Starting phenix.real_space_refine on Fri Sep 27 05:06:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sxo_10344/09_2024/6sxo_10344.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sxo_10344/09_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_10344/09_2024/6sxo_10344.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sxo_10344/09_2024/6sxo_10344.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sxo_10344/09_2024/6sxo_10344.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sxo_10344/09_2024/6sxo_10344.cif" } 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. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 10.90, per 1000 atoms: 0.73 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.64 Conformation dependent library (CDL) restraints added in 1.2 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: 6.45 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: 6.10 Time building geometry restraints manager: 4.32 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: 0.00 - 3.49: 22224 3.49 - 6.98: 556 6.98 - 10.46: 78 10.46 - 13.95: 10 13.95 - 17.44: 3 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 3.040 nonbonded pdb=" N2 GL52941 " pdb=" O2 CL53254 " model vdw 2.270 3.120 nonbonded pdb=" O2' AL8 48 " pdb=" OP2 CL8 50 " model vdw 2.278 3.040 nonbonded pdb=" O2' AL5 410 " pdb=" O2' CL5 414 " model vdw 2.282 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 7.960 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: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 41.750 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.720 ------------------------------------------------------------------------------- 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 : 1.203 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: 0.3620 time to fit residues: 122.7733 Evaluate side-chains 160 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 158 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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: 0.8980 chunk 32 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS A 209 GLN A 213 HIS Lh 20 GLN 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: 0.7023 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15829 Z= 0.213 Angle : 0.727 9.738 22871 Z= 0.364 Chirality : 0.041 0.265 2814 Planarity : 0.005 0.042 1675 Dihedral : 24.095 171.065 6263 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.24 % Allowed : 9.85 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.23), residues: 961 helix: -2.07 (0.22), residues: 406 sheet: -1.06 (0.46), residues: 115 loop : -1.95 (0.24), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRPLR 95 HIS 0.009 0.002 HISLR 143 PHE 0.014 0.002 PHE A 117 TYR 0.020 0.001 TYRLY 74 ARG 0.008 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 215 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 187 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 MET cc_start: 0.4901 (mmm) cc_final: 0.4245 (mmm) REVERT: A 331 MET cc_start: 0.1840 (ttp) cc_final: -0.0585 (mtt) REVERT: Lh 22 ASP cc_start: 0.6937 (p0) cc_final: 0.6585 (p0) REVERT: LR 27 ASN cc_start: 0.7716 (m-40) cc_final: 0.7488 (m-40) REVERT: LR 34 ASN cc_start: 0.7384 (p0) cc_final: 0.7126 (p0) REVERT: LR 88 ARG cc_start: 0.7852 (mtp180) cc_final: 0.6408 (mmp-170) REVERT: LR 89 MET cc_start: 0.7692 (tpp) cc_final: 0.7135 (tpt) REVERT: LR 96 MET cc_start: 0.7008 (OUTLIER) cc_final: 0.6703 (ttt) REVERT: LX 69 ASN cc_start: 0.7618 (t0) cc_final: 0.6755 (t0) REVERT: LX 131 ASP cc_start: 0.6242 (t0) cc_final: 0.5724 (t0) outliers start: 28 outliers final: 18 residues processed: 201 average time/residue: 0.3040 time to fit residues: 86.4928 Evaluate side-chains 161 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 1.271 ------------------------------------------------------------------------------- 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 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 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 111 LEU 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: 0.9990 chunk 31 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 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: 0.1980 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 175 HIS Lh 20 GLN LR 7 GLN LR 134 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15829 Z= 0.331 Angle : 0.754 9.139 22871 Z= 0.376 Chirality : 0.042 0.263 2814 Planarity : 0.005 0.046 1675 Dihedral : 23.942 169.549 6263 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.06 % Allowed : 13.21 % Favored : 82.73 % 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: -2.46 (0.24), residues: 961 helix: -1.51 (0.24), residues: 400 sheet: -1.12 (0.47), residues: 115 loop : -1.79 (0.25), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRPLR 95 HIS 0.007 0.002 HISLR 75 PHE 0.012 0.002 PHE A 265 TYR 0.023 0.002 TYRLY 74 ARG 0.005 0.001 ARGLX 56 *********************** 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 177 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 142 time to evaluate : 1.300 Fit side-chains revert: symmetry clash REVERT: A 331 MET cc_start: 0.2172 (ttp) cc_final: 0.0068 (mtt) REVERT: LR 27 ASN cc_start: 0.7762 (m-40) cc_final: 0.7525 (m-40) REVERT: LR 88 ARG cc_start: 0.8018 (mtp180) cc_final: 0.6456 (mmp-170) REVERT: LR 96 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.7127 (ttt) REVERT: LX 69 ASN cc_start: 0.7930 (t0) cc_final: 0.7105 (t0) REVERT: LX 133 GLU cc_start: 0.7988 (mp0) cc_final: 0.7147 (mp0) REVERT: LY 27 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8433 (ttp80) outliers start: 35 outliers final: 20 residues processed: 170 average time/residue: 0.2880 time to fit residues: 70.9401 Evaluate side-chains 152 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 LY residue 10 ASP Chi-restraints excluded: chain LY residue 27 ARG Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 111 LEU 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: 3.9990 chunk 59 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 115 optimal weight: 20.0000 chunk 121 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 109 optimal weight: 20.0000 chunk 32 optimal weight: 0.5980 overall best weight: 1.3982 ------------------------------------------------------------------------------- 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: 0.7043 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15829 Z= 0.172 Angle : 0.620 8.553 22871 Z= 0.312 Chirality : 0.037 0.241 2814 Planarity : 0.004 0.043 1675 Dihedral : 23.747 171.296 6262 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.13 % Allowed : 15.41 % Favored : 81.46 % 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: -1.99 (0.25), residues: 961 helix: -0.98 (0.25), residues: 400 sheet: -1.01 (0.47), residues: 117 loop : -1.64 (0.25), 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 0.008 0.001 PHELR 132 TYR 0.017 0.001 TYRLY 74 ARG 0.006 0.001 ARGLY 84 *********************** 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: 27 poor density : 160 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LR 27 ASN cc_start: 0.7673 (m-40) cc_final: 0.7450 (m-40) REVERT: LR 88 ARG cc_start: 0.7872 (mtp180) cc_final: 0.6465 (mmt180) REVERT: LR 96 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.7107 (ttt) REVERT: LX 69 ASN cc_start: 0.7836 (t0) cc_final: 0.6972 (t0) outliers start: 27 outliers final: 20 residues processed: 177 average time/residue: 0.2945 time to fit residues: 74.7316 Evaluate side-chains 166 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 145 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 36 VAL Chi-restraints excluded: chain LR residue 96 MET 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 10 ASP Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 111 LEU 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: 8.9990 chunk 1 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 84 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 109 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 overall best weight: 4.6166 ------------------------------------------------------------------------------- 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 120 ASN ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 20 GLN LR 134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 15829 Z= 0.420 Angle : 0.792 9.856 22871 Z= 0.392 Chirality : 0.044 0.252 2814 Planarity : 0.006 0.052 1675 Dihedral : 23.782 168.852 6262 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.75 % Allowed : 13.90 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.24), residues: 961 helix: -1.25 (0.24), residues: 399 sheet: -0.80 (0.50), residues: 109 loop : -1.84 (0.25), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRPLR 95 HIS 0.008 0.002 HISLR 75 PHE 0.019 0.002 PHELh 72 TYR 0.024 0.002 TYRLY 74 ARG 0.006 0.001 ARGLY 26 *********************** 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 186 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 145 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ASN cc_start: 0.3393 (OUTLIER) cc_final: 0.2596 (m-40) REVERT: A 331 MET cc_start: 0.2282 (ttp) cc_final: 0.0134 (mtt) REVERT: LR 27 ASN cc_start: 0.7842 (m-40) cc_final: 0.7629 (m-40) REVERT: LR 88 ARG cc_start: 0.8149 (mtp180) cc_final: 0.6463 (mmt180) REVERT: LR 96 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.7206 (ttt) REVERT: LX 69 ASN cc_start: 0.7932 (t0) cc_final: 0.7111 (t0) outliers start: 41 outliers final: 33 residues processed: 172 average time/residue: 0.2985 time to fit residues: 73.1663 Evaluate side-chains 167 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 132 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU 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 120 ASN 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 323 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain Lh residue 15 GLU Chi-restraints excluded: chain Lh residue 33 VAL Chi-restraints excluded: chain Lh residue 65 GLN 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 55 VAL Chi-restraints excluded: chain LR residue 78 ILE 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 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 55 VAL 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: 0.8980 chunk 109 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 117 optimal weight: 20.