Starting phenix.real_space_refine (version: dev) on Tue Feb 21 12:26:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sxo_10344/02_2023/6sxo_10344.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sxo_10344/02_2023/6sxo_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_10344/02_2023/6sxo_10344.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sxo_10344/02_2023/6sxo_10344.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sxo_10344/02_2023/6sxo_10344.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sxo_10344/02_2023/6sxo_10344.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 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-4877/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: 8.57, per 1000 atoms: 0.58 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: 7.78 Conformation dependent library (CDL) restraints added in 1.5 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: 5.67 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: 6.21 Time building geometry restraints manager: 8.01 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: 8649 34.97 - 69.94: 299 69.94 - 104.91: 33 104.91 - 139.88: 8 139.88 - 174.85: 9 Dihedral angle restraints: 8998 sinusoidal: 6145 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 8995 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 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. 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: 8.300 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: 30.750 Check model and map are aligned: 0.290 Process input model: 46.740 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.150 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 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 : 16.448 174.846 7138 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 % 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 *********************** 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 : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 255 average time/residue: 0.3690 time to fit residues: 124.6402 Evaluate side-chains 159 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 157 time to evaluate : 1.287 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1196 time to fit residues: 1.9986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 32 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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: 0.7169 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 15829 Z= 0.217 Angle : 0.721 9.127 22871 Z= 0.362 Chirality : 0.041 0.254 2814 Planarity : 0.005 0.042 1675 Dihedral : 16.626 170.235 4969 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 3.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.23), residues: 961 helix: -2.02 (0.22), residues: 405 sheet: -0.95 (0.47), residues: 114 loop : -2.04 (0.24), residues: 442 *********************** 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 200 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 174 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 19 residues processed: 188 average time/residue: 0.3061 time to fit residues: 82.0280 Evaluate side-chains 158 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 139 time to evaluate : 1.377 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1389 time to fit residues: 6.6465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 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: 4.9990 chunk 91 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 161 ASN A 175 HIS Lh 20 GLN LR 7 GLN ** LR 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 15829 Z= 0.369 Angle : 0.782 10.711 22871 Z= 0.388 Chirality : 0.044 0.249 2814 Planarity : 0.006 0.048 1675 Dihedral : 16.456 168.833 4969 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer Outliers : 3.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.24), residues: 961 helix: -1.57 (0.23), residues: 402 sheet: -0.80 (0.49), residues: 109 loop : -1.97 (0.24), residues: 450 *********************** 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 174 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 146 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 17 residues processed: 164 average time/residue: 0.2799 time to fit residues: 66.6627 Evaluate side-chains 149 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 1.217 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1495 time to fit residues: 5.9632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 115 optimal weight: 20.0000 chunk 121 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 109 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 LR 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 15829 Z= 0.178 Angle : 0.621 8.870 22871 Z= 0.311 Chirality : 0.037 0.228 2814 Planarity : 0.004 0.043 1675 Dihedral : 16.089 170.157 4969 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 1.51 % 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: -2.01 (0.25), residues: 961 helix: -1.02 (0.25), residues: 400 sheet: -0.95 (0.48), residues: 117 loop : -1.65 (0.26), residues: 444 *********************** 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 172 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 159 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 163 average time/residue: 0.2918 time to fit residues: 69.4415 Evaluate side-chains 148 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 140 time to evaluate : 1.247 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1372 time to fit residues: 3.5000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 1 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 109 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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: 0.7240 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 15829 Z= 0.268 Angle : 0.666 7.880 22871 Z= 0.332 Chirality : 0.039 0.220 2814 Planarity : 0.005 0.050 1675 Dihedral : 16.019 168.033 4969 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 3.13 % 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: -1.93 (0.25), residues: 961 helix: -0.90 (0.25), residues: 400 sheet: -0.69 (0.50), residues: 109 loop : -1.73 (0.26), residues: 452 *********************** 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 170 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 24 residues processed: 161 average time/residue: 0.2752 time to fit residues: 65.1430 Evaluate side-chains 159 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 1.381 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1393 time to fit residues: 7.8502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 2.9990 chunk 109 optimal weight: 20.0000 chunk 24 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 chunk 117 optimal weight: 20.