Starting phenix.real_space_refine on Fri Jul 3 05:01:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ony_17002/07_2026/8ony_17002.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ony_17002/07_2026/8ony_17002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ony_17002/07_2026/8ony_17002.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ony_17002/07_2026/8ony_17002.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ony_17002/07_2026/8ony_17002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ony_17002/07_2026/8ony_17002.map" } resolution = 2.92 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 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= -0.004 sd= 0.150 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: 6 Type Number sf(0) Gaussians Co 2 6.85 5 P 214 5.49 5 S 38 5.16 5 C 6966 2.51 5 N 2321 2.21 5 O 2852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12393 Number of models: 1 Model: "" Number of chains: 9 Chain: "5" Number of atoms: 3348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3348 Classifications: {'RNA': 156} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 15, 'rna3p_pur': 73, 'rna3p_pyr': 51} Link IDs: {'rna2p': 32, 'rna3p': 123} Chain breaks: 6 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: "LY" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1075 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} 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: "LX" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 950 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 107} Chain: "LR" Number of atoms: 1292 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 153, 1281 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 3, 'TRANS': 149} Conformer: "B" Number of residues, atoms: 153, 1281 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 3, 'TRANS': 149} bond proxies already assigned to first conformer: 1285 Chain: "8" 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} Chain: "A" Number of atoms: 2905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2905 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 350} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CO': 2} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARGLR 16 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARGLR 16 " occ=0.50 Time building chain proxies: 2.47, per 1000 atoms: 0.20 Number of scatterers: 12393 At special positions: 0 Unit cell: (145.41, 123.21, 196.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Co 2 26.99 S 38 16.00 P 214 15.00 O 2852 8.00 N 2321 7.00 C 6966 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: 0.73 Conformation dependent library (CDL) restraints added in 381.3 milliseconds 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1822 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 13 sheets defined 44.5% alpha, 16.6% beta 45 base pairs and 105 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'Lk' and resid 7 through 17 removed outlier: 3.593A pdb=" N PHELk 11 " --> pdb=" O GLULk 7 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEULk 12 " --> pdb=" O ILELk 8 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARGLk 17 " --> pdb=" O LEULk 13 " (cutoff:3.500A) Processing helix chain 'Lk' and resid 49 through 59 removed outlier: 3.506A pdb=" N ALALk 53 " --> pdb=" O ASPLk 49 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYSLk 55 " --> pdb=" O GLULk 51 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLNLk 58 " --> pdb=" O GLULk 54 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SERLk 59 " --> pdb=" O LYSLk 55 " (cutoff:3.500A) Processing helix chain 'LY' and resid 10 through 20 Processing helix chain 'LY' and resid 22 through 30 removed outlier: 4.151A pdb=" N LYSLY 28 " --> pdb=" O HISLY 24 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILELY 29 " --> pdb=" O ILELY 25 " (cutoff:3.500A) Processing helix chain 'LY' and resid 35 through 43 removed outlier: 3.545A pdb=" N LYSLY 41 " --> pdb=" O GLULY 37 " (cutoff:3.500A) 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: 3.519A pdb=" N SERLY 125 " --> pdb=" O ARGLY 121 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARGLY 126 " --> pdb=" O LYSLY 122 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLYLY 129 " --> pdb=" O SERLY 125 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 5 through 10 removed outlier: 3.684A pdb=" N LEULh 9 " --> pdb=" O LYSLh 5 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 13 through 37 removed outlier: 3.588A pdb=" N VALLh 36 " --> pdb=" O ARGLh 32 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THRLh 37 " --> pdb=" O VALLh 33 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 