Starting phenix.real_space_refine (version: dev) on Thu Feb 23 00:49:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i2n_0333/02_2023/6i2n_0333.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i2n_0333/02_2023/6i2n_0333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i2n_0333/02_2023/6i2n_0333.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i2n_0333/02_2023/6i2n_0333.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i2n_0333/02_2023/6i2n_0333.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i2n_0333/02_2023/6i2n_0333.pdb" } resolution = 3.3 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= 0.002 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 Process input model Symmetric amino acids flipped Residue "D ARG 93": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D ARG 156": "NH1" <-> "NH2" Residue "D ARG 172": "NH1" <-> "NH2" Residue "D ARG 197": "NH1" <-> "NH2" Residue "D ARG 269": "NH1" <-> "NH2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 146": "NH1" <-> "NH2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B ARG 172": "NH1" <-> "NH2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "E ARG 93": "NH1" <-> "NH2" Residue "E ARG 146": "NH1" <-> "NH2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "E ARG 172": "NH1" <-> "NH2" Residue "E ARG 197": "NH1" <-> "NH2" Residue "E ARG 269": "NH1" <-> "NH2" Residue "E ARG 356": "NH1" <-> "NH2" Residue "G ARG 93": "NH1" <-> "NH2" Residue "G ARG 146": "NH1" <-> "NH2" Residue "G ARG 156": "NH1" <-> "NH2" Residue "G ARG 172": "NH1" <-> "NH2" Residue "G ARG 197": "NH1" <-> "NH2" Residue "G ARG 269": "NH1" <-> "NH2" Residue "G ARG 356": "NH1" <-> "NH2" Residue "I ARG 93": "NH1" <-> "NH2" Residue "I ARG 146": "NH1" <-> "NH2" Residue "I ARG 156": "NH1" <-> "NH2" Residue "I ARG 172": "NH1" <-> "NH2" Residue "I ARG 197": "NH1" <-> "NH2" Residue "I ARG 269": "NH1" <-> "NH2" Residue "I ARG 356": "NH1" <-> "NH2" Residue "K ARG 93": "NH1" <-> "NH2" Residue "K ARG 146": "NH1" <-> "NH2" Residue "K ARG 156": "NH1" <-> "NH2" Residue "K ARG 172": "NH1" <-> "NH2" Residue "K ARG 197": "NH1" <-> "NH2" Residue "K ARG 269": "NH1" <-> "NH2" Residue "K ARG 356": "NH1" <-> "NH2" Residue "M ARG 93": "NH1" <-> "NH2" Residue "M ARG 146": "NH1" <-> "NH2" Residue "M ARG 156": "NH1" <-> "NH2" Residue "M ARG 172": "NH1" <-> "NH2" Residue "M ARG 197": "NH1" <-> "NH2" Residue "M ARG 269": "NH1" <-> "NH2" Residue "M ARG 356": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 18970 Number of models: 1 Model: "" Number of chains: 14 Chain: "U" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'RNA': 3} Modifications used: {'rna3p_pyr': 3} Link IDs: {'rna3p': 2} Chain: "D" Number of atoms: 2650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2650 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain breaks: 1 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'RNA': 3} Modifications used: {'rna3p_pyr': 3} Link IDs: {'rna3p': 2} Chain: "B" Number of atoms: 2650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2650 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain breaks: 1 Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'RNA': 3} Modifications used: {'rna3p_pyr': 3} Link IDs: {'rna3p': 2} Chain: "E" Number of atoms: 2650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2650 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain breaks: 1 Chain: "F" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'RNA': 3} Modifications used: {'rna3p_pyr': 3} Link IDs: {'rna3p': 2} Chain: "G" Number of atoms: 2650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2650 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain breaks: 1 Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'RNA': 3} Modifications used: {'rna3p_pyr': 3} Link IDs: {'rna3p': 2} Chain: "I" Number of atoms: 2650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2650 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain breaks: 1 Chain: "J" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'RNA': 3} Modifications used: {'rna3p_pyr': 3} Link IDs: {'rna3p': 2} Chain: "K" Number of atoms: 2650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2650 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain breaks: 1 Chain: "L" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'RNA': 3} Modifications used: {'rna3p_pyr': 3} Link IDs: {'rna3p': 2} Chain: "M" Number of atoms: 2650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2650 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain breaks: 1 Time building chain proxies: 10.68, per 1000 atoms: 0.56 Number of scatterers: 18970 At special positions: 0 Unit cell: (106.7, 105.633, 190.993, 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 119 16.00 P 21 15.00 O 3654 8.00 N 3269 7.00 C 11907 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 7.28 Conformation dependent library (CDL) restraints added in 2.8 seconds 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4424 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 0 sheets defined 50.