Starting phenix.real_space_refine (version: dev) on Mon Apr 4 22:18:30 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuj_32130/04_2022/7vuj_32130_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuj_32130/04_2022/7vuj_32130.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuj_32130/04_2022/7vuj_32130_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuj_32130/04_2022/7vuj_32130_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuj_32130/04_2022/7vuj_32130_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuj_32130/04_2022/7vuj_32130.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuj_32130/04_2022/7vuj_32130.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuj_32130/04_2022/7vuj_32130_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuj_32130/04_2022/7vuj_32130_updated.pdb" } resolution = 3.8 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= 0.001 sd= 0.025 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 "B GLU 138": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 8286 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1943 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2295 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 12, 'TRANS': 266} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'GDP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'7ZQ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.05, per 1000 atoms: 0.61 Number of scatterers: 8286 At special positions: 0 Unit cell: (82.16, 100.88, 134.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 49 16.00 P 2 15.00 Mg 1 11.99 O 1523 8.00 N 1433 7.00 C 5277 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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: 3.30 Conformation dependent library (CDL) restraints added in 1.2 seconds 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 10 sheets defined 37.4% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 10 through 37 removed outlier: 3.906A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 61 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 253 through 268 removed outlier: 4.428A pdb=" N GLN A 257 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP A 267 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A 268 " --> pdb=" O SER A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 293 Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 322 through 341 removed outlier: 3.902A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 380 Processing helix chain 'B' and resid 4 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 7 through 23 Processing helix chain 'G' and resid 30 through 44 Processing helix chain 'R' and resid 28 through 52 removed outlier: 3.906A pdb=" N SER R 34 " --> pdb=" O VAL R 30 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU R 35 " --> pdb=" O VAL R 31 " (cutoff:3.500A) Proline residue: R 42 - end of helix Processing helix chain 'R' and resid 55 through 58 removed outlier: 4.086A pdb=" N ARG R 58 " --> pdb=" O VAL R 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 55 through 58' Processing helix chain 'R' and resid 61 through 90 removed outlier: 3.658A pdb=" N PHE R 85 " --> pdb=" O VAL R 81 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASP R 89 " --> pdb=" O PHE R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 131 removed outlier: 3.872A pdb=" N VAL R 106 " --> pdb=" O LYS R 102 " (cutoff:3.500A) Proline residue: R 121 - end of helix Processing helix chain 'R' and resid 136 through 139 No H-bonds generated for 'chain 'R' and resid 136 through 139' Processing helix chain 'R' and resid 142 through 165 removed outlier: 3.583A pdb=" N LYS R 147 " --> pdb=" O ALA R 143 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL R 152 " --> pdb=" O VAL R 148 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR R 153 " --> pdb=" O ILE R 149 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE R 161 " --> pdb=" O PHE R 157 " (cutoff:3.500A) Proline residue: R 162 - end of helix removed outlier: 5.316A pdb=" N TRP R 165 " --> pdb=" O ILE R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 191 removed outlier: 3.863A pdb=" N VAL R 182 " --> pdb=" O SER R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 212 removed outlier: 3.576A pdb=" N SER R 197 " --> pdb=" O LEU R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 252 Proline residue: R 243 - end of helix Processing helix chain 'R' and resid 260 through 285 removed outlier: 3.511A pdb=" N HIS R 264 " --> pdb=" O ARG R 260 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N MET R 266 " --> pdb=" O LEU R 262 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER R 267 " --> pdb=" O VAL R 263 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE R 282 " --> pdb=" O THR R 278 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N PHE R 283 " --> pdb=" O ALA R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 290 through 300 Processing sheet with id= A, first strand: chain 'A' and resid 349 through 352 removed outlier: 7.158A pdb=" N VAL A 277 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N HIS A 352 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU A 279 " --> pdb=" O HIS A 352 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 219 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 61 through 63 removed outlier: 3.607A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.670A pdb=" N ALA B 104 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU B 139 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 178 through 180 removed outlier: 3.508A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.830A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.625A pdb=" N CYS B 233 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR B 243 " --> pdb=" O ARG B 251 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.591A pdb=" N LEU B 286 " --> pdb=" O SER B 277 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 335 through 339 removed outlier: 4.298A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.682A pdb=" N LEU N 20 " --> pdb=" O LEU N 81 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU N 79 " --> pdb=" O CYS N 22 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR N 69 " --> pdb=" O GLN N 82 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 95 through 98 351 hydrogen bonds defined for protein. 