Starting phenix.real_space_refine on Sat Mar 16 13:50:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sxo_10344/03_2024/6sxo_10344.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sxo_10344/03_2024/6sxo_10344.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/6sxo_10344/03_2024/6sxo_10344.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sxo_10344/03_2024/6sxo_10344.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sxo_10344/03_2024/6sxo_10344.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sxo_10344/03_2024/6sxo_10344.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= 0.003 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 326 5.49 5 S 32 5.16 5 C 8094 2.51 5 N 2786 2.21 5 O 3656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 243": "NH1" <-> "NH2" Residue "A PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lh ARG 7": "NH1" <-> "NH2" Residue "Lh ARG 56": "NH1" <-> "NH2" Residue "Lh ARG 94": "NH1" <-> "NH2" Residue "Lk ARG 3": "NH1" <-> "NH2" Residue "Lk ARG 40": "NH1" <-> "NH2" Residue "LR ARG 38": "NH1" <-> "NH2" Residue "LR ARG 42": "NH1" <-> "NH2" Residue "LR ARG 52": "NH1" <-> "NH2" Residue "LR ARG 74": "NH1" <-> "NH2" Residue "LR ARG 117": "NH1" <-> "NH2" Residue "LR ARG 151": "NH1" <-> "NH2" Residue "LX ARG 53": "NH1" <-> "NH2" Residue "LX PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LX ARG 139": "NH1" <-> "NH2" Residue "LY ARG 27": "NH1" <-> "NH2" Residue "LY ARG 87": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14894 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2931 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 12, 'TRANS': 362} Chain: "Lh" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1015 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "Lk" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "LR" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1281 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 3, 'TRANS': 149} Chain: "LX" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 985 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 111} Chain: "LY" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1115 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "L5" Number of atoms: 5761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 5761 Classifications: {'RNA': 268} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 15, 'rna3p_pur': 135, 'rna3p_pyr': 105} Link IDs: {'rna2p': 28, 'rna3p': 239} Chain breaks: 6 Chain: "L8" Number of atoms: 1237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1237 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 3, 'rna3p_pur': 22, 'rna3p_pyr': 23} Link IDs: {'rna2p': 13, 'rna3p': 44} Time building chain proxies: 8.29, per 1000 atoms: 0.56 Number of scatterers: 14894 At special positions: 0 Unit cell: (155.15, 212.93, 126.26, 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 32 16.00 P 326 15.00 O 3656 8.00 N 2786 7.00 C 8094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.21 Conformation dependent library (CDL) restraints added in 1.7 seconds 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1860 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 11 sheets defined 43.7% alpha, 13.3% beta 98 base pairs and 176 stacking pairs defined. Time for finding SS restraints: 6.23 Creating SS restraints... Processing helix chain 'A' and resid 14 through 38 removed outlier: 3.881A pdb=" N VAL A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 27 " --> pdb=" O MET A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 63 Processing helix chain 'A' and resid 136 through 157 removed outlier: 3.522A pdb=" N VAL A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 177 removed outlier: 4.394A pdb=" N VAL A 166 " --> pdb=" O GLN A 162 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 212 Processing helix chain 'A' and resid 259 through 273 Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 285 through 299 removed outlier: 3.871A pdb=" N ALA A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 343 removed outlier: 3.608A pdb=" N LEU A 342 " --> pdb=" O GLU A 339 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR A 343 " --> pdb=" O PRO A 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 339 through 343' Processing helix chain 'A' and resid 351 through 361 removed outlier: 4.026A pdb=" N SER A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.672A pdb=" N ALA A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 5 through 10 removed outlier: 3.565A pdb=" N ARGLh 10 " --> pdb=" O ALALh 6 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 13 through 34 removed outlier: 3.567A pdb=" N ASPLh 23 " --> pdb=" O LYSLh 19 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEULh 24 " --> pdb=" O GLNLh 20 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VALLh 26 " --> pdb=" O ASPLh 22 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEULh 28 " --> pdb=" O LEULh 24 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SERLh 29 " --> pdb=" O LYSLh 25 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 40 through 45 Processing helix chain 'Lh' and resid 46 through 73 removed outlier: 3.662A pdb=" N ARGLh 56 " --> pdb=" O LYSLh 52 