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'D' and resid 121 through 128 removed outlier: 3.794A pdb=" N SER D 128 " --> pdb=" O VAL D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 142 Processing helix chain 'D' and resid 145 through 151 Processing helix chain 'D' and resid 195 through 205 Processing helix chain 'D' and resid 207 through 213 Processing helix chain 'D' and resid 218 through 221 No H-bonds generated for 'chain 'D' and resid 218 through 221' Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 232 through 240 removed outlier: 3.741A pdb=" N GLU D 237 " --> pdb=" O SER D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 275 Processing helix chain 'D' and resid 279 through 291 removed outlier: 3.518A pdb=" N ALA D 290 " --> pdb=" O GLN D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 308 No H-bonds generated for 'chain 'D' and resid 305 through 308' Processing helix chain 'D' and resid 326 through 346 Processing helix chain 'D' and resid 351 through 357 Processing helix chain 'D' and resid 361 through 372 removed outlier: 4.046A pdb=" N MET D 372 " --> pdb=" O ARG D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 388 Processing helix chain 'D' and resid 390 through 395 Processing helix chain 'D' and resid 404 through 421 Processing helix chain 'B' and resid 121 through 128 removed outlier: 3.795A pdb=" N SER B 128 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 145 through 151 Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 207 through 213 Processing helix chain 'B' and resid 218 through 221 No H-bonds generated for 'chain 'B' and resid 218 through 221' Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 232 through 240 removed outlier: 3.740A pdb=" N GLU B 237 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 275 Processing helix chain 'B' and resid 279 through 291 removed outlier: 3.518A pdb=" N ALA B 290 " --> pdb=" O GLN B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 308 No H-bonds generated for 'chain 'B' and resid 305 through 308' Processing helix chain 'B' and resid 326 through 346 Processing helix chain 'B' and resid 351 through 357 Processing helix chain 'B' and resid 361 through 372 removed outlier: 4.047A pdb=" N MET B 372 " --> pdb=" O ARG B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 388 Processing helix chain 'B' and resid 390 through 395 Processing helix chain 'B' and resid 404 through 421 Processing helix chain 'E' and resid 121 through 128 removed outlier: 3.793A pdb=" N SER E 128 " --> pdb=" O VAL E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 142 Processing helix chain 'E' and resid 145 through 151 Processing helix chain 'E' and resid 195 through 205 Processing helix chain 'E' and resid 207 through 213 Processing helix chain 'E' and resid 218 through 221 No H-bonds generated for 'chain 'E' and resid 218 through 221' Processing helix chain 'E' and resid 225 through 230 Processing helix chain 'E' and resid 232 through 240 removed outlier: 3.740A pdb=" N GLU E 237 " --> pdb=" O SER E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 275 Processing helix chain 'E' and resid 279 through 291 removed outlier: 3.518A pdb=" N ALA E 290 " --> pdb=" O GLN E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 308 No H-bonds generated for 'chain 'E' and resid 305 through 308' Processing helix chain 'E' and resid 326 through 346 Processing helix chain 'E' and resid 351 through 357 Processing helix chain 'E' and resid 361 through 372 removed outlier: 4.047A pdb=" N MET E 372 " --> pdb=" O ARG E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 388 Processing helix chain 'E' and resid 390 through 395 Processing helix chain 'E' and resid 404 through 421 Processing helix chain 'G' and resid 121 through 128 removed outlier: 3.794A pdb=" N SER G 128 " --> pdb=" O VAL G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 142 Processing helix chain 'G' and resid 145 through 151 Processing helix chain 'G' and resid 195 through 205 Processing helix chain 'G' and resid 207 through 213 Processing helix chain 'G' and resid 218 