Starting phenix.real_space_refine on Thu Aug 6 10:07:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8onz_17003/08_2026/8onz_17003.cif Found real_map, /net/cci-nas-00/data/ceres_data/8onz_17003/08_2026/8onz_17003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8onz_17003/08_2026/8onz_17003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8onz_17003/08_2026/8onz_17003.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8onz_17003/08_2026/8onz_17003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8onz_17003/08_2026/8onz_17003.map" } resolution = 2.94 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= -0.003 sd= 0.106 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 329 5.49 5 S 15 5.16 5 C 8151 2.51 5 N 2794 2.21 5 O 3701 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14990 Number of models: 1 Model: "" Number of chains: 8 Chain: "LR" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1251 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 3, 'TRANS': 149} Chain: "LX" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 965 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 8, 'TRANS': 112} Chain: "LY" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1065 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 6, 'TRANS': 127} Chain: "Lh" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1003 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "Lk" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 632 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 4, 'TRANS': 71} Chain: "1" Number of atoms: 5777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 5777 Classifications: {'RNA': 270} Modifications used: {'rna2p_pur': 19, 'rna2p_pyr': 17, 'rna3p_pur': 126, 'rna3p_pyr': 108} Link IDs: {'rna2p': 35, 'rna3p': 234} Chain breaks: 7 Chain: "2" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1261 Classifications: {'RNA': 59} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 1, 'rna3p_pur': 24, 'rna3p_pyr': 24} Link IDs: {'rna2p': 11, 'rna3p': 47} Chain: "A" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3036 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 365} Time building chain proxies: 2.85, per 1000 atoms: 0.19 Number of scatterers: 14990 At special positions: 0 Unit cell: (134.54, 151.032, 190.96, 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 15 16.00 P 329 15.00 O 3701 8.00 N 2794 7.00 C 8151 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: 0.98 Conformation dependent library (CDL) restraints added in 318.3 milliseconds 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1866 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 12 sheets defined 46.4% alpha, 15.7% beta 91 base pairs and 150 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'LR' and resid 4 through 16 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: 3.578A pdb=" N ASNLR 34 " --> pdb=" O SERLR 30 " (cutoff:3.500A) Processing helix chain 'LR' and resid 37 through 47 Processing helix chain 'LR' and resid 60 through 72 removed outlier: 3.539A pdb=" N ILELR 72 " --> pdb=" O LEULR 68 " (cutoff:3.500A) Processing helix chain 'LR' and resid 77 through 81 Processing helix chain 'LR' and resid 84 through 89 Processing helix chain 'LR' and resid 90 through 112 Processing helix chain 'LR' and resid 116 through 129 Processing helix chain 'LR' and resid 134 through 152 Processing helix chain 'LX' and resid 71 through 75 Processing helix chain 'LX' and resid 82 through 91 Processing helix chain 'LX' and resid 104 through 117 Processing helix chain 'LX' and resid 144 through 152 Processing helix chain 'LY' and resid 10 through 20 Processing helix chain 'LY' and resid 22 through 30 removed outlier: 3.944A pdb=" N VALLY 28 " --> pdb=" O SERLY 24 " (cutoff:3.500A) Processing helix chain 'LY' and resid 35 through 43 Processing helix chain 'LY' and resid 74 through 