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15829 Z= 0.226 Angle : 0.658 7.903 22871 Z= 0.330 Chirality : 0.039 0.234 2814 Planarity : 0.005 0.044 1675 Dihedral : 23.696 170.062 6262 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.75 % Allowed : 15.64 % Favored : 79.61 % 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: -2.00 (0.25), residues: 961 helix: -0.89 (0.25), residues: 399 sheet: -1.11 (0.49), residues: 115 loop : -1.72 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPLR 95 HIS 0.004 0.001 HISLR 75 PHE 0.011 0.002 PHELR 132 TYR 0.018 0.001 TYRLY 74 ARG 0.005 0.001 ARGLR 16 *********************** 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 : 1.264 Fit side-chains revert: symmetry clash REVERT: A 163 ASN cc_start: 0.3318 (OUTLIER) cc_final: 0.2603 (m-40) REVERT: A 331 MET cc_start: 0.2069 (ttp) cc_final: -0.0024 (mtt) REVERT: LR 27 ASN cc_start: 0.7697 (m-40) cc_final: 0.7471 (m-40) REVERT: LR 88 ARG cc_start: 0.8053 (mtp180) cc_final: 0.6540 (mmt180) REVERT: LX 69 ASN cc_start: 0.7892 (t0) cc_final: 0.7059 (t0) REVERT: LX 133 GLU cc_start: 0.8071 (mp0) cc_final: 0.7707 (mp0) outliers start: 41 outliers final: 31 residues processed: 167 average time/residue: 0.2891 time to fit residues: 69.5762 Evaluate side-chains 170 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 138 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 121 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 65 GLN 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 86 ASN Chi-restraints excluded: chain LR residue 111 GLU 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 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 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: 0.7980 chunk 69 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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: 0.7044 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15829 Z= 0.168 Angle : 0.588 7.116 22871 Z= 0.295 Chirality : 0.036 0.203 2814 Planarity : 0.004 0.043 1675 Dihedral : 23.526 174.437 6262 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.48 % Allowed : 17.50 % Favored : 79.03 % 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: -1.62 (0.25), residues: 961 helix: -0.46 (0.26), residues: 399 sheet: -1.12 (0.48), residues: 117 loop : -1.57 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPLR 95 HIS 0.005 0.001 HIS A 147 PHE 0.013 0.001 PHE A 177 TYR 0.015 0.001 TYRLY 74 ARG 0.007 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 188 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 158 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 MET cc_start: 0.1935 (ttp) cc_final: -0.0191 (mtt) REVERT: Lk 69 LEU cc_start: 0.7467 (mm) cc_final: 0.7161 (mt) REVERT: LR 27 ASN cc_start: 0.7562 (m-40) cc_final: 0.7330 (m-40) REVERT: LR 88 ARG cc_start: 0.7897 (mtp180) cc_final: 0.6480 (mmt180) REVERT: LX 69 ASN cc_start: 0.7813 (t0) cc_final: 0.6959 (t0) REVERT: LX 133 GLU cc_start: 0.8056 (mp0) cc_final: 0.7745 (mp0) outliers start: 30 outliers final: 23 residues processed: 174 average time/residue: 0.2961 time to fit residues: 72.4347 Evaluate side-chains 168 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 145 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 273 PHE Chi-restraints excluded: chain A residue 291 MET 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 chunk 60 optimal weight: 0.0570 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: 10.0000 overall best weight: 1.5104 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15829 Z= 0.175 Angle : 0.591 8.980 22871 Z= 0.295 Chirality : 0.036 0.200 2814 Planarity : 0.004 0.043 1675 Dihedral : 23.471 179.111 6262 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % 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: -1.49 (0.26), residues: 961 helix: -0.32 (0.26), residues: 401 sheet: -1.11 (0.47), residues: 117 loop : -1.52 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPLR 95 HIS 0.003 0.001 HIS A 147 PHE 0.010 0.001 PHELR 132 TYR 0.014 0.001 TYRLY 74 ARG 0.006 0.000 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 181 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 150 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 MET cc_start: 0.1925 (ttp) cc_final: -0.0228 (mtt) REVERT: Lk 69 LEU cc_start: 0.7515 (mm) cc_final: 0.7215 (mt) REVERT: LR 81 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.6978 (ptp-170) REVERT: LR 88 ARG cc_start: 0.7928 (mtp180) cc_final: 0.6461 (mmt180) REVERT: LX 69 ASN cc_start: 0.7877 (t0) cc_final: 0.7070 (t0) REVERT: LX 133 GLU cc_start: 0.8076 (mp0) cc_final: 0.7805 (mp0) outliers start: 31 outliers final: 24 residues processed: 168 average time/residue: 0.3097 time to fit residues: 73.7628 Evaluate side-chains 167 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 142 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 291 MET 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 36 VAL Chi-restraints excluded: chain Lk residue 68 GLU Chi-restraints excluded: chain LR residue 81 ARG 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 95 THR Chi-restraints excluded: chain LX residue 97 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 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: 0.0470 chunk 49 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 102 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 112 optimal weight: 20.0000 chunk 74 optimal weight: 0.6980 chunk 119 optimal weight: 20.0000 overall best weight: 2.