through 221 No H-bonds generated for 'chain 'G' and resid 218 through 221' Processing helix chain 'G' and resid 225 through 230 Processing helix chain 'G' and resid 232 through 240 removed outlier: 3.741A pdb=" N GLU G 237 " --> pdb=" O SER G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 275 Processing helix chain 'G' and resid 279 through 291 removed outlier: 3.519A pdb=" N ALA G 290 " --> pdb=" O GLN G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 308 No H-bonds generated for 'chain 'G' and resid 305 through 308' Processing helix chain 'G' and resid 326 through 346 Processing helix chain 'G' and resid 351 through 357 Processing helix chain 'G' and resid 361 through 372 removed outlier: 4.047A pdb=" N MET G 372 " --> pdb=" O ARG G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 378 through 388 Processing helix chain 'G' and resid 390 through 395 Processing helix chain 'G' and resid 404 through 421 Processing helix chain 'I' and resid 121 through 128 removed outlier: 3.794A pdb=" N SER I 128 " --> pdb=" O VAL I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 142 Processing helix chain 'I' and resid 145 through 151 Processing helix chain 'I' and resid 195 through 205 Processing helix chain 'I' and resid 207 through 213 Processing helix chain 'I' and resid 218 through 221 No H-bonds generated for 'chain 'I' and resid 218 through 221' Processing helix chain 'I' and resid 225 through 230 Processing helix chain 'I' and resid 232 through 240 removed outlier: 3.742A pdb=" N GLU I 237 " --> pdb=" O SER I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 262 through 275 Processing helix chain 'I' and resid 279 through 291 removed outlier: 3.518A pdb=" N ALA I 290 " --> pdb=" O GLN I 286 " (cutoff:3.500A) Processing helix chain 'I' and resid 305 through 308 No H-bonds generated for 'chain 'I' and resid 305 through 308' Processing helix chain 'I' and resid 326 through 346 Processing helix chain 'I' and resid 351 through 357 Processing helix chain 'I' and resid 361 through 372 removed outlier: 4.046A pdb=" N MET I 372 " --> pdb=" O ARG I 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 378 through 388 Processing helix chain 'I' and resid 390 through 395 Processing helix chain 'I' and resid 404 through 421 Processing helix chain 'K' and resid 121 through 128 removed outlier: 3.795A pdb=" N SER K 128 " --> pdb=" O VAL K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 142 Processing helix chain 'K' and resid 145 through 151 Processing helix chain 'K' and resid 195 through 205 Processing helix chain 'K' and resid 207 through 213 Processing helix chain 'K' and resid 218 through 221 No H-bonds generated for 'chain 'K' and resid 218 through 221' Processing helix chain 'K' and resid 225 through 230 Processing helix chain 'K' and resid 232 through 240 removed outlier: 3.741A pdb=" N GLU K 237 " --> pdb=" O SER K 233 " (cutoff:3.500A) Processing helix chain 'K' and resid 262 through 275 Processing helix chain 'K' and resid 279 through 291 removed outlier: 3.519A pdb=" N ALA K 290 " --> pdb=" O GLN K 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 305 through 308 No H-bonds generated for 'chain 'K' and resid 305 through 308' Processing helix chain 'K' and resid 326 through 346 Processing helix chain 'K' and resid 351 through 357 Processing helix chain 'K' and resid 361 through 372 removed outlier: 4.045A pdb=" N MET K 372 " --> pdb=" O ARG K 368 " (cutoff:3.500A) Processing helix chain 'K' and resid 378 through 388 Processing helix chain 'K' and resid 390 through 395 Processing helix chain 'K' and resid 404 through 421 Processing helix chain 'M' and resid 121 through 128 removed outlier: 3.794A pdb=" N SER M 128 " --> pdb=" O VAL M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 142 Processing helix chain 'M' and resid 145 through 151 Processing helix chain 'M' and resid 195 through 205 Processing helix chain 'M' and resid 207 through 213 Processing helix chain 'M' and resid 218 through 221 No H-bonds generated for 'chain 'M' and resid 218 through 221' Processing helix chain 'M' and resid 225 through 230 Processing helix chain 'M' and resid 232 through 240 removed outlier: 3.741A pdb=" N GLU M 237 " --> pdb=" O SER M 233 " (cutoff:3.500A) Processing helix chain 'M' and resid 262 through 275 Processing helix chain 'M' and resid 279 through 291 removed outlier: 3.518A pdb=" N ALA M 290 " --> pdb=" O GLN M 286 " (cutoff:3.500A) Processing helix chain 'M' and resid 305 through 308 No H-bonds generated for 'chain 'M' and resid 305 through 308' Processing helix chain 'M' and resid 326 through 346 Processing helix chain 'M' and resid 351 through 357 Processing helix chain 'M' and resid 361 through 372 removed outlier: 4.047A pdb=" N MET M 372 " --> pdb=" O ARG M 368 " (cutoff:3.500A) Processing helix chain 'M' and resid 378 through 388 Processing helix chain 'M' and resid 390 through 395 Processing helix chain 'M' and resid 404 through 421 686 hydrogen bonds defined for protein. 