77 Processing helix chain 'LY' and resid 99 through 101 No H-bonds generated for 'chain 'LY' and resid 99 through 101' Processing helix chain 'LY' and resid 111 through 133 removed outlier: 3.571A pdb=" N ASNLY 116 " --> pdb=" O LYSLY 112 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 8 through 13 removed outlier: 3.555A pdb=" N LEULh 12 " --> pdb=" O LYSLh 8 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRPLh 13 " --> pdb=" O ALALh 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'Lh' and resid 8 through 13' Processing helix chain 'Lh' and resid 16 through 37 removed outlier: 3.566A pdb=" N GLNLh 37 " --> pdb=" O GLNLh 33 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 45 through 75 removed outlier: 4.173A pdb=" N ILELh 49 " --> pdb=" O LYSLh 45 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 90 through 96 Processing helix chain 'Lh' and resid 98 through 103 Processing helix chain 'Lh' and resid 106 through 116 Processing helix chain 'Lk' and resid 7 through 17 removed outlier: 3.652A pdb=" N PHELk 11 " --> pdb=" O ASPLk 7 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLULk 13 " --> pdb=" O LYSLk 9 " (cutoff:3.500A) Processing helix chain 'Lk' and resid 51 through 60 removed outlier: 3.816A pdb=" N LYSLk 57 " --> pdb=" O ASPLk 53 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLNLk 60 " --> pdb=" O GLULk 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 89 removed outlier: 3.638A pdb=" N LEU A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 111 removed outlier: 4.906A pdb=" N TYR A 108 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 122 removed outlier: 3.974A pdb=" N GLN A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 147 Processing helix chain 'A' and resid 152 through 169 Processing helix chain 'A' and resid 176 through 180 Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 239 through 257 removed outlier: 4.329A pdb=" N LEU A 243 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU A 244 " --> pdb=" O ASN A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 276 removed outlier: 3.680A pdb=" N ILE A 266 " --> pdb=" O ARG A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 376 removed outlier: 4.068A pdb=" N ASN A 370 " --> pdb=" O LYS A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 394 through 405 Processing sheet with id=AA1, first strand: chain 'LR' and resid 22 through 24 Processing sheet with id=AA2, first strand: chain 'LX' and resid 76 through 79 removed outlier: 6.994A pdb=" N ILELX 98 " --> pdb=" O ILELX 77 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VALLX 96 " --> pdb=" O PROLX 79 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYSLX 133 " --> pdb=" O VALLX 99 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYSLX 122 " --> pdb=" O ARGLX 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'LY' and resid 31 through 33 Processing sheet with id=AA4, first strand: chain 'LY' and resid 78 through 81 removed outlier: 7.056A pdb=" N VALLY 78 " --> pdb=" O VALLY 72 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N VALLY 72 " --> pdb=" O VALLY 78 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N HISLY 80 " --> pdb=" O THRLY 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'LY' and resid 85 through 87 Processing sheet with id=AA6, first strand: chain 'Lk' and resid 3 through 4 removed outlier: 6.670A pdb=" N GLNLk 3 " --> pdb=" O THRLk 46 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N VALLk 48 " --> pdb=" O GLNLk 3 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SERLk 22 " --> pdb=" O ARGLk 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.627A pdb=" N PHE A 424 " --> pdb=" O THR A 331 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.627A pdb=" N PHE A 424 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS A 297 " --> pdb=" O ALA A 328 