Starting phenix.real_space_refine on Sun Mar 17 21:02:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i2n_0333/03_2024/6i2n_0333.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i2n_0333/03_2024/6i2n_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_0333/03_2024/6i2n_0333.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i2n_0333/03_2024/6i2n_0333.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i2n_0333/03_2024/6i2n_0333.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i2n_0333/03_2024/6i2n_0333.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 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. 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 9.40, per 1000 atoms: 0.50 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: 6.85 Conformation dependent library (CDL) restraints added in 3.3 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: 1.80 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: 5.22 Time building geometry restraints manager: 7.42 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: 11049 14.80 - 29.59: 634 29.59 - 44.39: 169 44.39 - 59.18: 48 59.18 - 73.98: 35 Dihedral angle restraints: 11935 sinusoidal: 5110 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 11932 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 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: 3.630 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: 13.720 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 48.170 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 : 11.929 73.978 7511 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 % Allowed : 4.79 % Favored : 95.21 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP E 119 HIS 0.018 0.003 HIS K 89 PHE 0.023 0.004 PHE M 384 TYR 0.028 0.003 TYR B 178 ARG 0.006 0.001 ARG E 197 *********************** 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 : 2.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 348 VAL cc_start: 0.8873 (p) cc_final: 0.8528 (t) REVERT: B 109 ILE cc_start: 0.7388 (mt) cc_final: 0.6783 (mt) REVERT: B 406 LEU cc_start: 0.9048 (tm) cc_final: 0.8843 (tp) REVERT: E 88 ASP cc_start: 0.7880 (t70) cc_final: 0.6469 (t0) REVERT: G 88 ASP cc_start: 0.7383 (t70) cc_final: 0.6585 (t0) REVERT: G 183 ASN cc_start: 0.7802 (t0) cc_final: 0.7496 (t0) REVERT: G 343 MET cc_start: 0.8784 (mmm) cc_final: 0.8527 (mmm) REVERT: G 402 MET cc_start: 0.8335 (ttm) cc_final: 0.8010 (mtp) REVERT: K 415 ASP cc_start: 0.7601 (m-30) cc_final: 0.7232 (m-30) REVERT: M 340 ASN cc_start: 0.8497 (m-40) cc_final: 0.8283 (m-40) outliers start: 0 outliers final: 0 residues processed: 533 average time/residue: 0.3875 time to fit residues: 288.6592 Evaluate side-chains 261 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 2.261 ------------------------------------------------------------------------------- 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 340 ASN 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: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2422 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= 0.201 Angle : 0.562 7.803 26201 Z= 0.277 Chirality : 0.039 0.148 2975 Planarity : 0.005 0.037 3297 Dihedral : 7.732 58.007 2863 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.05 % Allowed : 11.11 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.16), residues: 2324 helix: -0.59 (0.13), residues: 1323 sheet: -1.06 (0.44), residues: 126 loop : -1.93 (0.18), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 388 HIS 0.009 0.002 HIS B 89 PHE 0.013 0.002 PHE G 384 TYR 0.025 0.001 TYR M 362 ARG 0.005 0.000 ARG K 93 *********************** 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 327 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 285 time to evaluate : 2.