2058 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: 4.31 Time building geometry restraints manager: 7.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5039 1.33 - 1.45: 3199 1.45 - 1.57: 10872 1.57 - 1.69: 35 1.69 - 1.80: 203 Bond restraints: 19348 Sorted by residual: bond pdb=" C PHE G 129 " pdb=" N VAL G 130 " ideal model delta sigma weight residual 1.330 1.308 0.022 1.42e-02 4.96e+03 2.37e+00 bond pdb=" C PHE E 129 " pdb=" N VAL E 130 " ideal model delta sigma weight residual 1.330 1.309 0.022 1.42e-02 4.96e+03 2.34e+00 bond pdb=" C PHE K 129 " pdb=" N VAL K 130 " ideal model delta sigma weight residual 1.330 1.309 0.022 1.42e-02 4.96e+03 2.30e+00 bond pdb=" C PHE I 129 " pdb=" N VAL I 130 " ideal model delta sigma weight residual 1.330 1.309 0.021 1.42e-02 4.96e+03 2.28e+00 bond pdb=" C PHE D 129 " pdb=" N VAL D 130 " ideal model delta sigma weight residual 1.330 1.309 0.021 1.42e-02 4.96e+03 2.24e+00 ... (remaining 19343 not shown) Histogram of bond angle deviations from ideal: 99.20 - 106.17: 612 106.17 - 113.15: 10494 113.15 - 120.12: 7392 120.12 - 127.10: 7464 127.10 - 134.07: 239 Bond angle restraints: 26201 Sorted by residual: angle pdb=" N VAL G 131 " pdb=" CA VAL G 131 " pdb=" C VAL G 131 " ideal model delta sigma weight residual 108.88 119.38 -10.50 2.16e+00 2.14e-01 2.36e+01 angle pdb=" N VAL E 131 " pdb=" CA VAL E 131 " pdb=" C VAL E 131 " ideal model delta sigma weight residual 108.88 119.37 -10.49 2.16e+00 2.14e-01 2.36e+01 angle pdb=" N VAL D 131 " pdb=" CA VAL D 131 " pdb=" C VAL D 131 " ideal model delta sigma weight residual 108.88 119.36 -10.48 2.16e+00 2.14e-01 2.36e+01 angle pdb=" N VAL K 131 " pdb=" CA VAL K 131 " pdb=" C VAL K 131 " ideal model delta sigma weight residual 108.88 119.35 -10.47 2.16e+00 2.14e-01 2.35e+01 angle pdb=" N VAL I 131 " pdb=" CA VAL I 131 " pdb=" C VAL I 131 " ideal model delta sigma weight residual 108.88 119.34 -10.46 2.16e+00 2.14e-01 2.35e+01 ... (remaining 26196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.80: 11028 14.80 - 29.59: 627 29.59 - 44.39: 154 44.39 - 59.18: 7 59.18 - 73.98: 35 Dihedral angle restraints: 11851 sinusoidal: 5026 harmonic: 6825 Sorted by residual: dihedral pdb=" CA PHE I 165 " pdb=" C PHE I 165 " pdb=" N GLU I 166 " pdb=" CA GLU I 166 " ideal model delta harmonic sigma weight residual 180.00 157.61 22.39 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA PHE E 165 " pdb=" C PHE E 165 " pdb=" N GLU E 166 " pdb=" CA GLU E 166 " ideal model delta harmonic sigma weight residual 180.00 157.63 22.37 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA PHE G 165 " pdb=" C PHE G 165 " pdb=" N GLU G 166 " pdb=" CA GLU G 166 " ideal model delta harmonic sigma weight residual 180.00 157.63 22.37 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 11848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1735 0.039 - 0.078: 876 0.078 - 0.117: 239 0.117 - 0.156: 82 0.156 - 0.195: 43 Chirality restraints: 2975 Sorted by residual: chirality pdb=" CG LEU E 413 " pdb=" CB LEU E 413 " pdb=" CD1 LEU E 413 " pdb=" CD2 LEU E 413 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 9.48e-01 chirality pdb=" CG LEU M 413 " pdb=" CB LEU M 413 " pdb=" CD1 LEU M 413 " pdb=" CD2 LEU M 413 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 9.35e-01 chirality pdb=" CG LEU D 413 " pdb=" CB LEU D 413 " pdb=" CD1 LEU D 413 " pdb=" CD2 LEU D 413 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 9.35e-01 ... (remaining 2972 not shown) Planarity restraints: 3297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 131 " -0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO G 132 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO G 132 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO G 132 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL M 131 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.12e+00 pdb=" N PRO M 132 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO M 132 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO M 132 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 131 " -0.034 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO E 132 