40 through 73 removed outlier: 4.029A pdb=" N ILELh 47 " --> pdb=" O LYSLh 43 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ARGLh 48 " --> pdb=" O LEULh 44 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VALLh 49 " --> pdb=" O SERLh 45 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYSLh 66 " --> pdb=" O ASNLh 62 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLULh 67 " --> pdb=" O GLNLh 63 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHELh 72 " --> pdb=" O ASNLh 68 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYRLh 73 " --> pdb=" O LEULh 69 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 90 through 94 Processing helix chain 'Lh' and resid 96 through 101 removed outlier: 3.756A pdb=" N ASNLh 101 " --> pdb=" O LYSLh 97 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 104 through 114 removed outlier: 3.518A pdb=" N LYSLh 110 " --> pdb=" O LYSLh 106 " (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 removed outlier: 3.683A pdb=" N VALLX 149 " --> pdb=" O ASPLX 145 " (cutoff:3.500A) Processing helix chain 'LR' and resid 4 through 15 removed outlier: 3.618A pdb=" N ARGLR 9 " --> pdb=" O ARGLR 5 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALALR 11 " --> pdb=" O GLNLR 7 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SERLR 12 " --> pdb=" O LYSLR 8 " (cutoff:3.500A) Processing helix chain 'LR' and resid 28 through 35 removed outlier: 3.651A pdb=" N ASNLR 34 " --> pdb=" O ASNLR 30 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALALR 35 " --> pdb=" O GLULR 31 " (cutoff:3.500A) Processing helix chain 'LR' and resid 37 through 47 Processing helix chain 'LR' and resid 60 through 72 removed outlier: 3.956A pdb=" N LYSLR 72 " --> pdb=" O LEULR 68 " (cutoff:3.500A) Processing helix chain 'LR' and resid 84 through 89 Processing helix chain 'LR' and resid 90 through 112 removed outlier: 3.757A pdb=" N LEULR 106 " --> pdb=" O LEULR 102 " (cutoff:3.500A) Processing helix chain 'LR' and resid 116 through 129 removed outlier: 3.648A pdb=" N SERLR 122 " --> pdb=" O HISLR 118 " (cutoff:3.500A) Processing helix chain 'LR' and resid 134 through 154 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 153 through 161 removed outlier: 3.537A pdb=" N ALA A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 187 removed outlier: 3.921A pdb=" N ASP A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TRP A 186 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 209 Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 273 through 291 Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.669A pdb=" N VAL A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER A 310 " --> pdb=" O GLU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 410 removed outlier: 3.511A pdb=" N HIS A 401 " --> pdb=" O PRO A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 424 Processing helix chain 'A' and resid 428 through 439 Processing sheet with id=AA1, first strand: chain 'Lk' and resid 3 through 4 removed outlier: 4.047A pdb=" N SERLk 22 " --> pdb=" O ARGLk 37 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VALLk 23 " --> pdb=" O LYSLk 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'LY' and resid 31 through 33 removed outlier: 3.565A pdb=" N METLY 47 " --> pdb=" O SERLY 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'LY' and resid 79 through 82 removed outlier: 7.081A pdb=" N VALLY 79 " --> pdb=" O VALLY 73 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N VALLY 73 " --> pdb=" O VALLY 79 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N TYRLY 81 " --> pdb=" O VALLY 71 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLULY 54 " --> pdb=" O THRLY 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'LY' and resid 86 through 88 Processing sheet with id=AA5, first strand: chain 'LX' and resid 77 through 80 removed outlier: 3.502A pdb=" N PHELX 79 " --> pdb=" O ILELX 99 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYSLX 134 " --> pdb=" O VALLX 100 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYSLX 123 " --> pdb=" O ARGLX 139 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'LR' and resid 22 through 24 removed outlier: 3.569A pdb=" N ILELR 51 " --> pdb=" O TRPLR 23 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 133 through 135 Processing sheet with id=AA8, first strand: chain 'A' and resid 133 through 135 removed outlier: 4.538A pdb=" N VAL A 360 " --> pdb=" O ILE A 333 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 215 through 216 removed outlier: 3.575A pdb=" N GLY A 216 " --> pdb=" O HIS A 255 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 215 through 216 removed outlier: 3.575A pdb=" N GLY A 216 " --> pdb=" O HIS A 255 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 252 " --> pdb=" O CYS A 263 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS A 263 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 228 through 230 removed outlier: 6.816A pdb=" N LEU A 447 " --> pdb=" O ALA A 229 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 312 through 315 Processing sheet with id=AB4, first strand: chain 'A' and resid 415 through 416 removed outlier: 3.959A pdb=" N HIS A 382 " --> pdb=" O TYR A 444 " (cutoff:3.500A) 344 hydrogen bonds defined for protein. 