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THRLh 64 " --> pdb=" O VALLh 60 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 98 through 102 removed outlier: 4.176A pdb=" N ASNLh 101 " --> pdb=" O HISLh 98 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEULh 102 " --> pdb=" O GLULh 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'Lh' and resid 98 through 102' Processing helix chain 'Lh' and resid 106 through 114 removed outlier: 3.768A pdb=" N ARGLh 112 " --> pdb=" O GLNLh 108 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYRLh 114 " --> pdb=" O LYSLh 110 " (cutoff:3.500A) Processing helix chain 'Lk' and resid 8 through 16 removed outlier: 3.538A pdb=" N LEULk 12 " --> pdb=" O ILELk 8 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEULk 13 " --> pdb=" O LYSLk 9 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THRLk 14 " --> pdb=" O ASPLk 10 " (cutoff:3.500A) Processing helix chain 'Lk' and resid 49 through 59 removed outlier: 3.571A pdb=" N GLULk 54 " --> pdb=" O LYSLk 50 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYSLk 55 " --> pdb=" O GLULk 51 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLNLk 58 " --> pdb=" O GLULk 54 " (cutoff:3.500A) Processing helix chain 'LR' and resid 4 through 15 Processing helix chain 'LR' and resid 18 through 20 No H-bonds generated for 'chain 'LR' and resid 18 through 20' Processing helix chain 'LR' and resid 28 through 34 removed outlier: 3.591A pdb=" N ILELR 32 " --> pdb=" O GLULR 28 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASNLR 34 " --> pdb=" O ASNLR 30 " (cutoff:3.500A) Processing helix chain 'LR' and resid 37 through 47 removed outlier: 3.740A pdb=" N LEULR 44 " --> pdb=" O GLNLR 40 " (cutoff:3.500A) Processing helix chain 'LR' and resid 60 through 71 removed outlier: 3.806A pdb=" N LYSLR 65 " --> pdb=" O ALALR 61 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASNLR 66 " --> pdb=" O ARGLR 62 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THRLR 67 " --> pdb=" O CYSLR 63 " (cutoff:3.500A) Processing helix chain 'LR' and resid 84 through 89 removed outlier: 3.704A pdb=" N METLR 89 " --> pdb=" O ALALR 85 " (cutoff:3.500A) Processing helix chain 'LR' and resid 90 through 112 removed outlier: 3.623A pdb=" N TRPLR 95 " --> pdb=" O GLULR 91 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARGLR 100 " --> pdb=" O METLR 96 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARGLR 110 " --> pdb=" O LEULR 106 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLULR 111 " --> pdb=" O ARGLR 107 " (cutoff:3.500A) Processing helix chain 'LR' and resid 116 through 129 removed outlier: 4.504A pdb=" N SERLR 122 " --> pdb=" O HISLR 118 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEULR 125 " --> pdb=" O HISLR 121 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLYLR 129 " --> pdb=" O LEULR 125 " (cutoff:3.500A) Processing helix chain 'LR' and resid 134 through 150 removed outlier: 4.835A pdb=" N GLULR 140 " --> pdb=" O ARGLR 136 " (cutoff:3.500A) Processing helix chain 'LX' and resid 72 through 76 Processing helix chain 'LX' and resid 105 through 118 Processing helix chain 'LX' and resid 145 through 154 Processing helix chain 'LY' and resid 10 through 20 removed outlier: 3.597A pdb=" N HISLY 18 " --> pdb=" O ASNLY 14 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASNLY 20 " --> pdb=" O LYSLY 16 " (cutoff:3.500A) Processing helix chain 'LY' and resid 24 through 30 removed outlier: 4.094A pdb=" N LYSLY 28 " --> pdb=" O HISLY 24 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N METLY 30 " --> pdb=" O ARGLY 26 " (cutoff:3.500A) Processing helix chain 'LY' and resid 37 through 42 removed outlier: 3.543A pdb=" N TYRLY 42 " --> pdb=" O LEULY 38 " (cutoff:3.500A) Processing helix chain 'LY' and resid 75 through 78 Processing helix chain 'LY' and resid 100 through 102 No H-bonds generated for 'chain 'LY' and resid 100 through 102' Processing helix chain 'LY' and resid 112 through 129 removed outlier: 3.503A pdb=" N LYSLY 117 " --> pdb=" O LYSLY 113 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILELY 118 " --> pdb=" O ASPLY 114 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALALY 123 " --> pdb=" O LEULY 119 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SERLY 125 " --> pdb=" O ARGLY 121 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARGLY 126 " --> pdb=" O LYSLY 122 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLNLY 127 " --> pdb=" O ALALY 123 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VALLY 128 " --> pdb=" O LYSLY 124 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 81 removed outlier: 5.747A pdb=" N ALA A 75 " --> pdb=" O HIS A 113 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N HIS A 113 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLY A 111 " --> pdb=" O PRO A 77 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS A 107 " --> pdb=" O SER A 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 180 through 181 removed outlier: 4.478A pdb=" N VAL A 223 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 187 removed outlier: 4.326A pdb=" N MET A 185 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN A 203 " --> pdb=" O MET A 185 