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 343 MET cc_start: 0.8840 (mmm) cc_final: 0.8367 (mmm) REVERT: D 398 LEU cc_start: 0.8253 (mt) cc_final: 0.7943 (mt) REVERT: B 362 TYR cc_start: 0.8983 (t80) cc_final: 0.8748 (t80) REVERT: B 385 MET cc_start: 0.8596 (tpp) cc_final: 0.8326 (tpp) REVERT: B 414 ILE cc_start: 0.9152 (mt) cc_final: 0.8866 (mt) REVERT: E 91 LYS cc_start: 0.8345 (mmtp) cc_final: 0.7996 (mtmm) REVERT: E 136 LYS cc_start: 0.8239 (mmtt) cc_final: 0.8001 (mmtt) REVERT: G 226 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8214 (tp) REVERT: I 151 ASP cc_start: 0.7209 (m-30) cc_final: 0.6984 (m-30) REVERT: I 168 VAL cc_start: 0.8854 (OUTLIER) cc_final: 0.8648 (m) REVERT: I 415 ASP cc_start: 0.7484 (m-30) cc_final: 0.7228 (m-30) REVERT: K 338 MET cc_start: 0.8609 (mtp) cc_final: 0.8396 (mtm) REVERT: M 178 TYR cc_start: 0.8626 (m-80) cc_final: 0.8387 (m-80) outliers start: 42 outliers final: 24 residues processed: 319 average time/residue: 0.3173 time to fit residues: 152.6194 Evaluate side-chains 278 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 252 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain I residue 100 ASN Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 231 ASP Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain K residue 100 ASN Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 277 GLU Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 348 VAL 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: 0.7980 chunk 175 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 211 optimal weight: 0.9980 chunk 228 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 169 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 M 105 ASN M 287 HIS M 340 ASN M 424 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2997 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= 0.257 Angle : 0.567 7.740 26201 Z= 0.280 Chirality : 0.040 0.136 2975 Planarity : 0.004 0.037 3297 Dihedral : 7.433 58.075 2863 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.03 % Allowed : 12.87 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.16), residues: 2324 helix: 0.16 (0.14), residues: 1316 sheet: -0.32 (0.45), residues: 112 loop : -1.73 (0.18), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 388 HIS 0.008 0.002 HIS I 89 PHE 0.015 0.002 PHE I 129 TYR 0.025 0.002 TYR M 362 ARG 0.004 0.000 ARG K 93 *********************** 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 304 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 242 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 366 LEU cc_start: 0.8839 (tp) cc_final: 0.8564 (tt) REVERT: D 429 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8029 (tp) REVERT: B 362 TYR cc_start: 0.9071 (t80) cc_final: 0.8783 (t80) REVERT: B 429 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7647 (tt) REVERT: E 91 LYS cc_start: 0.8409 (mmtp) cc_final: 0.8070 (mtmm) REVERT: I 152 ASN cc_start: 0.8602 (OUTLIER) cc_final: 0.8375 (p0) REVERT: I 415 ASP cc_start: 0.7452 (m-30) cc_final: 0.7210 (m-30) REVERT: K 372 MET cc_start: 0.9065 (mtp) cc_final: 0.8822 (mtp) REVERT: M 152 ASN cc_start: 0.8788 (OUTLIER) cc_final: 0.8461 (p0) REVERT: M 178 TYR cc_start: 0.8704 (m-80) cc_final: 0.8446 (m-80) outliers start: 62 outliers final: 35 residues processed: 290 average time/residue: 0.3195 time to fit residues: 141.3685 Evaluate side-chains 264 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 225 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain I residue 100 ASN Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 152 ASN Chi-restraints excluded: chain I residue 231 ASP Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain K residue 100 ASN Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 277 GLU Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 152 ASN Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 264 ASP Chi-restraints excluded: chain M residue 348 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 211 optimal weight: 0.6980 chunk 224 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 200 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN M 287 HIS M 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19348 Z= 0.249 Angle : 0.564 7.558 26201 Z= 0.276 Chirality : 0.039 0.134 2975 Planarity : 0.004 0.038 3297 Dihedral : 7.284 58.066 2863 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.23 % Allowed : 13.75 % Favored : 83.02 % 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 (0.17), residues: 2324 helix: 0.53 (0.14), residues: 1316 sheet: -0.22 (0.45), residues: 112 loop : -1.51 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 388 HIS 0.009 0.001 HIS K 89 PHE 0.017 0.002 PHE D 129 TYR 0.027 0.001 TYR M 362 ARG 0.003 0.000 ARG I 197 *********************** 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 307 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 241 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 89 HIS cc_start: 0.8955 (OUTLIER) cc_final: 0.8745 (p-80) REVERT: D 343 MET cc_start: 0.8840 (mmm) cc_final: 0.8435 (mmm) REVERT: D 366 LEU cc_start: 0.8860 (tp) cc_final: 0.8603 (tt) REVERT: D 398 LEU cc_start: 0.8213 (mt) cc_final: 0.7987 (mt) REVERT: D 429 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8028 (tp) REVERT: B 362 TYR cc_start: 0.9074 (t80) cc_final: 0.8758 (t80) REVERT: B 370 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8036 (mt0) REVERT: B 429 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7627 (tt) REVERT: E 91 LYS cc_start: 0.8392 (mmtp) cc_final: 0.8106 (mtmm) REVERT: E 385 MET cc_start: 0.8636 (tpp) cc_final: 0.8223 (tpp) REVERT: G 226 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8346 (tp) REVERT: I 152 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8359 (p0) REVERT: I 415 ASP cc_start: 0.7444 (m-30) cc_final: 0.7227 (m-30) REVERT: K 188 MET cc_start: 0.7945 (mmm) cc_final: 0.7714 (mmm) REVERT: K 372 MET cc_start: 0.9070 (mtp) cc_final: 0.8837 (mtp) REVERT: M 152 ASN cc_start: 0.8758 (OUTLIER) cc_final: 0.8437 (p0) REVERT: M 178 TYR cc_start: 0.8703 (m-80) cc_final: 0.8473 (m-80) outliers start: 66 outliers final: 44 residues processed: 298 average time/residue: 0.3050 time to fit residues: 138.4025 Evaluate side-chains 279 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 228 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 89 HIS Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain I residue 89 HIS Chi-restraints excluded: chain I residue 100 ASN Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 152 ASN Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain K residue 89 HIS Chi-restraints excluded: chain K residue 100 ASN Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 152 ASN Chi-restraints excluded: chain K residue 167 ASP Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 277 GLU Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain K residue 429 LEU Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 152 ASN Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 348 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 0.7980 chunk 127 optimal weight: 0.6980 chunk 3 optimal weight: 0.0060 chunk 166 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 191 optimal weight: 2.9990 chunk 155 optimal weight: 0.0070 chunk 0 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 201 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 overall best weight: 0.4614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 270 GLN B 340 ASN E 275 ASN M 287 HIS M 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19348 Z= 0.170 Angle : 0.524 7.955 26201 Z= 0.253 Chirality : 0.037 0.136 2975 Planarity : 0.003 0.039 3297 Dihedral : 7.051 57.980 2863 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.42 % Allowed : 14.58 % Favored : 82.00 % 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: -0.03 (0.17), residues: 2324 helix: 0.87 (0.14), residues: 1316 sheet: -0.03 (0.45), residues: 112 loop : -1.33 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 388 HIS 0.009 0.001 HIS K 89 PHE 0.010 0.001 PHE G 384 TYR 0.028 0.001 TYR M 362 ARG 0.003 0.000 ARG G 197 *********************** 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 320 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 250 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 89 HIS cc_start: 0.8997 (OUTLIER) cc_final: 0.8786 (p-80) REVERT: D 343 MET cc_start: 0.8819 (mmm) cc_final: 0.8292 (mmm) REVERT: D 366 LEU cc_start: 0.8825 (tp) cc_final: 0.8588 (tt) REVERT: D 429 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8025 (tp) REVERT: B 362 TYR cc_start: 0.9089 (t80) cc_final: 0.8774 (t80) REVERT: E 91 LYS cc_start: 0.8353 (mmtp) cc_final: 0.8047 (mtmm) REVERT: G 379 ARG cc_start: 0.8224 (tpp-160) cc_final: 0.7809 (mmm160) REVERT: I 167 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7550 (t70) REVERT: K 188 MET cc_start: 0.7963 (mmm) cc_final: 0.7698 (mmm) REVERT: K 372 MET cc_start: 0.9025 (mtp) cc_final: 0.8776 (mtp) REVERT: M 178 TYR cc_start: 0.8666 (m-80) cc_final: 0.8406 (m-80) REVERT: M 240 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.7875 (mt) outliers start: 70 outliers final: 42 residues processed: 311 average time/residue: 0.3039 time to fit residues: 144.3257 Evaluate side-chains 284 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 238 time to evaluate : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 89 HIS Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 262 