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15829 Z= 0.229 Angle : 0.628 8.097 22871 Z= 0.312 Chirality : 0.037 0.201 2814 Planarity : 0.005 0.042 1675 Dihedral : 23.458 178.420 6262 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.94 % Allowed : 17.15 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.25), residues: 961 helix: -0.42 (0.26), residues: 401 sheet: -1.09 (0.48), residues: 115 loop : -1.58 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPLR 95 HIS 0.004 0.001 HIS A 147 PHE 0.010 0.002 PHELR 132 TYR 0.017 0.001 TYRLY 74 ARG 0.007 0.001 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 176 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 142 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 MET cc_start: 0.2041 (ttp) cc_final: -0.0158 (mtt) REVERT: LR 81 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.6903 (ptp-170) REVERT: LR 88 ARG cc_start: 0.8022 (mtp180) cc_final: 0.6519 (mmt180) REVERT: LX 69 ASN cc_start: 0.7882 (t0) cc_final: 0.7089 (t0) REVERT: LX 133 GLU cc_start: 0.8076 (mp0) cc_final: 0.7853 (mp0) outliers start: 34 outliers final: 24 residues processed: 162 average time/residue: 0.3295 time to fit residues: 76.1950 Evaluate side-chains 160 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 135 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 27 GLU Chi-restraints excluded: chain Lh residue 65 GLN Chi-restraints excluded: chain Lh residue 100 GLU Chi-restraints excluded: chain Lh residue 121 VAL Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain LR residue 81 ARG 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 83 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 115 optimal weight: 20.0000 chunk 99 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 106 optimal weight: 9.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.3843 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= 0.161 Angle : 0.580 8.210 22871 Z= 0.290 Chirality : 0.035 0.201 2814 Planarity : 0.004 0.041 1675 Dihedral : 23.411 179.788 6262 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.67 % Allowed : 18.42 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.26), residues: 961 helix: -0.19 (0.26), residues: 402 sheet: -1.05 (0.48), residues: 111 loop : -1.57 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPLR 95 HIS 0.004 0.001 HIS A 147 PHE 0.008 0.001 PHELR 132 TYR 0.015 0.001 TYRLY 74 ARG 0.006 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 168 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 145 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 MET cc_start: 0.1999 (ttp) cc_final: -0.0150 (mtt) REVERT: Lk 69 LEU cc_start: 0.7506 (mm) cc_final: 0.7228 (mt) REVERT: LR 88 ARG cc_start: 0.7860 (mtp180) cc_final: 0.6474 (mmt180) REVERT: LX 69 ASN cc_start: 0.7888 (t0) cc_final: 0.7088 (t0) REVERT: LX 133 GLU cc_start: 0.8028 (mp0) cc_final: 0.7788 (mp0) outliers start: 23 outliers final: 21 residues processed: 159 average time/residue: 0.3047 time to fit residues: 69.8350 Evaluate side-chains 163 residues out of total 863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 142 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 273 PHE 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 100 GLU 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 83 THR 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 99 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.4409 r_free = 0.4409 target = 0.197448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.159910 restraints weight = 29530.760| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.83 r_work: 0.3614 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15829 Z= 0.167 Angle : 0.578 8.412 22871 Z= 0.289 Chirality : 0.035 0.202 2814 Planarity : 0.004 0.043 1675 Dihedral : 23.357 179.404 6262 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.13 % Allowed : 17.61 % Favored : 79.26 % 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: -1.36 (0.26), residues: 961 helix: -0.12 (0.26), residues: 408 sheet: -1.03 (0.48), residues: 111 loop : -1.57 (0.26), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPLR 95 HIS 0.004 0.001 HIS A 147 PHE 0.014 0.001 PHE A 177 TYR 0.015 0.001 TYRLY 74 ARG 0.006 0.000 ARGLY 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3408.62 seconds wall clock time: 61 minutes 50.05 seconds (3710.05 seconds total)