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 278 through 279 Processing sheet with id=AA6, first strand: chain 'Lk' and resid 4 through 5 removed outlier: 4.421A pdb=" N VALLk 46 " --> pdb=" O ILELk 5 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SERLk 22 " --> pdb=" O ARGLk 37 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'LR' and resid 22 through 23 Processing sheet with id=AA8, first strand: chain 'LX' and resid 77 through 80 removed outlier: 3.609A pdb=" N PHELX 79 " --> pdb=" O ILELX 99 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYSLX 134 " --> pdb=" O VALLX 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'LX' and resid 121 through 123 Processing sheet with id=AB1, first strand: chain 'LY' and resid 31 through 33 Processing sheet with id=AB2, first strand: chain 'LY' and resid 94 through 99 removed outlier: 3.861A pdb=" N VALLY 97 " --> pdb=" O VALLY 85 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VALLY 85 " --> pdb=" O VALLY 97 " (cutoff:3.500A) removed outlier: 11.462A pdb=" N ILELY 99 " --> pdb=" O GLULY 83 " (cutoff:3.500A) removed outlier: 10.812A pdb=" N GLULY 83 " --> pdb=" O ILELY 99 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLNLY 72 " --> pdb=" O TYRLY 81 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLULY 83 " --> pdb=" O VALLY 70 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N VALLY 70 " --> pdb=" O GLULY 83 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VALLY 85 " --> pdb=" O GLYLY 68 " (cutoff:3.500A) removed outlier: 10.148A pdb=" N GLYLY 68 " --> pdb=" O VALLY 85 " (cutoff:3.500A) 296 hydrogen bonds defined for protein. 846 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 257 hydrogen bonds 436 hydrogen bond angles 0 basepair planarities 98 basepair parallelities 176 stacking parallelities Total time for adding SS restraints: 6.08 Time building geometry restraints manager: 7.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2201 1.32 - 1.44: 5593 1.44 - 1.57: 7333 1.57 - 1.69: 647 1.69 - 1.81: 55 Bond restraints: 15829 Sorted by residual: bond pdb=" C1' CL53241 " pdb=" N1 CL53241 " ideal model delta sigma weight residual 1.480 1.558 -0.078 1.50e-02 4.44e+03 2.67e+01 bond pdb=" C1' CL53579 " pdb=" N1 CL53579 " ideal model delta sigma weight residual 1.470 1.513 -0.043 1.50e-02 4.44e+03 8.03e+00 bond pdb=" CG LEULk 69 " pdb=" CD1 LEULk 69 " ideal model delta sigma weight residual 1.521 1.441 0.080 3.30e-02 9.18e+02 5.94e+00 bond pdb=" CG LEULR 15 " pdb=" CD1 LEULR 15 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.29e+00 bond pdb=" CB ARGLh 7 " pdb=" CG ARGLh 7 " ideal model delta sigma weight residual 1.520 1.451 0.069 3.00e-02 1.11e+03 5.22e+00 ... (remaining 15824 not shown) Histogram of bond angle deviations from ideal: 93.96 - 102.22: 466 102.22 - 110.48: 6580 110.48 - 118.73: 7699 118.73 - 126.99: 7268 126.99 - 135.25: 858 Bond angle restraints: 22871 Sorted by residual: angle pdb=" O3' CL53294 " pdb=" P GL53295 " pdb=" O5' GL53295 " ideal model delta sigma weight residual 104.00 119.07 -15.07 1.50e+00 4.44e-01 1.01e+02 angle pdb=" P GL53295 " pdb=" O5' GL53295 " pdb=" C5' GL53295 " ideal model delta sigma weight residual 120.90 133.63 -12.73 1.50e+00 4.44e-01 7.20e+01 angle pdb=" O3' UL53583 " pdb=" P CL53584 " pdb=" O5' CL53584 " ideal model delta sigma weight residual 104.00 115.57 -11.57 1.50e+00 4.44e-01 5.95e+01 angle pdb=" C3' UL53583 " pdb=" O3' UL53583 " pdb=" P CL53584 " ideal model delta sigma weight residual 120.20 131.51 -11.31 1.50e+00 4.44e-01 5.68e+01 angle pdb=" C3' GL53256 " pdb=" O3' GL53256 " pdb=" P GL53257 " ideal model delta sigma weight residual 120.20 130.53 -10.33 1.50e+00 4.44e-01 4.75e+01 ... (remaining 22866 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.97: 9300 34.97 - 69.94: 852 69.94 - 104.91: 121 104.91 - 139.88: 8 139.88 - 174.85: 9 Dihedral angle restraints: 10290 sinusoidal: 7437 harmonic: 2853 Sorted by residual: dihedral pdb=" O4' CL52709 " pdb=" C1' CL52709 " pdb=" N1 CL52709 " pdb=" C2 CL52709 " ideal model delta sinusoidal sigma weight residual -160.00 -29.77 -130.23 1 1.50e+01 4.44e-03 7.02e+01 dihedral pdb=" O4' UL8 51 " pdb=" C1' UL8 51 " pdb=" N1 UL8 51 " pdb=" C2 UL8 51 " ideal model delta sinusoidal sigma weight residual 232.00 57.15 174.85 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' UL52707 " pdb=" C1' UL52707 " pdb=" N1 UL52707 " pdb=" C2 UL52707 " ideal model delta sinusoidal sigma weight residual -128.00 38.07 -166.07 1 1.70e+01 3.46e-03 6.55e+01 ... (remaining 10287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 2608 0.111 - 0.222: 183 0.222 - 0.333: 16 0.333 - 0.443: 3 0.443 - 0.554: 4 Chirality restraints: 2814 Sorted by residual: chirality pdb=" C4' CL52943 " pdb=" C5' CL52943 " pdb=" O4' CL52943 " pdb=" C3' CL52943 " both_signs ideal model delta sigma weight residual False -2.50 -1.94 -0.55 2.00e-01 2.50e+01 7.68e+00 chirality pdb=" CB ILELh 4 " pdb=" CA ILELh 4 " pdb=" CG1 ILELh 4 " pdb=" CG2 ILELh 4 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.34e+00 chirality pdb=" P GL53580 " pdb=" OP1 GL53580 " pdb=" OP2 GL53580 " pdb=" O5' GL53580 " both_signs ideal model delta sigma weight residual True 2.41 -2.87 -0.46 2.00e-01 2.50e+01 5.21e+00 ... (remaining 2811 not shown) Planarity restraints: 1675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' UL52932 " -0.024 2.00e-02 2.50e+03 2.23e-02 1.12e+01 pdb=" N1 UL52932 " 0.053 2.00e-02 2.50e+03 pdb=" C2 UL52932 " -0.029 2.00e-02 2.50e+03 pdb=" O2 UL52932 " 0.009 2.00e-02 2.50e+03 pdb=" N3 UL52932 " 0.004 2.00e-02 2.50e+03 pdb=" C4 UL52932 " -0.004 2.00e-02 2.50e+03 pdb=" O4 UL52932 " -0.004 2.00e-02 2.50e+03 pdb=" C5 UL52932 " 0.004 2.00e-02 2.50e+03 pdb=" C6 UL52932 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' CL52942 " 0.038 2.00e-02 2.50e+03 2.17e-02 1.06e+01 pdb=" N1 CL52942 " -0.046 2.00e-02 2.50e+03 pdb=" C2 CL52942 " 0.010 2.00e-02 2.50e+03 pdb=" O2 CL52942 " -0.011 2.00e-02 2.50e+03 pdb=" N3 CL52942 " 0.008 2.00e-02 2.50e+03 pdb=" C4 CL52942 " 0.002 2.00e-02 2.50e+03 pdb=" N4 CL52942 " 0.004 2.00e-02 2.50e+03 pdb=" C5 CL52942 " 0.011 2.00e-02 2.50e+03 pdb=" C6 CL52942 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GL52941 " -0.013 2.00e-02 2.50e+03 1.87e-02 1.05e+01 pdb=" N9 GL52941 " 0.051 2.00e-02 2.50e+03 pdb=" C8 GL52941 " -0.007 2.00e-02 2.50e+03 pdb=" N7 GL52941 " -0.002 2.00e-02 2.50e+03 pdb=" C5 GL52941 " 0.001 2.00e-02 2.50e+03 pdb=" C6 GL52941 " -0.002 2.00e-02 2.50e+03 pdb=" O6 GL52941 " 0.001 2.00e-02 2.50e+03 pdb=" N1 GL52941 " 0.006 2.00e-02 2.50e+03 pdb=" C2 GL52941 " 0.001 2.00e-02 2.50e+03 pdb=" N2 GL52941 " 0.004 2.00e-02 2.50e+03 pdb=" N3 GL52941 " -0.004 2.00e-02 2.50e+03 pdb=" C4 GL52941 " -0.036 2.00e-02 2.50e+03 ... (remaining 1672 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3156 2.78 - 3.31: 12283 3.31 - 3.84: 27225 3.84 - 4.37: 32008 4.37 - 4.90: 45682 Nonbonded interactions: 120354 Sorted by model distance: nonbonded pdb=" O6 GL52950 " pdb=" O4 UL53244 " model vdw 2.255 2.432 nonbonded pdb=" O6 GL8 60 " pdb=" O2' CL8 96 " model vdw 2.264 2.440 nonbonded pdb=" N2 GL52941 " pdb=" O2 CL53254 " model vdw 2.270 2.520 nonbonded pdb=" O2' AL8 48 " pdb=" OP2 CL8 50 " model vdw 2.278 2.440 nonbonded pdb=" O2' AL5 410 " pdb=" O2' CL5 414 " model vdw 2.282 2.440 ... (remaining 120349 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.870 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: 27.630 Check model and map are aligned: 0.000 Set scattering table: 0.970 Process input model: 46.100 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 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 : 0.009 0.087 15829 Z= 0.545 Angle : 1.352 17.441 22871 Z= 0.700 Chirality : 0.066 0.554 2814 Planarity : 0.007 0.058 1675 Dihedral : 22.524 174.846 8430 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.16 % Allowed : 5.33 % Favored : 93.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -4.39 (0.20), residues: 961 helix: -3.72 (0.16), residues: 386 sheet: -1.40 (0.45), residues: 115 loop : -2.50 (0.21), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRPLR 23 HIS 0.034 0.004 HISLR 143 PHE 0.032 0.004 PHELR 132 TYR 0.032 0.004 TYRLY 74 ARG 0.021 0.002 ARGLh 7 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 248 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.6803 (mmtt) cc_final: 0.6376 (mmtm) REVERT: Lk 40 ARG cc_start: 0.7638 (ttt90) cc_final: 0.7411 (ttt-90) REVERT: LR 27 ASN cc_start: 0.7847 (m-40) cc_final: 0.7587 (m-40) REVERT: LR 88 ARG cc_start: 0.8292 (mtp180) cc_final: 0.6700 (mmt-90) REVERT: LR 89 MET cc_start: 0.7736 (tpp) cc_final: 0.7353 (tpt) REVERT: LR 96 MET cc_start: 0.6948 (tmt) cc_final: 0.6597 (ttt) REVERT: LX 50 LYS cc_start: 0.7904 (ptmt) cc_final: 0.7655 (tptp) REVERT: LX 53 ARG cc_start: 0.7869 (mtt180) cc_final: 0.6562 (mtt-85) REVERT: LX 69 ASN cc_start: 0.7599 (t0) cc_final: 0.6835 (t0) REVERT: LX 133 GLU cc_start: 0.7682 (mp0) cc_final: 0.7444 (mp0) outliers start: 10 outliers final: 2 residues processed: 255 average time/residue: 0.3791 time to fit residues: 129.9505 Evaluate side-chains 160 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 158 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LX residue 97 VAL Chi-restraints excluded: chain LY residue 79 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 73 optimal weight: 0.2980 chunk 114 optimal weight: 10.0000 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 84 ASN ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS A 209 GLN A 213 HIS Lh 20 GLN LR 66 ASN LR 86 ASN LR 130 ASN LR 143 HIS LX 73 HIS LX 108 GLN LY 4 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15829 Z= 0.223 Angle : 0.715 9.478 22871 Z= 0.357 Chirality : 0.041 0.245 2814 Planarity : 0.005 0.042 1675 Dihedral : 24.142 170.417 6263 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.59 % Allowed : 9.85 % Favored : 86.56 % 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: -2.93 (0.23), residues: 961 helix: -2.03 (0.22), residues: 406 sheet: -1.01 (0.47), residues: 114 loop : -2.01 (0.24), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRPLR 95 HIS 0.008 0.001 HISLR 143 PHE 0.011 0.002 PHELR 132 TYR 0.017 0.001 TYRLY 74 ARG 0.006 0.001 ARGLh 7 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 180 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ASN cc_start: 0.3078 (OUTLIER) cc_final: 0.2850 (m-40) REVERT: A 326 MET cc_start: 0.4900 (mmm) cc_final: 