ASN Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain I residue 89 HIS Chi-restraints excluded: chain I residue 100 ASN Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain K residue 89 HIS Chi-restraints excluded: chain K residue 100 ASN Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 167 ASP Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 277 GLU Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 348 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 3.9990 chunk 201 optimal weight: 0.0170 chunk 44 optimal weight: 0.6980 chunk 131 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 224 optimal weight: 0.1980 chunk 186 optimal weight: 0.0370 chunk 103 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- 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 262 ASN M 287 HIS M 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19348 Z= 0.151 Angle : 0.517 8.179 26201 Z= 0.249 Chirality : 0.037 0.135 2975 Planarity : 0.003 0.038 3297 Dihedral : 6.945 57.968 2863 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.84 % Allowed : 15.12 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.17), residues: 2324 helix: 1.08 (0.15), residues: 1316 sheet: 0.14 (0.46), residues: 112 loop : -1.17 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 388 HIS 0.009 0.001 HIS K 89 PHE 0.010 0.001 PHE G 384 TYR 0.026 0.001 TYR M 362 ARG 0.004 0.000 ARG I 146 *********************** 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 309 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 251 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 366 LEU cc_start: 0.8790 (tp) cc_final: 0.8558 (tt) REVERT: D 398 LEU cc_start: 0.8264 (mt) cc_final: 0.8056 (mt) REVERT: D 429 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8027 (tp) REVERT: B 414 ILE cc_start: 0.9272 (mt) cc_final: 0.9035 (mt) REVERT: E 91 LYS cc_start: 0.8327 (mmtp) cc_final: 0.8023 (mtmm) REVERT: E 428 LYS cc_start: 0.8253 (mmmt) cc_final: 0.7646 (mptt) REVERT: G 362 TYR cc_start: 0.8970 (t80) cc_final: 0.8572 (t80) REVERT: I 167 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7538 (t70) REVERT: K 188 MET cc_start: 0.7956 (mmm) cc_final: 0.7618 (mmm) REVERT: K 240 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8549 (mm) REVERT: K 372 MET cc_start: 0.8982 (mtp) cc_final: 0.8710 (mtp) REVERT: M 231 ASP cc_start: 0.7292 (p0) cc_final: 0.6785 (p0) REVERT: M 240 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.7879 (mt) REVERT: M 295 MET cc_start: 0.6302 (mmm) cc_final: 0.5872 (mmm) outliers start: 58 outliers final: 42 residues processed: 304 average time/residue: 0.3053 time to fit residues: 142.2560 Evaluate side-chains 284 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 238 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 262 ASN Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain I residue 100 ASN Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain K residue 89 HIS Chi-restraints excluded: chain K residue 100 ASN Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 167 ASP Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 240 LEU Chi-restraints excluded: chain K residue 277 GLU Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 92 GLU Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 262 ASN Chi-restraints excluded: chain M residue 348 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 127 optimal weight: 0.5980 chunk 163 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 138 optimal weight: 0.3980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN B 375 GLN G 378 GLN ** M 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 287 HIS M 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3785 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= 0.271 Angle : 0.580 11.418 26201 Z= 0.283 Chirality : 0.039 0.136 2975 Planarity : 0.004 0.039 3297 Dihedral : 7.124 58.148 2863 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.08 % Allowed : 15.36 % Favored : 81.56 % 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: 0.25 (0.17), residues: 2324 helix: 1.04 (0.14), residues: 1316 sheet: 0.14 (0.47), residues: 112 loop : -1.12 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 388 HIS 0.010 0.002 HIS K 89 PHE 0.014 0.002 PHE I 129 TYR 0.025 0.002 TYR M 362 ARG 0.005 0.000 ARG M 263 *********************** 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 304 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 241 time to evaluate : 2.