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 181 through 191 removed outlier: 6.910A pdb=" N GLY A 219 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASP A 217 " --> pdb=" O PRO A 186 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N GLY A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LYS A 215 " --> pdb=" O GLY A 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 194 through 196 removed outlier: 6.661A pdb=" N LEU A 413 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 278 through 281 Processing sheet with id=AB3, first strand: chain 'A' and resid 381 through 382 removed outlier: 3.928A pdb=" N HIS A 348 " --> pdb=" O TYR A 410 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 1080 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 233 hydrogen bonds 382 hydrogen bond angles 0 basepair planarities 91 basepair parallelities 150 stacking parallelities Total time for adding SS restraints: 2.83 Time building geometry restraints manager: 1.29 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: 2903 1.33 - 1.45: 5122 1.45 - 1.57: 7248 1.57 - 1.69: 649 1.69 - 1.81: 25 Bond restraints: 15947 Sorted by residual: bond pdb=" N1 C 11958 " pdb=" C2 C 11958 " ideal model delta sigma weight residual 1.397 1.370 0.027 1.00e-02 1.00e+04 7.46e+00 bond pdb=" N1 C 11957 " pdb=" C2 C 11957 " ideal model delta sigma weight residual 1.397 1.424 -0.027 1.00e-02 1.00e+04 7.04e+00 bond pdb=" C2 C 11957 " pdb=" N3 C 11957 " ideal model delta sigma weight residual 1.353 1.370 -0.017 8.00e-03 1.56e+04 4.71e+00 bond pdb=" N9 A 2 62 " pdb=" C4 A 2 62 " ideal model delta sigma weight residual 1.374 1.361 0.013 6.00e-03 2.78e+04 4.52e+00 bond pdb=" C8 G 12049 " pdb=" N7 G 12049 " ideal model delta sigma weight residual 1.305 1.293 0.012 6.00e-03 2.78e+04 4.16e+00 ... (remaining 15942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 22666 2.74 - 5.48: 389 5.48 - 8.22: 23 8.22 - 10.96: 5 10.96 - 13.70: 1 Bond angle restraints: 23084 Sorted by residual: angle pdb=" C3' U 12024 " pdb=" O3' U 12024 " pdb=" P U 12025 " ideal model delta sigma weight residual 119.70 129.74 -10.04 1.20e+00 6.94e-01 7.01e+01 angle pdb=" C1' C 11957 " pdb=" N1 C 11957 " pdb=" C2 C 11957 " ideal model delta sigma weight residual 118.80 127.82 -9.02 1.10e+00 8.26e-01 6.72e+01 angle pdb=" C2 C 11958 " pdb=" N1 C 11958 " pdb=" C6 C 11958 " ideal model delta sigma weight residual 120.30 117.20 3.10 4.00e-01 6.25e+00 6.01e+01 angle pdb=" C3' C 12028 " pdb=" O3' C 12028 " pdb=" P A 12029 " ideal model delta sigma weight residual 119.70 128.89 -9.19 1.20e+00 6.94e-01 5.87e+01 angle pdb=" N1 C 11957 " pdb=" C2 C 11957 " pdb=" O2 C 11957 " ideal model delta sigma weight residual 118.90 123.48 -4.58 6.00e-01 2.78e+00 5.82e+01 ... (remaining 23079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.74: 8990 27.74 - 55.49: 708 55.49 - 83.23: 478 83.23 - 110.98: 18 110.98 - 138.72: 5 Dihedral angle restraints: 10199 sinusoidal: 7321 harmonic: 2878 Sorted by residual: dihedral pdb=" O4' U 12041 " pdb=" C1' U 12041 " pdb=" N1 U 12041 " pdb=" C2 U 12041 " ideal model delta sinusoidal sigma weight residual 200.00 61.54 138.46 1 1.50e+01 4.44e-03 7.46e+01 dihedral pdb=" O4' U 11478 " pdb=" C1' U 11478 " pdb=" N1 U 11478 " pdb=" C2 U 11478 " ideal model delta sinusoidal sigma weight residual 200.00 67.06 132.94 1 1.50e+01 4.44e-03 7.17e+01 dihedral pdb=" O4' C 11955 " pdb=" C1' C 11955 " pdb=" N1 C 11955 " pdb=" C2 C 11955 " ideal model delta sinusoidal sigma weight residual -160.00 -77.80 -82.20 1 1.50e+01 4.44e-03 3.69e+01 ... (remaining 10196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2473 0.104 - 0.209: 369 0.209 - 0.313: 6 0.313 - 0.417: 1 0.417 - 0.522: 2 Chirality restraints: 2851 Sorted by residual: chirality pdb=" C3' A 12029 " pdb=" C4' A 12029 " pdb=" O3' A 12029 " pdb=" C2' A 12029 " both_signs ideal model delta sigma weight