0.4264 (mmm) REVERT: A 331 MET cc_start: 0.1876 (ttp) cc_final: -0.0602 (mtt) REVERT: Lh 22 ASP cc_start: 0.6976 (p0) cc_final: 0.6658 (p0) REVERT: LR 34 ASN cc_start: 0.7227 (p0) cc_final: 0.6952 (p0) REVERT: LR 86 ASN cc_start: 0.7110 (m-40) cc_final: 0.6784 (m110) REVERT: LR 88 ARG cc_start: 0.8175 (mtp180) cc_final: 0.6528 (mmp-170) REVERT: LR 96 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6919 (ttt) REVERT: LX 69 ASN cc_start: 0.7648 (t0) cc_final: 0.6808 (t0) REVERT: LX 131 ASP cc_start: 0.6215 (t0) cc_final: 0.5646 (t0) REVERT: LX 133 GLU cc_start: 0.7518 (mp0) cc_final: 0.7265 (mp0) outliers start: 31 outliers final: 19 residues processed: 195 average time/residue: 0.2784 time to fit residues: 77.1907 Evaluate side-chains 165 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 144 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain Lh residue 113 LEU Chi-restraints excluded: chain Lh residue 121 VAL Chi-restraints excluded: chain LR residue 15 LEU Chi-restraints excluded: chain LR residue 96 MET Chi-restraints excluded: chain LR residue 130 ASN Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 51 THR Chi-restraints excluded: chain LX residue 83 THR Chi-restraints excluded: chain LX residue 95 THR Chi-restraints excluded: chain LX residue 97 VAL Chi-restraints excluded: chain LX residue 138 VAL Chi-restraints excluded: chain LY residue 10 ASP Chi-restraints excluded: chain LY residue 79 VAL Chi-restraints excluded: chain LY residue 93 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 123 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 113 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 ASN A 175 HIS ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 20 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 15829 Z= 0.390 Angle : 0.800 9.309 22871 Z= 0.398 Chirality : 0.044 0.241 2814 Planarity : 0.006 0.048 1675 Dihedral : 24.015 169.394 6263 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.75 % Allowed : 12.63 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.24), residues: 961 helix: -1.63 (0.23), residues: 402 sheet: -0.86 (0.49), residues: 109 loop : -1.99 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRPLR 95 HIS 0.008 0.002 HISLR 75 PHE 0.016 0.002 PHELh 72 TYR 0.025 0.002 TYRLY 74 ARG 0.006 0.001 ARGLY 26 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 141 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 MET cc_start: 0.2162 (ttp) cc_final: 0.0066 (mtt) REVERT: LR 88 ARG cc_start: 0.8189 (mtp180) cc_final: 0.6476 (mmt180) REVERT: LR 91 GLU cc_start: 0.7140 (mp0) cc_final: 0.6650 (mp0) REVERT: LR 96 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.7259 (ttt) REVERT: LX 69 ASN cc_start: 0.7961 (t0) cc_final: 0.7147 (t0) outliers start: 41 outliers final: 27 residues processed: 171 average time/residue: 0.2816 time to fit residues: 69.0231 Evaluate side-chains 156 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 128 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain Lh residue 65 GLN Chi-restraints excluded: chain Lh residue 121 VAL Chi-restraints excluded: chain Lk residue 14 THR Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain LR residue 96 MET Chi-restraints excluded: chain LR residue 145 LEU Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 51 THR Chi-restraints excluded: chain LX residue 83 THR Chi-restraints excluded: chain LX residue 84 GLU Chi-restraints excluded: chain LX residue 97 VAL Chi-restraints excluded: chain LX residue 120 ASP Chi-restraints excluded: chain LY residue 10 ASP Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 112 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 20.0000 chunk 86 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 115 optimal weight: 20.0000 chunk 121 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 109 optimal weight: 20.0000 chunk 32 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15829 Z= 0.190 Angle : 0.621 8.555 22871 Z= 0.312 Chirality : 0.038 0.227 2814 Planarity : 0.004 0.043 1675 Dihedral : 23.791 170.902 6262 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.36 % Allowed : 14.83 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.25), residues: 961 helix: -1.08 (0.25), residues: 400 sheet: -1.05 (0.49), residues: 117 loop : -1.65 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPLR 95 HIS 0.005 0.001 HIS A 175 PHE 0.010 0.001 PHELR 132 TYR 0.015 0.001 TYRLY 74 ARG 0.006 0.000 ARGLR 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 158 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ASN cc_start: 0.3144 (p0) cc_final: 0.2941 (m-40) REVERT: A 331 MET cc_start: 0.2007 (ttp) cc_final: 0.0000 (mtt) REVERT: A 360 SER cc_start: 0.6846 (p) cc_final: 0.6514 (t) REVERT: LR 88 ARG cc_start: 0.8194 (mtp180) cc_final: 0.6560 (mmt180) REVERT: LX 69 ASN cc_start: 0.7807 (t0) cc_final: 0.6944 (t0) REVERT: LX 131 ASP cc_start: 0.6258 (t0) cc_final: 0.5982 (t0) outliers start: 29 outliers final: 22 residues processed: 174 average time/residue: 0.2867 time to fit residues: 71.9428 Evaluate side-chains 164 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain Lh residue 27 GLU Chi-restraints excluded: chain Lh residue 100 GLU Chi-restraints excluded: chain Lh residue 121 VAL Chi-restraints excluded: chain Lk residue 14 THR Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain LR residue 134 ASN Chi-restraints excluded: chain LX residue 51 THR Chi-restraints excluded: chain LX residue 84 GLU Chi-restraints excluded: chain LX residue 95 THR Chi-restraints excluded: chain LX residue 97 VAL Chi-restraints excluded: chain LX residue 138 VAL Chi-restraints excluded: chain LY residue 10 ASP Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 112 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 62 optimal weight: 0.0030 chunk 109 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 overall best weight: 2.