981 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 116 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 45 basepair parallelities 105 stacking parallelities Total time for adding SS restraints: 2.52 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2722 1.33 - 1.45: 3722 1.45 - 1.57: 6139 1.57 - 1.69: 420 1.69 - 1.81: 58 Bond restraints: 13061 Sorted by residual: bond pdb=" N9 A 8 82 " pdb=" C4 A 8 82 " ideal model delta sigma weight residual 1.374 1.389 -0.015 6.00e-03 2.78e+04 6.20e+00 bond pdb=" CB ILE A 394 " pdb=" CG2 ILE A 394 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.15e+00 bond pdb=" N9 G 8 58 " pdb=" C4 G 8 58 " ideal model delta sigma weight residual 1.375 1.388 -0.013 8.00e-03 1.56e+04 2.52e+00 bond pdb=" C8 G 52522 " pdb=" N7 G 52522 " ideal model delta sigma weight residual 1.305 1.296 0.009 6.00e-03 2.78e+04 2.08e+00 bond pdb=" N9 G 52528 " pdb=" C4 G 52528 " ideal model delta sigma weight residual 1.375 1.386 -0.011 8.00e-03 1.56e+04 1.86e+00 ... (remaining 13056 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 18495 2.96 - 5.92: 106 5.92 - 8.88: 2 8.88 - 11.84: 0 11.84 - 14.79: 1 Bond angle restraints: 18604 Sorted by residual: angle pdb=" C1' C 52410 " pdb=" N1 C 52410 " pdb=" C2 C 52410 " ideal model delta sigma weight residual 118.80 123.91 -5.11 1.10e+00 8.26e-01 2.15e+01 angle pdb=" CA LEU A 396 " pdb=" CB LEU A 396 " pdb=" CG LEU A 396 " ideal model delta sigma weight residual 116.30 131.09 -14.79 3.50e+00 8.16e-02 1.79e+01 angle pdb=" C1' G 52528 " pdb=" N9 G 52528 " pdb=" C4 G 52528 " ideal model delta sigma weight residual 126.50 131.99 -5.49 1.30e+00 5.92e-01 1.78e+01 angle pdb=" C2 C 52410 " pdb=" N1 C 52410 " pdb=" C6 C 52410 " ideal model delta sigma weight residual 120.30 118.67 1.63 4.00e-01 6.25e+00 1.66e+01 angle pdb=" C1' C 52532 " pdb=" N1 C 52532 " pdb=" C2 C 52532 " ideal model delta sigma weight residual 118.80 123.12 -4.32 1.10e+00 8.26e-01 1.54e+01 ... (remaining 18599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.74: 7001 18.74 - 37.48: 737 37.48 - 56.22: 268 56.22 - 74.96: 272 74.96 - 93.69: 14 Dihedral angle restraints: 8292 sinusoidal: 5480 harmonic: 2812 Sorted by residual: dihedral pdb=" C5' A 52529 " pdb=" C4' A 52529 " pdb=" C3' A 52529 " pdb=" O3' A 52529 " ideal model delta sinusoidal sigma weight residual 147.00 103.28 43.72 1 8.00e+00 1.56e-02 4.16e+01 dihedral pdb=" O4' A 52529 " pdb=" C4' A 52529 " pdb=" C3' A 52529 " pdb=" C2' A 52529 " ideal model delta sinusoidal sigma weight residual 24.00 -18.65 42.65 1 8.00e+00 1.56e-02 3.97e+01 dihedral pdb=" C4' A 52529 " pdb=" C3' A 52529 " pdb=" C2' A 52529 " pdb=" C1' A 52529 " ideal model delta sinusoidal sigma weight residual -35.00 0.92 -35.92 1 8.00e+00 1.56e-02 2.85e+01 ... (remaining 8289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1728 0.048 - 0.097: 403 0.097 - 0.145: 94 0.145 - 0.193: 12 0.193 - 0.241: 2 Chirality restraints: 2239 Sorted by residual: chirality pdb=" CB THR A 399 " pdb=" CA THR A 399 " pdb=" OG1 THR A 399 " pdb=" CG2 THR A 399 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C1' U 8 69 " pdb=" O4' U 8 69 " pdb=" C2' U 8 69 " pdb=" N1 U 8 69 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.19 2.00e-01 2.50e+01 9.48e-01 chirality pdb=" C1' A 52382 " pdb=" O4' A 52382 " pdb=" C2' A 52382 " pdb=" N9 A 52382 " both_signs ideal model delta sigma weight residual False 2.46 2.27 0.19 2.00e-01 2.50e+01 9.13e-01 ... (remaining 2236 not shown) Planarity restraints: 1565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C 52419 " 0.028 2.00e-02 2.50e+03 3.00e-02 2.02e+01 pdb=" N1 C 52419 " -0.070 2.00e-02 2.50e+03 pdb=" C2 C 52419 " 0.045 2.00e-02 2.50e+03 pdb=" O2 C 52419 " -0.012 2.00e-02 2.50e+03 pdb=" N3 C 52419 " -0.008 2.00e-02 2.50e+03 pdb=" C4 C 52419 " 0.001 2.00e-02 2.50e+03 pdb=" N4 C 52419 " 0.002 2.00e-02 2.50e+03 pdb=" C5 C 52419 " 0.006 2.00e-02 2.50e+03 pdb=" C6 C 52419 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 52418 " 0.024 2.00e-02 2.50e+03 2.35e-02 1.51e+01 pdb=" N9 A 52418 " -0.062 2.00e-02 2.50e+03 pdb=" C8 A 52418 