residual False -2.48 -1.96 -0.52 2.00e-01 2.50e+01 6.81e+00 chirality pdb=" C3' C 12028 " pdb=" C4' C 12028 " pdb=" O3' C 12028 " pdb=" C2' C 12028 " both_signs ideal model delta sigma weight residual False -2.74 -2.32 -0.43 2.00e-01 2.50e+01 4.53e+00 chirality pdb=" C4' A 12029 " pdb=" C5' A 12029 " pdb=" O4' A 12029 " pdb=" C3' A 12029 " both_signs ideal model delta sigma weight residual False -2.50 -2.13 -0.37 2.00e-01 2.50e+01 3.41e+00 ... (remaining 2848 not shown) Planarity restraints: 1715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C 11958 " -0.028 2.00e-02 2.50e+03 4.00e-02 3.60e+01 pdb=" N1 C 11958 " 0.072 2.00e-02 2.50e+03 pdb=" C2 C 11958 " -0.083 2.00e-02 2.50e+03 pdb=" O2 C 11958 " 0.037 2.00e-02 2.50e+03 pdb=" N3 C 11958 " 0.008 2.00e-02 2.50e+03 pdb=" C4 C 11958 " -0.007 2.00e-02 2.50e+03 pdb=" N4 C 11958 " 0.007 2.00e-02 2.50e+03 pdb=" C5 C 11958 " -0.004 2.00e-02 2.50e+03 pdb=" C6 C 11958 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 11488 " -0.038 2.00e-02 2.50e+03 3.46e-02 2.69e+01 pdb=" N1 C 11488 " 0.082 2.00e-02 2.50e+03 pdb=" C2 C 11488 " -0.046 2.00e-02 2.50e+03 pdb=" O2 C 11488 " 0.015 2.00e-02 2.50e+03 pdb=" N3 C 11488 " 0.005 2.00e-02 2.50e+03 pdb=" C4 C 11488 " -0.001 2.00e-02 2.50e+03 pdb=" N4 C 11488 " -0.005 2.00e-02 2.50e+03 pdb=" C5 C 11488 " -0.003 2.00e-02 2.50e+03 pdb=" C6 C 11488 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 11487 " -0.028 2.00e-02 2.50e+03 2.60e-02 1.86e+01 pdb=" N9 A 11487 " 0.068 2.00e-02 2.50e+03 pdb=" C8 A 11487 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A 11487 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A 11487 " -0.007 2.00e-02 2.50e+03 pdb=" C6 A 11487 " -0.001 2.00e-02 2.50e+03 pdb=" N6 A 11487 " -0.002 2.00e-02 2.50e+03 pdb=" N1 A 11487 " 0.005 2.00e-02 2.50e+03 pdb=" C2 A 11487 " 0.007 2.00e-02 2.50e+03 pdb=" N3 A 11487 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A 11487 " -0.043 2.00e-02 2.50e+03 ... (remaining 1712 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 130 2.57 - 3.15: 11378 3.15 - 3.73: 26811 3.73 - 4.32: 36405 4.32 - 4.90: 50996 Nonbonded interactions: 125720 Sorted by model distance: nonbonded pdb=" O2' G 12030 " pdb=" OP1 G 12031 " model vdw 1.983 3.040 nonbonded pdb=" OD2 ASP A 128 " pdb=" NH2 ARG A 225 " model vdw 2.058 3.120 nonbonded pdb=" N2 G 11963 " pdb=" O2 C 12008 " model vdw 2.074 2.496 nonbonded pdb=" N2 G 11968 " pdb=" O2 C 12003 " model vdw 2.085 2.496 nonbonded pdb=" N2 G 11962 " pdb=" O2 C 12009 " model vdw 2.093 2.496 ... (remaining 125715 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: 32.850 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: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 13.440 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0279 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 : 0.004 0.060 15947 Z= 0.308 Angle : 0.884 13.703 23084 Z= 0.710 Chirality : 0.063 0.522 2851 Planarity : 0.007 0.110 1715 Dihedral : 21.845 138.723 8333 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.33 (0.25), residues: 979 helix: 0.58 (0.25), residues: 413 sheet: 0.62 (0.43), residues: 114 loop : -0.09 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG A 384 TYR 0.020 0.002 TYR A 339 PHE 0.016 0.002 PHE A 185 TRP 0.009 0.001 TRP A 142 HIS 0.004 0.001 HISLR 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.31 (15947) covalent geometry : angle 0.88385 / 0.71 (23084) hydrogen bonds : bond 0.17864 / 11.78 ( 600) hydrogen bonds : angle 6.27643 / 4.70 ( 1462) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: LR 89 MET cc_start: 0.3230 (tpp) cc_final: 0.1878 (ppp) REVERT: LX 94 THR cc_start: 0.2165 (p) cc_final: 0.1853 (p) REVERT: LY 11 ARG cc_start: 0.3418 (ttt90) cc_final: 0.2124 (mmt-90) REVERT: A 302 TYR cc_start: 0.1015 (m-80) cc_final: 0.0422 (m-80) REVERT: A 321 MET cc_start: 0.0862 (ttm) cc_final: 0.0069 (mpt) REVERT: A 346 VAL cc_start: 0.3921 (p) cc_final: 0.2749 (p) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.4654 time to fit residues: 40.3878 Evaluate side-chains 36 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 30.