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15829 Z= 0.238 Angle : 0.643 7.391 22871 Z= 0.321 Chirality : 0.038 0.246 2814 Planarity : 0.005 0.044 1675 Dihedral : 23.702 169.618 6262 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.52 % Allowed : 14.37 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.25), residues: 961 helix: -0.81 (0.25), residues: 399 sheet: -0.79 (0.50), residues: 111 loop : -1.72 (0.25), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRPLR 95 HIS 0.005 0.002 HIS A 175 PHE 0.011 0.002 PHELR 132 TYR 0.018 0.002 TYRLY 74 ARG 0.007 0.001 ARGLR 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 148 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 MET cc_start: 0.2010 (ttp) cc_final: -0.0063 (mtt) REVERT: A 360 SER cc_start: 0.6691 (p) cc_final: 0.6413 (t) REVERT: LR 88 ARG cc_start: 0.8141 (mtp180) cc_final: 0.6670 (mmt180) REVERT: LX 69 ASN cc_start: 0.7789 (t0) cc_final: 0.6899 (t0) REVERT: LX 133 GLU cc_start: 0.8135 (mp0) cc_final: 0.7256 (mp0) REVERT: LX 138 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8562 (p) outliers start: 39 outliers final: 30 residues processed: 170 average time/residue: 0.2765 time to fit residues: 67.9543 Evaluate side-chains 167 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 136 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain Lh residue 15 GLU Chi-restraints excluded: chain Lh residue 27 GLU Chi-restraints excluded: chain Lh residue 33 VAL Chi-restraints excluded: chain Lh residue 96 ASN Chi-restraints excluded: chain Lh residue 121 VAL Chi-restraints excluded: chain Lk residue 14 THR Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain LR residue 55 VAL Chi-restraints excluded: chain LR residue 145 LEU Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 51 THR Chi-restraints excluded: chain LX residue 83 THR Chi-restraints excluded: chain LX residue 84 GLU Chi-restraints excluded: chain LX residue 95 THR Chi-restraints excluded: chain LX residue 97 VAL Chi-restraints excluded: chain LX residue 138 VAL Chi-restraints excluded: chain LY residue 10 ASP Chi-restraints excluded: chain LY residue 79 VAL Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 112 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.2980 chunk 109 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 117 optimal weight: 20.0000 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 ASN Lh 20 GLN ** LR 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15829 Z= 0.197 Angle : 0.601 7.308 22871 Z= 0.301 Chirality : 0.037 0.207 2814 Planarity : 0.004 0.043 1675 Dihedral : 23.631 170.498 6262 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.75 % Allowed : 15.41 % Favored : 79.84 % 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: -1.65 (0.25), residues: 961 helix: -0.52 (0.25), residues: 401 sheet: -0.72 (0.51), residues: 111 loop : -1.69 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPLR 95 HIS 0.005 0.001 HIS A 175 PHE 0.009 0.001 PHELR 132 TYR 0.014 0.001 TYRLY 74 ARG 0.006 0.000 ARGLR 100 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 143 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 MET cc_start: 0.2036 (ttp) cc_final: -0.0152 (mtt) REVERT: LR 88 ARG cc_start: 0.8058 (mtp180) cc_final: 0.6645 (mmt-90) REVERT: LX 69 ASN cc_start: 0.7800 (t0) cc_final: 0.6941 (t0) REVERT: LX 133 GLU cc_start: 0.8255 (mp0) cc_final: 0.7945 (mp0) outliers start: 41 outliers final: 34 residues processed: 167 average time/residue: 0.2777 time to fit residues: 67.0891 Evaluate side-chains 170 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 136 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain Lh residue 15 GLU Chi-restraints excluded: chain Lh residue 27 GLU Chi-restraints excluded: chain Lh residue 37 THR Chi-restraints excluded: chain Lh residue 121 VAL Chi-restraints excluded: chain Lk residue 14 THR Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain LR residue 55 VAL Chi-restraints excluded: chain LR residue 145 LEU Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 51 THR Chi-restraints excluded: chain LX residue 83 THR Chi-restraints excluded: chain LX residue 84 GLU Chi-restraints excluded: chain LX residue 95 THR Chi-restraints excluded: chain LX residue 97 VAL Chi-restraints excluded: chain LX residue 120 ASP Chi-restraints excluded: chain LX residue 138 VAL Chi-restraints excluded: chain LY residue 10 ASP Chi-restraints excluded: chain LY residue 40 GLN Chi-restraints excluded: chain LY residue 79 