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 188 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7749 (mtp) REVERT: D 357 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8693 (mtpp) REVERT: D 366 LEU cc_start: 0.8891 (tp) cc_final: 0.8660 (tt) REVERT: D 429 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8025 (tp) REVERT: E 91 LYS cc_start: 0.8349 (mmtp) cc_final: 0.8049 (mtmm) REVERT: E 385 MET cc_start: 0.8619 (tpp) cc_final: 0.8403 (tpp) REVERT: E 428 LYS cc_start: 0.8274 (mmmt) cc_final: 0.7664 (mptt) REVERT: G 357 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8845 (mtpp) REVERT: I 131 VAL cc_start: 0.8901 (OUTLIER) cc_final: 0.8690 (t) REVERT: I 167 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7513 (t70) REVERT: K 240 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8631 (mm) REVERT: K 372 MET cc_start: 0.9076 (mtp) cc_final: 0.8803 (mtp) REVERT: M 131 VAL cc_start: 0.8883 (m) cc_final: 0.8614 (t) REVERT: M 231 ASP cc_start: 0.7544 (p0) cc_final: 0.7061 (p0) REVERT: M 240 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.7838 (mt) outliers start: 63 outliers final: 48 residues processed: 295 average time/residue: 0.3024 time to fit residues: 135.4107 Evaluate side-chains 287 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 231 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain D residue 357 LYS Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 89 HIS Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 262 ASN Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain I residue 89 HIS Chi-restraints excluded: chain I residue 100 ASN Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain K residue 89 HIS Chi-restraints excluded: chain K residue 100 ASN Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 167 ASP Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 240 LEU Chi-restraints excluded: chain K residue 277 GLU Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain M residue 89 HIS Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 348 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 0.2980 chunk 133 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 142 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 175 optimal weight: 0.2980 chunk 203 optimal weight: 0.6980 chunk 214 optimal weight: 0.0060 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 E 363 GLN M 287 HIS M 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19348 Z= 0.161 Angle : 0.525 9.959 26201 Z= 0.254 Chirality : 0.037 0.137 2975 Planarity : 0.003 0.039 3297 Dihedral : 6.924 57.989 2863 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.98 % Allowed : 15.95 % Favored : 81.07 % 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 (0.15), residues: 1316 sheet: 0.28 (0.47), residues: 112 loop : -1.03 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 388 HIS 0.008 0.001 HIS K 89 PHE 0.010 0.001 PHE G 384 TYR 0.028 0.001 TYR M 362 ARG 0.007 0.000 ARG K 267 *********************** 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 300 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 239 time to evaluate : 2.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 131 VAL cc_start: 0.9030 (OUTLIER) cc_final: 0.8798 (t) REVERT: D 188 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7567 (mtp) REVERT: D 343 MET cc_start: 0.8878 (mmm) cc_final: 0.8605 (mmm) REVERT: D 366 LEU cc_start: 0.8816 (tp) cc_final: 0.8584 (tt) REVERT: D 429 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8019 (tp) REVERT: E 91 LYS cc_start: 0.8298 (mmtp) cc_final: 0.8015 (mtmm) REVERT: E 355 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8537 (mp) REVERT: E 357 LYS cc_start: 0.9415 (OUTLIER) cc_final: 0.9185 (ttmm) REVERT: E 428 LYS cc_start: 0.8276 (mmmt) cc_final: 0.7670 (mptt) REVERT: G 220 MET cc_start: 0.7482 (mmt) cc_final: 0.7181 (mmt) REVERT: G 357 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8846 (mtpp) REVERT: I 167 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7488 (t70) REVERT: K 240 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8488 (mm) REVERT: K 372 MET cc_start: 0.9021 (mtp) cc_final: 0.8727 (mtp) REVERT: M 131 VAL cc_start: 0.8859 (m) cc_final: 0.8625 (t) REVERT: M 231 ASP cc_start: 0.7415 (p0) cc_final: 0.6915 (p0) REVERT: M 240 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8104 (mt) outliers start: 61 outliers final: 