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A 52418 " 0.005 2.00e-02 2.50e+03 pdb=" C5 A 52418 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A 52418 " -0.001 2.00e-02 2.50e+03 pdb=" N6 A 52418 " 0.001 2.00e-02 2.50e+03 pdb=" N1 A 52418 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A 52418 " -0.006 2.00e-02 2.50e+03 pdb=" N3 A 52418 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A 52418 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 52526 " -0.038 2.00e-02 2.50e+03 2.07e-02 9.68e+00 pdb=" N1 C 52526 " 0.047 2.00e-02 2.50e+03 pdb=" C2 C 52526 " 0.001 2.00e-02 2.50e+03 pdb=" O2 C 52526 " 0.004 2.00e-02 2.50e+03 pdb=" N3 C 52526 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C 52526 " -0.005 2.00e-02 2.50e+03 pdb=" N4 C 52526 " -0.010 2.00e-02 2.50e+03 pdb=" C5 C 52526 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C 52526 " 0.005 2.00e-02 2.50e+03 ... (remaining 1562 not shown) Histogram of nonbonded interaction distances: 0.91 - 1.71: 1 1.71 - 2.51: 28 2.51 - 3.30: 12110 3.30 - 4.10: 31114 4.10 - 4.90: 50961 Warning: very small nonbonded interaction distances. Nonbonded interactions: 94214 Sorted by model distance: nonbonded pdb="CO CO A 501 " pdb="CO CO A 502 " model vdw 0.911 2.880 nonbonded pdb=" OE2 GLU A 364 " pdb="CO CO A 501 " model vdw 2.114 2.960 nonbonded pdb=" OD2 ASPLh 82 " pdb=" OG SERLX 64 " model vdw 2.271 3.040 nonbonded pdb=" OE1 GLNLR 39 " pdb=" NH1 ARGLR 42 " model vdw 2.352 3.120 nonbonded pdb=" OH TYRLY 74 " pdb=" OP2 G 8 75 " model vdw 2.359 3.040 ... (remaining 94209 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=0.50 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: 33.440 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.590 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:7.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 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 : 0.003 0.059 13061 Z= 0.219 Angle : 0.638 14.794 18604 Z= 0.466 Chirality : 0.045 0.241 2239 Planarity : 0.005 0.061 1565 Dihedral : 19.924 93.694 6470 Min Nonbonded Distance : 0.911 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.25), residues: 951 helix: 1.67 (0.26), residues: 379 sheet: 1.60 (0.52), residues: 107 loop : -0.98 (0.24), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGLk 37 TYR 0.012 0.001 TYRLX 137 PHE 0.011 0.001 PHELX 98 TRP 0.018 0.001 TRP A 148 HIS 0.005 0.001 HISLY 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.22 (13061) covalent geometry : angle 0.63808 / 0.47 (18604) hydrogen bonds : bond 0.24680 / 25.75 ( 445) hydrogen bonds : angle 5.59135 / 7.48 ( 1185) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.302 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.7444 time to fit residues: 93.2331 Evaluate side-chains 98 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.2980 chunk 106 optimal weight: 10.0000 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Lk 58 GLN LY 43 ASN LX 151 ASN LR 134 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.102869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.087518 restraints weight = 41787.961| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.70 r_work: 0.2947 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13061 Z= 0.144 Angle : 0.554 11.568 18604 Z= 0.325 Chirality : 0.041 0.275 2239 Planarity : 0.005 0.048 1565 Dihedral : 21.264 90.321 4363 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.17 % Allowed : 8.44 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.26), residues: 951 helix: 2.07 (0.26), residues: 403 sheet: 1.77 (0.50), residues: 105 loop : -0.91 (0.24), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGLR 9 TYR 0.016 0.001 TYRLX 137 PHE 0.013 0.001 PHE A 366 TRP 0.009 0.001 TRP A 186 HIS 0.014 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 (13061) covalent geometry : angle 0.55380 / 0.33 (18604) hydrogen bonds : bond 0.07960 / 7.48 ( 445) hydrogen bonds : angle 4.16302 / 5.61 ( 1185) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.507 Fit side-chains REVERT: Lk 31 ASN cc_start: 0.8433 (p0) cc_final: 0.8072 (p0) REVERT: LY 52 ASP cc_start: 0.6437 (t0) cc_final: 0.6212 (t0) REVERT: LY 112 ASP cc_start: 0.6179 (OUTLIER) cc_final: 0.5861 (m-30) REVERT: A 457 GLN cc_start: 0.9017 (tt0) cc_final: 0.8802 (tt0) outliers start: 10 outliers final: 2 residues processed: 111 average time/residue: 0.7285 time to fit residues: 86.9481 Evaluate side-chains 97 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 94 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LY residue 112 ASP Chi-restraints excluded: chain LX residue 119 ILE Chi-restraints excluded: chain LR residue 5 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 