VAL Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 112 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 5.9990 chunk 69 optimal weight: 0.0570 chunk 89 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 102 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.0500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 20 GLN LR 130 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15829 Z= 0.139 Angle : 0.554 7.999 22871 Z= 0.277 Chirality : 0.035 0.188 2814 Planarity : 0.004 0.042 1675 Dihedral : 23.525 172.788 6262 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.59 % Allowed : 17.03 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.26), residues: 961 helix: -0.14 (0.26), residues: 401 sheet: -0.46 (0.53), residues: 106 loop : -1.59 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPLR 95 HIS 0.004 0.001 HIS A 147 PHE 0.010 0.001 PHE A 177 TYR 0.013 0.001 TYR A 98 ARG 0.008 0.000 ARGLR 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 155 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ASN cc_start: 0.3025 (OUTLIER) cc_final: 0.2740 (m-40) REVERT: A 331 MET cc_start: 0.1881 (ttp) cc_final: -0.0244 (mtt) REVERT: LR 88 ARG cc_start: 0.8148 (mtp180) cc_final: 0.6748 (mmt-90) REVERT: LX 69 ASN cc_start: 0.7753 (t0) cc_final: 0.6910 (t0) REVERT: LX 133 GLU cc_start: 0.8236 (mp0) cc_final: 0.7971 (mp0) outliers start: 31 outliers final: 22 residues processed: 173 average time/residue: 0.2851 time to fit residues: 70.9852 Evaluate side-chains 166 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 143 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain Lh residue 27 GLU Chi-restraints excluded: chain Lh residue 96 ASN Chi-restraints excluded: chain Lh residue 121 VAL Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain LR residue 145 LEU Chi-restraints excluded: chain LX residue 51 THR Chi-restraints excluded: chain LX residue 95 THR Chi-restraints excluded: chain LX residue 97 VAL Chi-restraints excluded: chain LX residue 138 VAL Chi-restraints excluded: chain LY residue 40 GLN Chi-restraints excluded: chain LY residue 79 VAL Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 112 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 chunk 110 optimal weight: 20.0000 chunk 116 optimal weight: 30.0000 chunk 106 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LR 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 15829 Z= 0.390 Angle : 0.739 10.623 22871 Z= 0.364 Chirality : 0.042 0.205 2814 Planarity : 0.005 0.055 1675 Dihedral : 23.604 167.728 6262 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.75 % Allowed : 17.50 % Favored : 77.75 % 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: -1.78 (0.25), residues: 961 helix: -0.63 (0.25), residues: 401 sheet: -0.67 (0.52), residues: 109 loop : -1.79 (0.25), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRPLR 95 HIS 0.007 0.002 HISLR 75 PHE 0.018 0.002 PHELh 72 TYR 0.020 0.002 TYRLY 74 ARG 0.006 0.001 ARGLR 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 144 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 MET cc_start: 0.1924 (ttp) cc_final: -0.0365 (mtt) REVERT: LR 81 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.6896 (ptp-170) REVERT: LR 86 ASN cc_start: 0.7680 (t0) cc_final: 0.7347 (t0) REVERT: LR 88 ARG cc_start: 0.8251 (mtp180) cc_final: 0.6539 (mmt180) REVERT: LX 69 ASN cc_start: 0.7796 (t0) cc_final: 0.6989 (t0) REVERT: LX 133 GLU cc_start: 0.8318 (mp0) cc_final: 0.7965 (mp0) outliers start: 41 outliers final: 35 residues processed: 169 average time/residue: 0.2826 time to fit residues: 68.7060 Evaluate side-chains 174 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 138 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain Lh residue 15 GLU Chi-restraints excluded: chain Lh residue 22 ASP Chi-restraints excluded: chain Lh residue 96 ASN Chi-restraints excluded: chain Lh residue 121 VAL Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain LR residue 55 VAL Chi-restraints excluded: chain LR residue 78 ILE Chi-restraints excluded: chain LR residue 81 ARG Chi-restraints excluded: chain LR residue 116 ASP Chi-restraints excluded: chain LR residue 134 ASN Chi-restraints excluded: chain LR residue 145 LEU Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 51 THR Chi-restraints excluded: chain LX residue 83 THR Chi-restraints excluded: chain LX residue 84 GLU Chi-restraints excluded: chain LX residue 95 THR Chi-restraints excluded: chain LX residue 97 VAL Chi-restraints excluded: chain LX residue 120 ASP Chi-restraints excluded: chain LY residue 10 ASP Chi-restraints excluded: chain LY residue 79 VAL Chi-restraints excluded: chain LY residue 83 GLU Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 112 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 20.0000 chunk 116 optimal weight: 30.0000 chunk 68 optimal weight: 0.9990 chunk 49 optimal weight: 0.0870 chunk 88 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 112 optimal weight: 20.0000 chunk 74 optimal weight: 0.9980 chunk 119 optimal weight: 20.0000 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 ASN Lh 20 GLN LR 86 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15829 Z= 0.176 Angle : 0.589 7.809 22871 Z= 0.294 