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 40.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 50.0000 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 overall best weight: 4.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** LR 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LR 75 HIS ** LX 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LY 80 HIS Lk 33 GLN ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN A 400 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5361 r_free = 0.5361 target = 0.295945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.5296 r_free = 0.5296 target = 0.289001 restraints weight = 51710.679| |-----------------------------------------------------------------------------| r_work (start): 0.5290 rms_B_bonded: 0.98 r_work: 0.5209 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.5209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0669 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 15947 Z= 0.232 Angle : 0.770 10.607 23084 Z= 0.422 Chirality : 0.049 0.349 2851 Planarity : 0.008 0.065 1715 Dihedral : 23.010 142.339 6221 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.62 % Allowed : 6.94 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.22 (0.26), residues: 979 helix: 0.36 (0.24), residues: 429 sheet: 0.58 (0.46), residues: 121 loop : -0.04 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 130 TYR 0.018 0.003 TYR A 394 PHE 0.026 0.004 PHELY 19 TRP 0.014 0.002 TRP A 235 HIS 0.010 0.002 HIS A 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.23 (15947) covalent geometry : angle 0.76996 / 0.42 (23084) hydrogen bonds : bond 0.09765 / 6.71 ( 600) hydrogen bonds : angle 4.84080 / 3.60 ( 1462) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: LY 11 ARG cc_start: 0.4415 (ttt90) cc_final: 0.1567 (ttp-170) REVERT: LY 86 ARG cc_start: 0.0168 (ttm-80) cc_final: -0.0087 (ptt180) REVERT: A 62 LYS cc_start: 0.1604 (mttt) cc_final: 0.0897 (ptmm) REVERT: A 302 TYR cc_start: 0.1139 (m-80) cc_final: 0.0882 (m-80) outliers start: 14 outliers final: 4 residues processed: 53 average time/residue: 0.4445 time to fit residues: 26.6066 Evaluate side-chains 36 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LR residue 146 LYS Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 316 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 32 optimal weight: 8.9990 chunk 106 optimal weight: 20.0000 chunk 33 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 77 optimal weight: 50.0000 chunk 66 optimal weight: 40.0000 chunk 123 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... LR 67 ASN ** LX 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LY 80 HIS Lh 16 ASN ** Lh 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lk 28 ASN ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5360 r_free = 0.5360 target = 0.295318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.5295 r_free = 0.5295 target = 0.288770 restraints weight = 52179.318| |-----------------------------------------------------------------------------| r_work (start): 0.5291 rms_B_bonded: 1.04 r_work: 0.5231 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.5231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1076 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 15947 Z= 0.206 Angle : 0.793 20.952 23084 Z= 0.423 Chirality : 0.047 0.264 2851 Planarity : 0.008 0.163 1715 Dihedral : 23.010 149.149 6221 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.70 % Allowed : 10.06 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.67 (0.25), residues: 979 helix: -0.11 (0.23), residues: 420 sheet: -0.36 (0.45), residues: 117 loop : -0.66 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARGLR 144 TYR 0.041 0.003 TYRLY 73 PHE 0.030 0.004 PHELY 19 TRP 0.016 0.002 TRPLR 23 HIS 0.014 0.003 HISLX 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.21 (15947) covalent geometry : angle 0.79310 / 0.42 (23084) hydrogen bonds : bond 0.10227 / 7.09 ( 600) hydrogen bonds : angle 4.93860 / 3.62 ( 1462) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 44 time to evaluate : 0.238 Fit side-chains REVERT: LR 89 MET cc_start: 0.2800 (tpp) cc_final: 0.2429 (tpp) REVERT: LX 124 ASN cc_start: 0.5023 (p0) cc_final: 0.4048 (p0) REVERT: LY 11 ARG cc_start: 0.5322 (ttt90) cc_final: 0.2798 (pmm-80) REVERT: LY 86 ARG cc_start: 0.0332 (ttm-80) cc_final: 0.0002 (ttp-170) REVERT: Lh 83 LEU cc_start: 0.1491 (OUTLIER) cc_final: 0.0789 (tp) REVERT: Lk 12 ILE cc_start: 0.1891 (OUTLIER) cc_final: 0.1669 (mp) REVERT: A 122 GLN cc_start: 0.4242 (OUTLIER) cc_final: 0.3762 (pp30) REVERT: A 323 GLU cc_start: 0.3836 (OUTLIER) cc_final: 0.2745 (pp20) REVERT: A 373 LYS cc_start: -0.2072 (mtmt) cc_final: -0.2392 (tppt) outliers start: 32 outliers final: 9 residues processed: 73 average time/residue: 0.4453 time to fit residues: 36.4612 Evaluate side-chains 47 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LR residue 96 MET Chi-restraints excluded: chain LR residue 146 LYS Chi-restraints excluded: chain LY residue 19 PHE Chi-restraints excluded: chain LY residue 103 VAL Chi-restraints excluded: chain Lh residue 83 LEU Chi-restraints excluded: chain Lh residue 113 LEU Chi-restraints excluded: chain Lk residue 12 ILE Chi-restraints excluded: chain Lk residue 51 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 323 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 44 optimal weight: 0.2980 chunk 106 optimal weight: 2.9990 chunk 83 optimal weight: 50.0000 chunk 24 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 chunk 64 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... LR 67 ASN ** LX 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 50 HIS ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5365 r_free = 0.5365 target = 0.295711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5299 r_free = 0.5299 target = 0.289100 restraints weight = 51944.464| |-----------------------------------------------------------------------------| r_work (start): 0.5294 rms_B_bonded: 0.99 r_work: 0.5222 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.5222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1001 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 15947 Z= 0.124 Angle : 0.545 8.688 23084 Z= 0.310 Chirality : 0.038 0.260 2851 Planarity : 0.005 0.051 1715 Dihedral : 22.832 149.420 6221 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.89 % Allowed : 11.56 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.26 (0.26), residues: 979 helix: 0.35 (0.24), residues: 426 sheet: -0.39 (0.45), residues: 117 loop : -0.50 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGLk 24 TYR 0.024 0.002 TYRLY 73 PHE 0.016 0.002 PHE A 185 TRP 0.010 0.002 TRPLR 23 HIS 0.011 0.002 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (15947) covalent geometry : angle 0.54523 / 0.31 (23084) hydrogen bonds : bond 0.08184 / 5.72 ( 600) hydrogen bonds : angle 4.47835 / 3.34 ( 1462) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 31 time to evaluate : 0.293 Fit side-chains REVERT: LR 89 MET cc_start: 0.2208 (tpp) cc_final: 0.1788 (tpp) REVERT: LY 11 ARG cc_start: 0.5006 (ttt90) cc_final: 0.2596 (pmm-80) REVERT: LY 58 VAL cc_start: -0.0598 (OUTLIER) cc_final: -0.2304 (t) REVERT: Lh 83 LEU cc_start: 0.1596 (OUTLIER) cc_final: 0.0762 (tp) REVERT: Lk 12 ILE cc_start: 0.1427 (OUTLIER) cc_final: 0.1166 (mp) outliers start: 25 outliers final: 8 residues processed: 52 average time/residue: 0.4152 time to fit residues: 24.3715 