44 residues processed: 289 average time/residue: 0.3092 time to fit residues: 135.9022 Evaluate side-chains 285 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 232 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 357 LYS Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 100 ASN Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 262 ASN Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain I residue 89 HIS Chi-restraints excluded: chain I residue 100 ASN Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain K residue 100 ASN Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 167 ASP Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 240 LEU Chi-restraints excluded: chain K residue 277 GLU Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 348 VAL 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: 0.9990 chunk 214 optimal weight: 0.0070 chunk 125 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 163 optimal weight: 0.0070 chunk 63 optimal weight: 1.9990 chunk 188 optimal weight: 0.2980 chunk 197 optimal weight: 0.9980 chunk 207 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 214 GLN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 287 HIS M 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3939 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= 0.154 Angle : 0.519 9.799 26201 Z= 0.250 Chirality : 0.037 0.151 2975 Planarity : 0.003 0.037 3297 Dihedral : 6.861 57.980 2863 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.94 % Allowed : 16.19 % Favored : 80.87 % 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: 0.65 (0.17), residues: 2324 helix: 1.37 (0.15), residues: 1316 sheet: 0.36 (0.47), residues: 112 loop : -0.96 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 388 HIS 0.008 0.001 HIS I 89 PHE 0.010 0.001 PHE G 384 TYR 0.022 0.001 TYR M 362 ARG 0.007 0.000 ARG K 267 *********************** 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 306 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 246 time to evaluate : 2.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 131 VAL cc_start: 0.9005 (OUTLIER) cc_final: 0.8782 (t) REVERT: D 188 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7545 (mtp) REVERT: D 343 MET cc_start: 0.8900 (mmm) cc_final: 0.8626 (mmm) REVERT: D 357 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8609 (mtpp) REVERT: D 366 LEU cc_start: 0.8807 (tp) cc_final: 0.8565 (tt) REVERT: D 429 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8003 (tp) REVERT: B 298 ASP cc_start: 0.6858 (p0) cc_final: 0.6251 (p0) REVERT: B 414 ILE cc_start: 0.9241 (mt) cc_final: 0.9005 (mt) REVERT: E 357 LYS cc_start: 0.9431 (OUTLIER) cc_final: 0.9193 (ttmm) REVERT: E 385 MET cc_start: 0.8412 (tpp) cc_final: 0.8150 (tpp) REVERT: E 428 LYS cc_start: 0.8284 (mmmt) cc_final: 0.7672 (mptt) REVERT: G 220 MET cc_start: 0.7477 (mmt) cc_final: 0.7216 (mmt) REVERT: G 357 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8817 (mtpp) REVERT: I 167 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7512 (t70) REVERT: K 240 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8425 (mm) REVERT: K 372 MET cc_start: 0.9016 (mtp) cc_final: 0.8730 (mtp) REVERT: M 131 VAL cc_start: 0.8846 (m) cc_final: 0.8640 (t) REVERT: M 231 ASP cc_start: 0.7389 (p0) cc_final: 0.6892 (p0) REVERT: M 240 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8186 (mt) outliers start: 60 outliers final: 42 residues processed: 294 average time/residue: 0.3111 time to fit residues: 137.5025 Evaluate side-chains 285 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 234 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain D residue 357 LYS Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 357 LYS Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 262 ASN Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain I residue 89 HIS Chi-restraints excluded: chain I residue 100 ASN Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain K residue 100 ASN Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 167 ASP Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 240 LEU Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 348 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 0.0570 chunk 134 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 231 optimal weight: 0.7980 chunk 212 optimal weight: 0.7980 chunk 184 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 chunk 142 optimal