Chirality : 0.036 0.199 2814 Planarity : 0.004 0.041 1675 Dihedral : 23.533 170.673 6262 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.82 % Allowed : 19.12 % Favored : 77.06 % 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: -1.45 (0.26), residues: 961 helix: -0.28 (0.26), residues: 401 sheet: -0.63 (0.52), residues: 109 loop : -1.65 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRPLR 95 HIS 0.004 0.001 HIS A 147 PHE 0.008 0.001 PHELR 132 TYR 0.013 0.001 TYRLY 74 ARG 0.008 0.000 ARGLR 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 146 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 MET cc_start: 0.1872 (ttp) cc_final: -0.0286 (mtt) REVERT: LR 88 ARG cc_start: 0.8093 (mtp180) cc_final: 0.6670 (mmt-90) REVERT: LX 69 ASN cc_start: 0.7778 (t0) cc_final: 0.6928 (t0) REVERT: LX 133 GLU cc_start: 0.8280 (mp0) cc_final: 0.7775 (mp0) outliers start: 33 outliers final: 27 residues processed: 162 average time/residue: 0.2956 time to fit residues: 69.2852 Evaluate side-chains 169 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 142 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain Lh residue 27 GLU Chi-restraints excluded: chain Lh residue 121 VAL Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain LR residue 55 VAL Chi-restraints excluded: chain LR residue 78 ILE Chi-restraints excluded: chain LR residue 145 LEU Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 51 THR Chi-restraints excluded: chain LX residue 83 THR Chi-restraints excluded: chain LX residue 84 GLU Chi-restraints excluded: chain LX residue 95 THR Chi-restraints excluded: chain LX residue 97 VAL Chi-restraints excluded: chain LY residue 10 ASP Chi-restraints excluded: chain LY residue 79 VAL Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 112 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 83 optimal weight: 0.0470 chunk 125 optimal weight: 10.0000 chunk 115 optimal weight: 30.0000 chunk 99 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 79 optimal weight: 0.0050 chunk 106 optimal weight: 20.0000 overall best weight: 0.8094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15829 Z= 0.132 Angle : 0.541 8.348 22871 Z= 0.270 Chirality : 0.034 0.169 2814 Planarity : 0.004 0.039 1675 Dihedral : 23.392 174.628 6262 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.36 % Allowed : 19.00 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.26), residues: 961 helix: 0.16 (0.26), residues: 406 sheet: -0.74 (0.50), residues: 111 loop : -1.54 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPLR 95 HIS 0.005 0.001 HIS A 147 PHE 0.008 0.001 PHE A 338 TYR 0.012 0.001 TYR A 98 ARG 0.007 0.000 ARGLR 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 161 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 MET cc_start: 0.2006 (ttp) cc_final: -0.0451 (mtt) REVERT: LR 86 ASN cc_start: 0.7281 (t0) cc_final: 0.6927 (m110) REVERT: LR 88 ARG cc_start: 0.8122 (mtp180) cc_final: 0.6734 (mmt-90) REVERT: LX 69 ASN cc_start: 0.7833 (t0) cc_final: 0.7009 (t0) REVERT: LX 133 GLU cc_start: 0.8165 (mp0) cc_final: 0.7649 (mp0) outliers start: 29 outliers final: 22 residues processed: 176 average time/residue: 0.3156 time to fit residues: 79.3555 Evaluate side-chains 170 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 148 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain Lh residue 27 GLU Chi-restraints excluded: chain Lh residue 65 GLN Chi-restraints excluded: chain Lh residue 96 ASN Chi-restraints excluded: chain Lh residue 121 VAL Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain LR residue 15 LEU Chi-restraints excluded: chain LR residue 55 VAL Chi-restraints excluded: chain LR residue 145 LEU Chi-restraints excluded: chain LX residue 51 THR Chi-restraints excluded: chain LX residue 83 THR Chi-restraints excluded: chain LX residue 95 THR Chi-restraints excluded: chain LX residue 97 VAL Chi-restraints excluded: chain LY residue 79 VAL Chi-restraints excluded: chain LY residue 83 GLU Chi-restraints excluded: chain LY residue 112 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.0170 chunk 92 optimal weight: 0.0030 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.0980 chunk 87 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.4228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.201028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.163813 restraints weight = 29899.846| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 2.82 r_work: 0.3673 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15829 Z= 0.119 Angle : 0.534 7.317 22871 Z= 0.266 Chirality : 0.033 0.168 2814 Planarity : 0.004 0.042 1675 Dihedral : 23.327 176.034 6262 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.09 % Allowed : 20.39 % Favored : 77.52 % 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: -0.85 (0.26), residues: 961 helix: 0.42 (0.26), residues: 406 sheet: -0.64 (0.49), residues: 111 loop : -1.47 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPLR 95 HIS 0.005 0.001 HIS A 147 PHE 0.009 0.001 PHE A 338 TYR 0.013 0.001 TYR A 343 ARG 0.006 0.000 ARGLR 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3340.51 seconds wall clock time: 62 minutes 7.98 seconds (3727.98 seconds total)