987 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: 2.42 Time building geometry restraints manager: 3.56 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: 1327 1.31 - 1.44: 2381 1.44 - 1.56: 4686 1.56 - 1.69: 3 1.69 - 1.81: 70 Bond restraints: 8467 Sorted by residual: bond pdb=" C5 GDP A 402 " pdb=" C4 GDP A 402 " ideal model delta sigma weight residual 1.490 1.389 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" C3' GDP A 402 " pdb=" C2' GDP A 402 " ideal model delta sigma weight residual 1.524 1.447 0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C5 GDP A 402 " pdb=" C6 GDP A 402 " ideal model delta sigma weight residual 1.490 1.419 0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C6 GDP A 402 " pdb=" N1 GDP A 402 " ideal model delta sigma weight residual 1.337 1.388 -0.051 2.00e-02 2.50e+03 6.56e+00 bond pdb=" N7 GDP A 402 " pdb=" C5 GDP A 402 " ideal model delta sigma weight residual 1.350 1.394 -0.044 2.00e-02 2.50e+03 4.94e+00 ... (remaining 8462 not shown) Histogram of bond angle deviations from ideal: 99.50 - 107.27: 256 107.27 - 115.05: 5024 115.05 - 122.82: 5458 122.82 - 130.59: 706 130.59 - 138.37: 45 Bond angle restraints: 11489 Sorted by residual: angle pdb=" CA LEU A 260 " pdb=" CB LEU A 260 " pdb=" CG LEU A 260 " ideal model delta sigma weight residual 116.30 131.42 -15.12 3.50e+00 8.16e-02 1.87e+01 angle pdb=" O5' GDP A 402 " pdb=" PA GDP A 402 " pdb=" O3A GDP A 402 " ideal model delta sigma weight residual 102.60 112.22 -9.62 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C8 GDP A 402 " pdb=" N9 GDP A 402 " pdb=" C4 GDP A 402 " ideal model delta sigma weight residual 108.00 117.13 -9.13 3.00e+00 1.11e-01 9.26e+00 angle pdb=" N VAL R 150 " pdb=" CA VAL R 150 " pdb=" C VAL R 150 " ideal model delta sigma weight residual 112.35 108.47 3.88 1.41e+00 5.03e-01 7.57e+00 angle pdb=" N GLY N 66 " pdb=" CA GLY N 66 " pdb=" C GLY N 66 " ideal model delta sigma weight residual 115.61 110.97 4.64 1.74e+00 3.30e-01 7.13e+00 ... (remaining 11484 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 4568 17.58 - 35.17: 372 35.17 - 52.75: 63 52.75 - 70.34: 11 70.34 - 87.92: 9 Dihedral angle restraints: 5023 sinusoidal: 1994 harmonic: 3029 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -11.00 -75.00 1 1.00e+01 1.00e-02 7.11e+01 dihedral pdb=" CA PHE R 85 " pdb=" C PHE R 85 " pdb=" N LEU R 86 " pdb=" CA LEU R 86 " ideal model delta harmonic sigma weight residual 180.00 154.81 25.19 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA LYS G 29 " pdb=" C LYS G 29 " pdb=" N VAL G 30 " pdb=" CA VAL G 30 " ideal model delta harmonic sigma weight residual 180.00 -155.73 -24.27 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 5020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 792 0.034 - 0.069: 343 0.069 - 0.103: 116 0.103 - 0.137: 40 0.137 - 0.171: 5 Chirality restraints: 1296 Sorted by residual: chirality pdb=" CG LEU N 81 " pdb=" CB LEU N 81 " pdb=" CD1 LEU N 81 " pdb=" CD2 LEU N 81 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.32e-01 chirality pdb=" CA ARG A 270 " pdb=" N ARG A 270 " pdb=" C ARG A 270 " pdb=" CB ARG A 270 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CB THR A 55 " pdb=" CA THR A 55 " pdb=" OG1 THR A 55 " pdb=" CG2 THR A 55 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.37e-01 ... (remaining 1293 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 321 " -0.044 5.00e-02 4.00e+02 6.71e-02 7.20e+00 pdb=" N PRO A 322 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 310 " -0.040 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO A 311 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 311 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 311 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO R 100 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.72e+00 pdb=" C PRO R 100 " -0.038 2.00e-02 2.50e+03 pdb=" O PRO R 100 " 0.014 2.00e-02 2.50e+03 pdb=" N ASP R 101 " 0.013 2.00e-02 2.50e+03 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 91 2.55 - 3.14: 6787 3.14 - 3.72: 13347 3.72 - 4.31: 17666 4.31 - 4.90: 29123 Nonbonded interactions: 67014 Sorted by model distance: nonbonded pdb=" OG SER A 276 " pdb=" CD1 ILE A 372 " model vdw 1.960 3.460 nonbonded pdb=" O PRO N 88 " pdb=" OG1 THR N 91 " model vdw 2.172 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.178 2.440 nonbonded pdb=" OD1 ASN A 361 " pdb=" NH2 ARG A 364 " model vdw 2.187 2.520 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.198 2.520 ... (remaining 67009 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: 7 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 49 5.16 5 Cl 1 4.86 5 C 5277 2.51 5 N 1433 2.21 5 O 1523 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 group one per residue 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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 4.020 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.060 Process input model: 24.810 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.101 8467 