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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: 0.7226 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 15829 Z= 0.236 Angle : 0.628 7.465 22871 Z= 0.314 Chirality : 0.038 0.217 2814 Planarity : 0.005 0.045 1675 Dihedral : 15.909 167.748 4969 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 1.85 % 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: -1.80 (0.25), residues: 961 helix: -0.66 (0.25), residues: 399 sheet: -0.86 (0.50), residues: 114 loop : -1.72 (0.25), residues: 448 *********************** 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 165 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 149 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 154 average time/residue: 0.2915 time to fit residues: 65.3821 Evaluate side-chains 143 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 133 time to evaluate : 1.342 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1475 time to fit residues: 4.3698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 34 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 15829 Z= 0.176 Angle : 0.588 9.129 22871 Z= 0.294 Chirality : 0.036 0.203 2814 Planarity : 0.004 0.045 1675 Dihedral : 15.766 169.395 4969 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 1.51 % 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: -1.53 (0.25), residues: 961 helix: -0.43 (0.25), residues: 401 sheet: -0.58 (0.51), residues: 110 loop : -1.62 (0.26), residues: 450 *********************** 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 162 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 149 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 156 average time/residue: 0.3277 time to fit residues: 72.4091 Evaluate side-chains 144 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 1.343 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1299 time to fit residues: 3.4990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 23 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 0.0000 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 110 optimal weight: 20.0000 chunk 116 optimal weight: 30.0000 chunk 106 optimal weight: 20.0000 overall best weight: 1.7390 ------------------------------------------------------------------------------- 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: 0.7199 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 15829 Z= 0.189 Angle : 0.592 9.103 22871 Z= 0.295 Chirality : 0.036 0.192 2814 Planarity : 0.004 0.043 1675 Dihedral : 15.705 168.720 4969 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 1.04 % 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: -1.48 (0.25), residues: 961 helix: -0.37 (0.25), residues: 403 sheet: -0.54 (0.52), residues: 110 loop : -1.63 (0.26), residues: 448 *********************** 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 154 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 145 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 146 average time/residue: 0.3152 time to fit residues: 65.6934 Evaluate side-chains 146 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 139 time to evaluate : 1.459 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1317 time to fit residues: 3.2461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 49 optimal weight: 0.7980 chunk 88 optimal weight: 0.0010 chunk 34 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 112 optimal weight: 20.0000 chunk 74 optimal weight: 0.8980 chunk 119 optimal weight: 20.0000 overall best weight: 2.1390 ------------------------------------------------------------------------------- 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: 0.7217 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 15829 Z= 0.217 Angle : 0.610 9.266 22871 Z= 0.304 Chirality : 0.037 0.194 2814 Planarity : 0.005 0.065 1675 Dihedral : 15.740 168.798 4969 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer Outliers : 0.58 % 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: -1.53 (0.25), residues: 961 helix: -0.43 (0.25), residues: 403 sheet: -0.51 (0.53), residues: 109 loop : -1.65 (0.26), residues: 449 *********************** 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 146 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 141 time to evaluate : 1.268 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 142 average time/residue: 0.3046 time to fit residues: 61.9995 Evaluate side-chains 138 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 135 time to evaluate : 1.300 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1400 time to fit residues: 2.3345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 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: 6.9990 chunk 77 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 79 optimal weight: 0.4980 chunk 106 optimal weight: 20.0000 overall best weight: 1.0480 ------------------------------------------------------------------------------- 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: 0.7162 moved from start: 0.3766 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= 0.145 Angle : 0.564 8.922 22871 Z= 0.282 Chirality : 0.035 0.182 2814 Planarity : 0.004 0.042 1675 Dihedral : 15.623 171.218 4969 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 0.58 % 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: -1.25 (0.26), residues: 961 helix: -0.11 (0.26), residues: 401 sheet: -0.33 (0.53), residues: 104 loop : -1.58 (0.26), residues: 456 ********************** 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 154 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 149 time to evaluate : 1.205 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 151 average time/residue: 0.3079 time to fit residues: 66.4445 Evaluate side-chains 148 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 145 time to evaluate : 1.280 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1386 time to fit residues: 2.3013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 12 optimal weight: 0.0770 chunk 18 optimal weight: 0.0170 chunk 87 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.198267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.161015 restraints weight = 29574.417| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 2.83 r_work: 0.3625 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 15829 Z= 0.156 Angle : 0.566 8.771 22871 Z= 0.282 Chirality : 0.034 0.176 2814 Planarity : 0.004 0.041 1675 Dihedral : 15.524 171.416 4969 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 0.58 % 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: -1.17 (0.26), residues: 961 helix: -0.04 (0.26), residues: 407 sheet: -0.32 (0.53), residues: 104 loop : -1.56 (0.26), residues: 450 =============================================================================== Job complete usr+sys time: 3129.19 seconds wall clock time: 57 minutes 56.44 seconds (3476.44 seconds total)