104 optimal weight: 0.0870 chunk 91 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 75 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Lk 58 GLN LY 40 GLN LX 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.100856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.085040 restraints weight = 41488.025| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.88 r_work: 0.2897 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13061 Z= 0.164 Angle : 0.529 10.267 18604 Z= 0.310 Chirality : 0.041 0.252 2239 Planarity : 0.005 0.046 1565 Dihedral : 21.014 90.104 4363 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.64 % Allowed : 10.32 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.26), residues: 951 helix: 2.06 (0.26), residues: 400 sheet: 1.77 (0.51), residues: 103 loop : -0.96 (0.24), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGLR 88 TYR 0.017 0.002 TYRLX 137 PHE 0.011 0.002 PHELX 79 TRP 0.008 0.001 TRP A 186 HIS 0.005 0.001 HISLY 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (13061) covalent geometry : angle 0.52926 / 0.31 (18604) hydrogen bonds : bond 0.07978 / 7.53 ( 445) hydrogen bonds : angle 3.81286 / 5.13 ( 1185) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.407 Fit side-chains REVERT: Lk 31 ASN cc_start: 0.8486 (p0) cc_final: 0.8180 (p0) REVERT: LY 112 ASP cc_start: 0.6074 (OUTLIER) cc_final: 0.5771 (m-30) REVERT: LX 145 ASP cc_start: 0.8293 (t0) cc_final: 0.8056 (t0) REVERT: A 457 GLN cc_start: 0.9007 (tt0) cc_final: 0.8709 (tt0) outliers start: 14 outliers final: 5 residues processed: 102 average time/residue: 0.7524 time to fit residues: 82.4978 Evaluate side-chains 96 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LY residue 84 ARG Chi-restraints excluded: chain LY residue 112 ASP Chi-restraints excluded: chain LX residue 119 ILE Chi-restraints excluded: chain LR residue 5 ARG Chi-restraints excluded: chain LR residue 12 SER Chi-restraints excluded: chain LR residue 144 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 31 optimal weight: 0.0770 chunk 73 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 79 optimal weight: 0.0270 chunk 12 optimal weight: 30.0000 chunk 14 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Lk 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.101367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.085731 restraints weight = 41521.067| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.74 r_work: 0.2915 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13061 Z= 0.136 Angle : 0.490 8.057 18604 Z= 0.287 Chirality : 0.039 0.241 2239 Planarity : 0.005 0.049 1565 Dihedral : 20.898 90.416 4363 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.23 % Allowed : 9.85 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.26), residues: 951 helix: 2.06 (0.27), residues: 393 sheet: 1.67 (0.51), residues: 103 loop : -0.94 (0.24), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 395 TYR 0.014 0.001 TYRLX 137 PHE 0.010 0.001 PHELX 79 TRP 0.008 0.001 TRP A 186 HIS 0.004 0.001 HISLY 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (13061) covalent geometry : angle 0.48977 / 0.29 (18604) hydrogen bonds : bond 0.06784 / 6.32 ( 445) hydrogen bonds : angle 3.57599 / 4.76 ( 1185) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.450 Fit side-chains REVERT: Lk 31 ASN cc_start: 0.8512 (p0) cc_final: 0.8231 (p0) REVERT: LY 112 ASP cc_start: 0.6169 (m-30) cc_final: 0.5834 (m-30) REVERT: LX 145 ASP cc_start: 0.8294 (t0) cc_final: 0.7982 (t0) REVERT: A 457 GLN cc_start: 0.8991 (tt0) cc_final: 0.8721 (tt0) outliers start: 19 outliers final: 9 residues processed: 101 average time/residue: 0.7017 time to fit residues: 76.4755 Evaluate side-chains 101 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Lk residue 12 LEU Chi-restraints excluded: chain Lk residue 22 SER Chi-restraints excluded: chain Lh residue 22 ASP Chi-restraints excluded: chain Lh residue 94 ARG Chi-restraints excluded: chain LX residue 119 ILE Chi-restraints excluded: chain LR residue 5 ARG Chi-restraints excluded: chain LR residue 12 SER Chi-restraints excluded: chain LR residue 91 GLU Chi-restraints excluded: chain LR residue 144 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 97 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 64 optimal weight: 0.1980 chunk 109 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Lk 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.099624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.083396 restraints weight = 43680.376| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.91 r_work: 0.2871 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13061 Z= 