Z= 0.281 Angle : 0.733 15.125 11489 Z= 0.376 Chirality : 0.045 0.171 1296 Planarity : 0.005 0.067 1452 Dihedral : 13.441 87.920 3057 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.97 % Favored : 93.93 % 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: -0.35 (0.27), residues: 1022 helix: 0.81 (0.26), residues: 388 sheet: -0.64 (0.37), residues: 216 loop : -0.90 (0.30), residues: 418 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.2303 time to fit residues: 76.2317 Evaluate side-chains 231 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 0.960 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.1980 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.2980 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 0.2980 chunk 47 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN A 236 GLN ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 8467 Z= 0.209 Angle : 0.635 8.653 11489 Z= 0.325 Chirality : 0.043 0.180 1296 Planarity : 0.005 0.075 1452 Dihedral : 5.574 67.860 1148 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.19 % Favored : 94.72 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.27), residues: 1022 helix: 0.82 (0.26), residues: 392 sheet: -0.35 (0.38), residues: 206 loop : -0.82 (0.31), residues: 424 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 244 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 249 average time/residue: 0.2365 time to fit residues: 77.3411 Evaluate side-chains 256 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 243 time to evaluate : 0.974 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1071 time to fit residues: 3.7011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 90 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 GLN ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 277 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 8467 Z= 0.331 Angle : 0.701 7.387 11489 Z= 0.364 Chirality : 0.046 0.177 1296 Planarity : 0.006 0.087 1452 Dihedral : 5.713 47.402 1148 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 22.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.46 % Favored : 93.44 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.26), residues: 1022 helix: 0.73 (0.26), residues: 392 sheet: -0.60 (0.37), residues: 209 loop : -1.01 (0.30), residues: 421 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 243 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 11 residues processed: 252 average time/residue: 0.2293 time to fit residues: 75.4790 Evaluate side-chains 247 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 236 time to evaluate : 0.858 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0810 time to fit residues: 2.8778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 0.0870 chunk 91 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 chunk 80 optimal weight: 0.0070 chunk 54 optimal weight: 0.6980 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 GLN ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN N 53 GLN ** R 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8467 Z= 0.189 Angle : 0.614 8.781 11489 Z= 0.317 Chirality : 0.043 0.150 1296 Planarity : 0.005 0.066 1452 Dihedral : 5.224 40.634 1148 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.99 % Favored : 94.91 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.27), residues: 1022 helix: 0.79 (0.26), residues: 393 sheet: -0.59 (0.37), residues: 204 loop : -0.97 (0.31), residues: 425 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 239 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 245 average time/residue: 0.2285 time to fit residues: 74.0082 Evaluate side-chains 243 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 233 time to evaluate : 0.937 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1054 time to fit residues: 2.9909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 GLN ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 8467 Z= 0.249 Angle : 0.644 8.037 11489 Z= 0.334 Chirality : 0.044 0.149 1296 Planarity : 0.005 0.062 1452 Dihedral : 5.210 41.610 1148 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.36 % Favored : 93.54 % Rotamer Outliers : 2.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.27), residues: 1022 helix: 0.88 (0.27), residues: 386 sheet: -0.93 (0.36), residues: 211 loop : -0.91 (0.30), residues: 425 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 242 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 16 residues processed: 250 average time/residue: 0.2201 time to fit residues: 73.3132 Evaluate side-chains 251 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 235 time to evaluate : 0.935 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1373 time to fit residues: 4.6009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.0980 chunk 56 optimal weight: 0.8980 chunk 23 optimal weight: 8.9990 chunk 96 optimal weight: 0.0980 chunk 80 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 93 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 GLN A 261 ASN A 284 GLN A 375 GLN ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS G 18 GLN ** R 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 251 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 8467 Z= 0.188 Angle : 0.619 7.830 11489 Z= 0.319 Chirality : 0.042 0.148 1296 Planarity : 0.004 0.051 1452 Dihedral : 5.095 45.897 1148 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.09 % Favored : 94.81 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.27), residues: 1022 helix: 0.81 (0.27), residues: 381 sheet: -0.93 (0.37), residues: 205 loop : -0.95 (0.30), residues: 436 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 234 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 242 average time/residue: 0.2199 time to fit residues: 70.8187 Evaluate side-chains 236 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 228 time to evaluate : 0.956 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1164 time to fit residues: 2.8567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 60 optimal weight: 0.0060 chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS G 18 GLN ** R 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 8467 Z= 0.253 Angle : 0.674 9.131 11489 Z= 0.345 Chirality : 0.044 0.181 1296 Planarity : 0.005 0.056 1452 Dihedral : 5.162 41.554 1148 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 21.