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO E 132 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 132 " -0.029 5.00e-02 4.00e+02 ... (remaining 3294 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 6062 2.84 - 3.35: 18066 3.35 - 3.87: 30532 3.87 - 4.38: 35559 4.38 - 4.90: 60403 Nonbonded interactions: 150622 Sorted by model distance: nonbonded pdb=" OD1 ASP E 88 " pdb=" OH TYR E 98 " model vdw 2.323 2.440 nonbonded pdb=" OD1 ASP B 88 " pdb=" OH TYR B 98 " model vdw 2.323 2.440 nonbonded pdb=" OD1 ASP D 88 " pdb=" OH TYR D 98 " model vdw 2.323 2.440 nonbonded pdb=" OD1 ASP M 88 " pdb=" OH TYR M 98 " model vdw 2.323 2.440 nonbonded pdb=" OD1 ASP K 88 " pdb=" OH TYR K 98 " model vdw 2.323 2.440 ... (remaining 150617 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'U' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 21 5.49 5 S 119 5.16 5 C 11907 2.51 5 N 3269 2.21 5 O 3654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 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: 14.950 Check model and map are aligned: 0.270 Process input model: 45.840 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.150 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 : 0.007 0.060 19348 Z= 0.442 Angle : 0.970 10.499 26201 Z= 0.508 Chirality : 0.053 0.195 2975 Planarity : 0.007 0.051 3297 Dihedral : 11.089 73.978 7427 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % 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: -3.81 (0.13), residues: 2324 helix: -2.47 (0.10), residues: 1316 sheet: -0.73 (0.43), residues: 112 loop : -2.64 (0.17), residues: 896 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 533 time to evaluate : 2.345 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: 533 average time/residue: 0.3990 time to fit residues: 297.9383 Evaluate side-chains 259 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 2.431 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.5980 chunk 175 optimal weight: 0.2980 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 118 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 181 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 chunk 210 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 147 GLN D 287 HIS D 395 ASN B 270 GLN B 363 GLN B 370 GLN E 270 GLN E 275 ASN E 340 ASN E 395 ASN G 147 GLN G 270 GLN G 340 ASN G 395 ASN I 147 GLN I 340 ASN I 395 ASN K 340 ASN K 395 ASN ** M 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 287 HIS M 340 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 19348 Z= 0.201 Angle : 0.562 7.939 26201 Z= 0.277 Chirality : 0.039 0.145 2975 Planarity : 0.005 0.037 3297 Dihedral : 4.465 25.367 2779 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer Outliers : 2.15 % 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: -1.67 (0.16), residues: 2324 helix: -0.52 (0.13), residues: 1323 sheet: -1.05 (0.43), residues: 126 loop : -1.91 (0.18), residues: 875 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 288 time to evaluate : 2.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 23 residues processed: 324 average time/residue: 0.3220 time to fit residues: 158.0167 Evaluate side-chains 275 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 252 time to evaluate : 2.240 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1691 time to fit residues: 10.6616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 175 optimal weight: 0.9980 chunk 143 optimal weight: 0.3980 chunk 58 optimal weight: 0.6980 chunk 211 optimal weight: 0.6980 chunk 228 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 169 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN E 275 ASN G 378 GLN M 105 ASN M 287 HIS M 340 ASN M 424 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 19348 Z= 0.225 Angle : 0.550 7.408 26201 Z= 0.271 Chirality : 0.039 0.152 2975 Planarity : 0.004 0.037 3297 Dihedral : 4.311 26.472 2779 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.17), residues: 2324 helix: 0.25 (0.14), residues: 1316 sheet: -0.28 (0.46), residues: 112 loop : -1.72 (0.18), residues: 896 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 247 time to evaluate : 2.