weight: 0.4980 chunk 112 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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: 0.7841 moved from start: 0.3994 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= 0.172 Angle : 0.536 9.725 26201 Z= 0.257 Chirality : 0.037 0.147 2975 Planarity : 0.003 0.037 3297 Dihedral : 6.884 58.004 2863 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.94 % Allowed : 16.39 % Favored : 80.68 % 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: 0.66 (0.17), residues: 2324 helix: 1.37 (0.15), residues: 1316 sheet: 0.42 (0.46), residues: 112 loop : -0.96 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 388 HIS 0.008 0.001 HIS I 89 PHE 0.009 0.001 PHE G 384 TYR 0.020 0.001 TYR M 362 ARG 0.007 0.000 ARG D 213 ********************** 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 296 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 236 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 131 VAL cc_start: 0.8983 (OUTLIER) cc_final: 0.8756 (t) REVERT: D 188 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7575 (mtp) REVERT: D 343 MET cc_start: 0.8880 (mmm) cc_final: 0.8544 (mmm) REVERT: D 357 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8582 (mtpp) REVERT: D 366 LEU cc_start: 0.8808 (tp) cc_final: 0.8561 (tt) REVERT: D 429 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7993 (tp) REVERT: E 91 LYS cc_start: 0.8221 (mmtp) cc_final: 0.7842 (mtmm) REVERT: E 357 LYS cc_start: 0.9438 (OUTLIER) cc_final: 0.9198 (ttmm) REVERT: E 385 MET cc_start: 0.8437 (tpp) cc_final: 0.8158 (tpp) REVERT: G 220 MET cc_start: 0.7496 (mmt) cc_final: 0.7141 (mmt) REVERT: G 357 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8751 (mtpp) REVERT: I 167 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7521 (t70) REVERT: K 240 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8448 (mm) REVERT: K 372 MET cc_start: 0.9005 (mtp) cc_final: 0.8720 (mtp) REVERT: M 131 VAL cc_start: 0.8847 (m) cc_final: 0.8642 (t) REVERT: M 231 ASP cc_start: 0.7386 (p0) cc_final: 0.6896 (p0) REVERT: M 240 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8056 (mt) outliers start: 60 outliers final: 46 residues processed: 284 average time/residue: 0.3066 time to fit residues: 131.8634 Evaluate side-chains 288 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 233 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain D residue 357 LYS Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 357 LYS Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 100 ASN Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 262 ASN Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain I residue 89 HIS Chi-restraints excluded: chain I residue 100 ASN Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 262 ASN Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain K residue 100 ASN Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 167 ASP Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 240 LEU Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 348 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 2.9990 chunk 56 optimal weight: 0.2980 chunk 169 optimal weight: 0.4980 chunk 27 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 184 optimal weight: 0.7980 chunk 77 optimal weight: 0.2980 chunk 189 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 161 optimal weight: 0.0980 overall best weight: 0.3580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** M 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.132526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.102237 restraints weight = 28666.198| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.47 r_work: 0.3110 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19348 Z= 0.149 Angle : 0.521 9.027 26201 Z= 0.249 Chirality : 0.037 0.151 2975 Planarity : 0.003 0.036 3297 Dihedral : 6.815 57.978 2863 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.69 % Allowed : 16.49 % Favored : 80.82 % 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: 0.74 (0.17), residues: 2324 helix: 1.48 (0.15), residues: 1309 sheet: 0.48 (0.46), residues: 112 loop : -0.97 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 388 HIS 0.008 0.001 HIS M 287 PHE 0.010 0.001 PHE G 384 TYR 0.020 0.001 TYR M 362 ARG 0.007 0.000 ARG D 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4059.66 seconds wall clock time: 74 minutes 19.30 seconds (4459.30 seconds total)