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.75 % Favored : 93.15 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.26), residues: 1022 helix: 0.74 (0.26), residues: 381 sheet: -1.11 (0.37), residues: 205 loop : -0.96 (0.30), residues: 436 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 241 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 12 residues processed: 246 average time/residue: 0.2252 time to fit residues: 73.6067 Evaluate side-chains 250 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 238 time to evaluate : 0.909 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0819 time to fit residues: 3.0886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 61 optimal weight: 9.9990 chunk 65 optimal weight: 0.0870 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 75 optimal weight: 0.3980 chunk 87 optimal weight: 0.7980 chunk 92 optimal weight: 0.0030 chunk 84 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 overall best weight: 0.3768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN A 377 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN ** R 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.092 8467 Z= 0.202 Angle : 0.657 8.991 11489 Z= 0.338 Chirality : 0.044 0.164 1296 Planarity : 0.005 0.104 1452 Dihedral : 5.139 50.023 1148 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.28 % Favored : 94.62 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.27), residues: 1022 helix: 0.70 (0.27), residues: 381 sheet: -1.10 (0.37), residues: 193 loop : -0.98 (0.30), residues: 448 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 238 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 242 average time/residue: 0.2372 time to fit residues: 75.5257 Evaluate side-chains 240 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 235 time to evaluate : 0.892 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1539 time to fit residues: 2.4650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.124 8467 Z= 0.291 Angle : 0.724 13.434 11489 Z= 0.381 Chirality : 0.046 0.258 1296 Planarity : 0.006 0.149 1452 Dihedral : 5.197 42.080 1148 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 22.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.56 % Favored : 93.35 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.27), residues: 1022 helix: 0.67 (0.27), residues: 381 sheet: -1.17 (0.37), residues: 197 loop : -1.05 (0.30), residues: 444 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 238 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 243 average time/residue: 0.2298 time to fit residues: 73.6419 Evaluate side-chains 247 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 239 time to evaluate : 0.934 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0828 time to fit residues: 2.5319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 chunk 48 optimal weight: 0.0770 chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** R 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.107 8467 Z= 0.260 Angle : 0.720 9.864 11489 Z= 0.374 Chirality : 0.046 0.215 1296 Planarity : 0.006 0.125 1452 Dihedral : 5.224 43.368 1148 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 21.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.26 % Favored : 93.64 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.26), residues: 1022 helix: 0.53 (0.26), residues: 383 sheet: -1.10 (0.37), residues: 195 loop : -1.04 (0.30), residues: 444 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 243 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 246 average time/residue: 0.2313 time to fit residues: 74.9163 Evaluate side-chains 238 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 237 time to evaluate : 0.938 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0763 time to fit residues: 1.4969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 33 optimal weight: 0.0980 chunk 81 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 180 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.185352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.156133 restraints weight = 14243.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.161336 restraints weight = 8381.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.164901 restraints weight = 5551.671| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.147 8467 Z= 0.276 Angle : 0.752 13.383 11489 Z= 0.397 Chirality : 0.046 0.290 1296 Planarity : 0.007 0.146 1452 Dihedral : 5.262 45.066 1148 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 21.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.65 % Favored : 93.25 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.26), residues: 1022 helix: 0.44 (0.26), residues: 382 sheet: -1.02 (0.37), residues: 195 loop : -1.07 (0.30), residues: 445 =============================================================================== Job complete usr+sys time: 2127.39 seconds wall clock time: 39 minutes 12.70 seconds (2352.70 seconds total)