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 10 residues processed: 269 average time/residue: 0.3262 time to fit residues: 133.4858 Evaluate side-chains 243 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 233 time to evaluate : 2.244 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1681 time to fit residues: 6.2436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 0.8980 chunk 158 optimal weight: 0.3980 chunk 109 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 100 optimal weight: 3.9990 chunk 141 optimal weight: 0.5980 chunk 211 optimal weight: 0.7980 chunk 224 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 270 GLN E 378 GLN G 147 GLN ** M 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 19348 Z= 0.191 Angle : 0.539 7.361 26201 Z= 0.259 Chirality : 0.038 0.139 2975 Planarity : 0.004 0.038 3297 Dihedral : 4.103 26.544 2779 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer Outliers : 1.91 % 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: -0.27 (0.17), residues: 2324 helix: 0.69 (0.14), residues: 1316 sheet: -0.17 (0.45), residues: 112 loop : -1.46 (0.19), residues: 896 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 250 time to evaluate : 2.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 19 residues processed: 282 average time/residue: 0.3229 time to fit residues: 137.7864 Evaluate side-chains 260 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 241 time to evaluate : 1.942 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1705 time to fit residues: 9.2293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 3 optimal weight: 0.4980 chunk 166 optimal weight: 0.0270 chunk 92 optimal weight: 0.7980 chunk 191 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 201 optimal weight: 0.6980 chunk 56 optimal weight: 0.0770 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 GLN E 275 ASN M 262 ASN M 287 HIS M 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 19348 Z= 0.159 Angle : 0.528 8.100 26201 Z= 0.252 Chirality : 0.037 0.140 2975 Planarity : 0.003 0.038 3297 Dihedral : 3.958 25.073 2779 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer Outliers : 1.27 % 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: 0.07 (0.17), residues: 2324 helix: 0.94 (0.15), residues: 1316 sheet: -0.01 (0.45), residues: 112 loop : -1.28 (0.19), residues: 896 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 253 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 8 residues processed: 276 average time/residue: 0.3251 time to fit residues: 136.6140 Evaluate side-chains 246 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 238 time to evaluate : 2.299 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1816 time to fit residues: 5.8897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 0.9990 chunk 201 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 224 optimal weight: 0.6980 chunk 186 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 ASN M 287 HIS M 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 19348 Z= 0.251 Angle : 0.568 8.351 26201 Z= 0.276 Chirality : 0.039 0.138 2975 Planarity : 0.004 0.039 3297 Dihedral : 4.180 25.674 2779 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer Outliers : 1.17 % 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: 0.16 (0.17), residues: 2324 helix: 0.98 (0.14), residues: 1316 sheet: 0.05 (0.46), residues: 112 loop : -1.17 (0.19), residues: 896 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 249 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 9 residues processed: 270 average time/residue: 0.3325 time to fit residues: 135.0204 Evaluate side-chains 240 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 231 time to evaluate : 2.428 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1748 time to fit residues: 5.9795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 188 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 chunk 223 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 287 HIS M 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 19348 Z= 0.239 Angle : 0.566 11.272 26201 Z= 0.274 Chirality : 0.039 0.146 2975 Planarity : 0.004 0.039 3297 Dihedral : 4.176 26.143 2779 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 0.93 % 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: 0.28 (0.17), residues: 2324 helix: 1.05 (0.14), residues: 1316 sheet: 0.21 (0.47), residues: 112 loop : -1.09 (0.20), residues: 896 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 239 time to evaluate : 2.