0.192 Angle : 0.552 8.503 18604 Z= 0.319 Chirality : 0.042 0.241 2239 Planarity : 0.006 0.047 1565 Dihedral : 20.824 90.386 4363 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.11 % Allowed : 10.79 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.26), residues: 951 helix: 1.80 (0.27), residues: 396 sheet: 1.42 (0.50), residues: 103 loop : -1.04 (0.24), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGLR 88 TYR 0.018 0.002 TYRLX 137 PHE 0.012 0.002 PHE A 366 TRP 0.008 0.002 TRP A 186 HIS 0.005 0.001 HISLY 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (13061) covalent geometry : angle 0.55246 / 0.32 (18604) hydrogen bonds : bond 0.08070 / 7.60 ( 445) hydrogen bonds : angle 3.60977 / 4.80 ( 1185) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.393 Fit side-chains REVERT: Lk 31 ASN cc_start: 0.8564 (p0) cc_final: 0.8310 (p0) REVERT: Lk 68 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7347 (tm-30) REVERT: LY 112 ASP cc_start: 0.6128 (OUTLIER) cc_final: 0.5817 (m-30) REVERT: LX 145 ASP cc_start: 0.8313 (t0) cc_final: 0.8074 (t0) outliers start: 18 outliers final: 12 residues processed: 104 average time/residue: 0.6905 time to fit residues: 77.1538 Evaluate side-chains 109 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Lk residue 22 SER Chi-restraints excluded: chain LY residue 55 VAL Chi-restraints excluded: chain LY residue 84 ARG Chi-restraints excluded: chain LY residue 112 ASP Chi-restraints excluded: chain Lh residue 22 ASP Chi-restraints excluded: chain Lh residue 94 ARG Chi-restraints excluded: chain LX residue 119 ILE Chi-restraints excluded: chain LX residue 148 ASP Chi-restraints excluded: chain LR residue 5 ARG Chi-restraints excluded: chain LR residue 12 SER Chi-restraints excluded: chain LR residue 91 GLU Chi-restraints excluded: chain LR residue 112 SER Chi-restraints excluded: chain LR residue 144 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 25 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 64 optimal weight: 0.1980 chunk 86 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Lk 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.101077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.079814 restraints weight = 33206.961| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.91 r_work: 0.2973 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13061 Z= 0.119 Angle : 0.477 8.217 18604 Z= 0.282 Chirality : 0.038 0.233 2239 Planarity : 0.005 0.048 1565 Dihedral : 20.796 90.840 4363 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.99 % Allowed : 12.19 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.26), residues: 951 helix: 1.99 (0.27), residues: 395 sheet: 1.41 (0.50), residues: 103 loop : -0.98 (0.25), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGLR 88 TYR 0.013 0.001 TYRLX 137 PHE 0.009 0.001 PHE A 366 TRP 0.011 0.001 TRP A 186 HIS 0.003 0.001 HISLY 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (13061) covalent geometry : angle 0.47685 / 0.28 (18604) hydrogen bonds : bond 0.06560 / 6.09 ( 445) hydrogen bonds : angle 3.47526 / 4.62 ( 1185) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.388 Fit side-chains REVERT: Lk 19 ASP cc_start: 0.8441 (p0) cc_final: 0.8031 (p0) REVERT: Lk 31 ASN cc_start: 0.8593 (p0) cc_final: 0.8366 (p0) REVERT: LY 112 ASP cc_start: 0.6327 (m-30) cc_final: 0.6010 (m-30) REVERT: LX 145 ASP cc_start: 0.8313 (t0) cc_final: 0.8068 (t0) outliers start: 17 outliers final: 12 residues processed: 104 average time/residue: 0.6552 time to fit residues: 73.4504 Evaluate side-chains 106 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Lk residue 12 LEU Chi-restraints excluded: chain Lk residue 22 SER Chi-restraints excluded: chain LY residue 55 VAL Chi-restraints excluded: chain LY residue 84 ARG Chi-restraints excluded: chain LY residue 111 LEU Chi-restraints excluded: chain Lh residue 22 ASP Chi-restraints excluded: chain Lh residue 94 ARG Chi-restraints excluded: chain LX residue 119 ILE Chi-restraints excluded: chain LR residue 5 ARG Chi-restraints excluded: chain LR residue 12 SER Chi-restraints excluded: chain LR residue 91 GLU Chi-restraints excluded: chain LR residue 144 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 61 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 30.0000 chunk 41 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Lk 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.102723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.087001 restraints weight = 44148.237| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.96 r_work: 0.2944 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13061 Z= 0.100 Angle : 0.449 9.500 18604 Z= 0.264 Chirality : 0.036 0.217 2239 Planarity : 0.004 0.047 1565 Dihedral : 20.685 92.970 4363 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.64 % Allowed : 12.90 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.27), residues: 951 helix: 2.08 (0.28), residues: 395 sheet: 1.48 (0.49), residues: 103 loop : -0.88 (0.25), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 395 TYR 0.011 0.001 TYRLX 137 PHE 0.007 0.001 PHELX 79 TRP 0.016 0.001 TRP A 186 HIS 0.002 0.001 HISLY 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.10 (13061) covalent geometry : angle 0.44891 / 0.26 (18604) hydrogen bonds : bond 0.05412 / 4.97 ( 445) hydrogen bonds : angle 3.28836 / 4.39 ( 1185) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.393 Fit side-chains REVERT: Lk 19 ASP cc_start: 0.8382 (p0) cc_final: 0.7951 (p0) REVERT: Lk 31 ASN cc_start: 0.8568 (p0) cc_final: 0.8364 (p0) REVERT: Lk 68 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7265 (tm-30) REVERT: LY 112 ASP cc_start: 0.6146 (m-30) cc_final: 0.5897 (m-30) REVERT: LR 151 ARG cc_start: 0.7442 (tpt170) cc_final: 0.7215 (ttp80) outliers start: 14 outliers final: 9 residues processed: 102 average time/residue: 0.6042 time to fit residues: 66.2959 Evaluate side-chains 100 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LY residue 55 VAL Chi-restraints excluded: chain LY residue 84 ARG Chi-restraints excluded: chain LY residue 111 LEU Chi-restraints excluded: chain Lh residue 94 ARG Chi-restraints excluded: chain LX residue 119 ILE Chi-restraints excluded: chain LR residue 5 ARG Chi-restraints excluded: chain LR residue 12 SER Chi-restraints excluded: chain LR residue 91 GLU Chi-restraints excluded: chain LR residue 144 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 88 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Lk 58 GLN Lh 96 ASN A 434 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.100724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.079242 restraints weight = 32624.294| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.84 r_work: 0.2967 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13061 Z= 0.151 Angle : 0.497 9.610 18604 Z= 0.288 Chirality : 0.039 0.171 2239 Planarity : 0.005 0.045 1565 Dihedral : 20.615 90.996 4363 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.88 % Allowed : 13.48 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.27), residues: 951 helix: 1.96 (0.28), residues: 395 sheet: 1.12 (0.47), residues: 113 loop : -1.02 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 395 TYR 0.015 0.001 TYRLX 137 PHE 0.010 0.001 PHELX 79 TRP 0.013 0.002 TRP A 186 HIS 0.004 0.001 HISLR 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (13061) covalent geometry : angle 0.49678 / 0.29 (18604) hydrogen bonds : bond 0.06704 / 6.28 ( 445) hydrogen bonds : angle 3.36685 / 4.50 ( 1185) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.366 Fit side-chains REVERT: Lk 19 ASP cc_start: 0.8442 (p0) cc_final: 0.7999 (p0) REVERT: LY 112 ASP cc_start: 0.6362 (m-30) cc_final: 0.6094 (m-30) REVERT: Lh 100 GLU cc_start: 0.7432 (pt0) cc_final: 0.7176 (pt0) REVERT: LR 151 ARG cc_start: 0.7610 (tpt170) cc_final: 0.7201 (ttp80) outliers start: 16 outliers final: 11 residues processed: 99 average time/residue: 0.6090 time to fit residues: 64.9811 Evaluate side-chains 101 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Lk residue 22 SER Chi-restraints excluded: chain LY residue 55 VAL Chi-restraints excluded: chain LY residue 84 ARG Chi-restraints excluded: chain LY residue 111 LEU Chi-restraints excluded: chain Lh residue 94 ARG Chi-restraints excluded: chain LX residue 119 ILE Chi-restraints excluded: chain LX residue 148 ASP Chi-restraints excluded: chain LR residue 5 ARG Chi-restraints excluded: chain LR residue 12 SER Chi-restraints excluded: chain LR residue 91 GLU Chi-restraints excluded: chain LR residue 144 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 75 optimal weight: 20.0000 chunk 112 optimal weight: 20.0000 chunk 87 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Lk 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.098315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.082336 restraints weight = 43033.867| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 3.00 r_work: 0.2842 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13061 Z= 0.253 Angle : 0.629 9.912 18604 Z= 0.358 Chirality : 0.046 0.187 2239 Planarity : 0.007 0.064 1565 Dihedral : 20.709 94.046 4363 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.64 % Allowed : 13.95 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.26), residues: 951 helix: 1.49 (0.27), residues: 396 sheet: 0.84 (0.47), residues: 