3.1192 ------------------------------------------------------------------------------- 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: 6.9990 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 R 392 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5963 moved from start: 0.3334 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= 0.262 Angle : 0.592 12.945 10024 Z= 0.292 Chirality : 0.041 0.218 1172 Planarity : 0.003 0.035 1192 Dihedral : 8.617 130.254 1094 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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: 1.38 (0.30), residues: 854 helix: 2.82 (0.27), residues: 385 sheet: 0.51 (0.40), residues: 168 loop : -1.50 (0.34), 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 130 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 95 time to evaluate : 0.839 Fit side-chains outliers start: 35 outliers final: 23 residues processed: 119 average time/residue: 0.9644 time to fit residues: 123.1487 Evaluate side-chains 120 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 0.855 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 16 residues processed: 7 average time/residue: 0.3001 time to fit residues: 3.6169 ------------------------------------------------------------------------------- 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: 0.7980 chunk 70 optimal weight: 0.4980 chunk 83 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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: 0.5968 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 7377 Z= 0.260 Angle : 0.608 11.351 10024 Z= 0.300 Chirality : 0.041 0.212 1172 Planarity : 0.003 0.036 1192 Dihedral : 8.627 127.383 1094 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 4.18 % 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: 1.21 (0.30), residues: 854 helix: 2.69 (0.27), residues: 385 sheet: 0.41 (0.40), residues: 165 loop : -1.57 (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 123 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 92 time to evaluate : 0.822 Fit side-chains outliers start: 31 outliers final: 21 residues processed: 112 average time/residue: 0.9323 time to fit residues: 112.2107 Evaluate side-chains 112 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 91 time to evaluate : 0.756 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 15 residues processed: 6 average time/residue: 0.2843 time to fit residues: 3.0874 ------------------------------------------------------------------------------- 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: 0.6980 chunk 53 optimal weight: 0.0030 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 7 optimal weight: 0.1980 chunk 65 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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 119 ASN ** 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: 0.5912 moved from start: 0.3463 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= 0.147 Angle : 0.551 10.476 10024 Z= 0.271 Chirality : 0.038 0.203 1172 Planarity : 0.003 0.034 1192 Dihedral : 8.150 122.232 1094 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % 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: 1.35 (0.30), residues: 854 helix: 2.84 (0.27), residues: 390 sheet: 0.60 (0.43), residues: 140 loop : -1.53 (0.32), residues: 324 *********************** 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 121 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 94 time to evaluate : 0.873 Fit side-chains outliers start: 27 outliers final: 17 residues processed: 114 average time/residue: 0.9363 time to fit residues: 114.7977 Evaluate side-chains 103 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 0.821 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 2 average time/residue: 0.2248 time to fit residues: 1.6945 ------------------------------------------------------------------------------- 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: 0.7980 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.5924 moved from start: 0.3568 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= 0.174 Angle : 0.579 10.255 10024 Z= 0.283 Chirality : 0.039 0.207 1172 Planarity : 0.003 0.036 1192 Dihedral : 8.039 119.726 1094 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 3.24 % 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: 1.44 (0.30), residues: 854 helix: 2.86 (0.27), residues: 389 sheet: 0.54 (0.41), residues: 165 loop : -1.51 (0.33), residues: 300 *********************** 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 109 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 85 time to evaluate : 0.901 Fit side-chains outliers start: 24 outliers final: 18 residues processed: 103 average time/residue: 0.9671 time to fit residues: 107.1764 Evaluate side-chains 101 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 0.830 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 16 residues processed: 2 average time/residue: 0.1725 time to fit residues: 1.6244 ------------------------------------------------------------------------------- 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: 0.9980 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 73 optimal weight: 0.0970 chunk 21 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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: 0.5958 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 7377 Z= 0.232 Angle : 0.603 10.505 10024 Z= 0.296 Chirality : 0.040 0.212 1172 Planarity : 0.003 0.035 1192 Dihedral : 8.112 117.010 1094 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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: 1.33 (0.30), residues: 854 helix: 2.72 (0.27), residues: 390 sheet: 0.39 (0.41), residues: 167 loop : -1.43 (0.33), residues: 297 ********************** 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 108 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 83 time to evaluate : 0.806 Fit side-chains outliers start: 25 outliers final: 20 residues processed: 101 average time/residue: 1.0551 time to fit residues: 113.6606 Evaluate side-chains 102 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 82 time to evaluate : 0.801 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 4 average time/residue: 0.3704 time to fit residues: 2.7526 ------------------------------------------------------------------------------- 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: 0.9990 chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.170670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.126235 restraints weight = 8562.043| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 3.38 r_work: 0.3472 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5924 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 7377 Z= 0.177 Angle : 0.594 11.552 10024 Z= 0.289 Chirality : 0.039 0.211 1172 Planarity : 0.003 0.037 1192 Dihedral : 7.927 113.107 1094 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 2.83 % 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: 1.38 (0.30), residues: 854 helix: 2.79 (0.27), residues: 385 sheet: 0.46 (0.41), residues: 165 loop : -1.40 (0.33), residues: 304 =============================================================================== Job complete usr+sys time: 2675.78 seconds wall clock time: 48 minutes 26.16 seconds (2906.16 seconds total)