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 258 average time/residue: 0.3395 time to fit residues: 131.1216 Evaluate side-chains 233 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 225 time to evaluate : 2.362 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1764 time to fit residues: 5.8130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 1.9990 chunk 133 optimal weight: 0.0050 chunk 67 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 142 optimal weight: 0.3980 chunk 152 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 175 optimal weight: 0.6980 chunk 203 optimal weight: 0.0870 chunk 214 optimal weight: 3.9990 overall best weight: 0.3772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 ASN I 270 GLN ** M 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 19348 Z= 0.154 Angle : 0.529 10.064 26201 Z= 0.252 Chirality : 0.037 0.245 2975 Planarity : 0.003 0.037 3297 Dihedral : 3.900 25.489 2779 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer Outliers : 0.39 % 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: 0.54 (0.17), residues: 2324 helix: 1.27 (0.15), residues: 1316 sheet: 0.34 (0.47), residues: 112 loop : -0.99 (0.20), residues: 896 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 243 time to evaluate : 2.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 249 average time/residue: 0.3363 time to fit residues: 125.7693 Evaluate side-chains 237 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 234 time to evaluate : 2.190 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1599 time to fit residues: 3.9378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 188 optimal weight: 0.4980 chunk 197 optimal weight: 0.8980 chunk 207 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN E 275 ASN I 424 GLN M 287 HIS M 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 19348 Z= 0.311 Angle : 0.610 10.418 26201 Z= 0.297 Chirality : 0.041 0.236 2975 Planarity : 0.004 0.040 3297 Dihedral : 4.326 25.223 2779 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer Outliers : 0.54 % 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: 0.34 (0.17), residues: 2324 helix: 1.10 (0.14), residues: 1316 sheet: -0.36 (0.44), residues: 126 loop : -0.99 (0.20), residues: 882 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 233 time to evaluate : 2.415 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 242 average time/residue: 0.3435 time to fit residues: 124.5693 Evaluate side-chains 230 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 223 time to evaluate : 2.283 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1777 time to fit residues: 5.5326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 0.0040 chunk 134 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 153 optimal weight: 0.0470 chunk 231 optimal weight: 3.9990 chunk 212 optimal weight: 0.8980 chunk 184 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 overall best weight: 0.5290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN E 275 ASN I 147 GLN M 287 HIS M 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 19348 Z= 0.186 Angle : 0.546 9.779 26201 Z= 0.263 Chirality : 0.038 0.221 2975 Planarity : 0.003 0.037 3297 Dihedral : 4.039 25.291 2779 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer Outliers : 0.24 % 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: 0.51 (0.17), residues: 2324 helix: 1.26 (0.14), residues: 1316 sheet: -0.28 (0.45), residues: 126 loop : -0.94 (0.20), residues: 882 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 229 time to evaluate : 2.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 234 average time/residue: 0.3425 time to fit residues: 120.5791 Evaluate side-chains 226 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 225 time to evaluate : 2.492 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1760 time to fit residues: 3.6997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 0.7980 chunk 56 optimal weight: 0.0470 chunk 169 optimal weight: 0.0070 chunk 27 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 189 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 ASN E 363 GLN I 147 GLN ** M 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.130049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.100128 restraints weight = 28667.284| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.47 r_work: 0.3104 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 19348 Z= 0.161 Angle : 0.531 9.532 26201 Z= 0.255 Chirality : 0.037 0.217 2975 Planarity : 0.003 0.038 3297 Dihedral : 3.874 23.429 2779 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % 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: 0.66 (0.17), residues: 2324 helix: 1.39 (0.15), residues: 1309 sheet: 0.42 (0.47), residues: 112 loop : -0.97 (0.20), residues: 903 =============================================================================== Job complete usr+sys time: 3843.04 seconds wall clock time: 70 minutes 40.10 seconds (4240.10 seconds total)