113 loop : -1.35 (0.25), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGLR 88 TYR 0.021 0.002 TYRLX 137 PHE 0.015 0.002 PHE A 366 TRP 0.016 0.002 TRP A 186 HIS 0.005 0.001 HISLY 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.25 (13061) covalent geometry : angle 0.62938 / 0.36 (18604) hydrogen bonds : bond 0.09334 / 8.84 ( 445) hydrogen bonds : angle 3.67688 / 4.89 ( 1185) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.437 Fit side-chains REVERT: Lk 58 GLN cc_start: 0.7924 (mt0) cc_final: 0.7701 (mp10) REVERT: Lk 68 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7437 (tm-30) REVERT: LY 112 ASP cc_start: 0.6321 (OUTLIER) cc_final: 0.6033 (m-30) REVERT: LR 151 ARG cc_start: 0.7562 (tpt170) cc_final: 0.7241 (ttp80) outliers start: 14 outliers final: 9 residues processed: 98 average time/residue: 0.7231 time to fit residues: 76.3319 Evaluate side-chains 99 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Lk residue 22 SER Chi-restraints excluded: chain LY residue 55 VAL Chi-restraints excluded: chain LY residue 111 LEU Chi-restraints excluded: chain LY residue 112 ASP Chi-restraints excluded: chain LX residue 119 ILE Chi-restraints excluded: chain LX residue 148 ASP Chi-restraints excluded: chain LR residue 5 ARG Chi-restraints excluded: chain LR residue 12 SER Chi-restraints excluded: chain LR residue 91 GLU Chi-restraints excluded: chain LR residue 144 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 89 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.098756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.082762 restraints weight = 43741.291| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 3.03 r_work: 0.2850 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13061 Z= 0.218 Angle : 0.581 10.082 18604 Z= 0.334 Chirality : 0.043 0.185 2239 Planarity : 0.006 0.049 1565 Dihedral : 20.674 95.318 4363 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.64 % Allowed : 14.19 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.26), residues: 951 helix: 1.48 (0.27), residues: 395 sheet: 0.73 (0.47), residues: 113 loop : -1.40 (0.25), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGLh 92 TYR 0.018 0.002 TYRLX 137 PHE 0.013 0.002 PHE A 366 TRP 0.023 0.002 TRP A 186 HIS 0.005 0.001 HISLY 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.22 (13061) covalent geometry : angle 0.58072 / 0.33 (18604) hydrogen bonds : bond 0.08218 / 7.78 ( 445) hydrogen bonds : angle 3.62995 / 4.81 ( 1185) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.398 Fit side-chains REVERT: Lk 58 GLN cc_start: 0.7949 (mt0) cc_final: 0.7732 (mp10) REVERT: Lk 68 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7429 (tm-30) REVERT: LY 112 ASP cc_start: 0.6307 (OUTLIER) cc_final: 0.6045 (m-30) REVERT: LR 151 ARG cc_start: 0.7537 (tpt170) cc_final: 0.7199 (ttp80) outliers start: 14 outliers final: 9 residues processed: 97 average time/residue: 0.7152 time to fit residues: 74.6802 Evaluate side-chains 100 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Lk residue 22 SER Chi-restraints excluded: chain LY residue 55 VAL Chi-restraints excluded: chain LY residue 84 ARG Chi-restraints excluded: chain LY residue 111 LEU Chi-restraints excluded: chain LY residue 112 ASP Chi-restraints excluded: chain LX residue 119 ILE Chi-restraints excluded: chain LR residue 5 ARG Chi-restraints excluded: chain LR residue 12 SER Chi-restraints excluded: chain LR residue 91 GLU Chi-restraints excluded: chain LR residue 144 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 99 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.099584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.077184 restraints weight = 38729.892| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.08 r_work: 0.2924 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13061 Z= 0.163 Angle : 0.533 10.091 18604 Z= 0.309 Chirality : 0.040 0.179 2239 Planarity : 0.005 0.046 1565 Dihedral : 20.610 96.091 4363 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.17 % Allowed : 15.01 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.26), residues: 951 helix: 1.64 (0.27), residues: 395 sheet: 0.72 (0.46), residues: 113 loop : -1.35 (0.25), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 395 TYR 0.015 0.001 TYRLX 137 PHE 0.010 0.001 PHE A 366 TRP 0.028 0.002 TRP A 186 HIS 0.004 0.001 HISLY 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (13061) covalent geometry : angle 0.53296 / 0.31 (18604) hydrogen bonds : bond 0.07221 / 6.75 ( 445) hydrogen bonds : angle 3.51774 / 4.69 ( 1185) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5612.78 seconds wall clock time: 96 minutes 23.40 seconds (5783.40 seconds total)