Evaluate side-chains 39 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LR residue 146 LYS Chi-restraints excluded: chain LY residue 19 PHE Chi-restraints excluded: chain LY residue 58 VAL Chi-restraints excluded: chain Lh residue 83 LEU Chi-restraints excluded: chain Lh residue 90 THR Chi-restraints excluded: chain Lk residue 12 ILE Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 378 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 47 optimal weight: 0.0670 chunk 0 optimal weight: 20.0000 chunk 110 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 57 optimal weight: 8.9990 chunk 123 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... LY 80 HIS ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS A 423 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5366 r_free = 0.5366 target = 0.295920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.5305 r_free = 0.5305 target = 0.289697 restraints weight = 52126.875| |-----------------------------------------------------------------------------| r_work (start): 0.5300 rms_B_bonded: 0.97 r_work: 0.5227 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.5227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1032 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15947 Z= 0.111 Angle : 0.514 9.169 23084 Z= 0.292 Chirality : 0.037 0.267 2851 Planarity : 0.005 0.046 1715 Dihedral : 22.748 149.028 6221 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.47 % Allowed : 11.79 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.03 (0.26), residues: 979 helix: 0.64 (0.25), residues: 425 sheet: -0.40 (0.47), residues: 114 loop : -0.46 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARGLY 74 TYR 0.019 0.001 TYRLY 73 PHE 0.015 0.002 PHELY 19 TRP 0.009 0.002 TRP A 142 HIS 0.010 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.11 (15947) covalent geometry : angle 0.51374 / 0.29 (23084) hydrogen bonds : bond 0.07850 / 5.48 ( 600) hydrogen bonds : angle 4.33703 / 3.23 ( 1462) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 27 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: LR 89 MET cc_start: 0.2509 (tpp) cc_final: 0.2162 (tpp) REVERT: LY 11 ARG cc_start: 0.4898 (ttt90) cc_final: 0.2700 (mtt90) REVERT: Lh 83 LEU cc_start: 0.1644 (OUTLIER) cc_final: 0.0818 (tp) REVERT: Lk 12 ILE cc_start: 0.1374 (OUTLIER) cc_final: 0.1152 (mp) REVERT: A 233 MET cc_start: 0.1921 (OUTLIER) cc_final: 0.1287 (tpp) REVERT: A 431 ARG cc_start: 0.3905 (OUTLIER) cc_final: 0.2988 (tmm-80) outliers start: 30 outliers final: 13 residues processed: 54 average time/residue: 0.3977 time to fit residues: 24.7159 Evaluate side-chains 42 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 25 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LR residue 146 LYS Chi-restraints excluded: chain LY residue 19 PHE Chi-restraints excluded: chain LY residue 77 TYR Chi-restraints excluded: chain LY residue 85 THR Chi-restraints excluded: chain Lh residue 83 LEU Chi-restraints excluded: chain Lh residue 90 THR Chi-restraints excluded: chain Lh residue 113 LEU Chi-restraints excluded: chain Lk residue 12 ILE Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 51 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 431 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 56 optimal weight: 0.9990 chunk 90 optimal weight: 40.0000 chunk 91 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 75 optimal weight: 50.0000 chunk 65 optimal weight: 40.0000 chunk 97 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 chunk 61 optimal weight: 30.0000 chunk 74 optimal weight: 50.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Lk 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 GLN A 423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5352 r_free = 0.5352 target = 0.293708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.5288 r_free = 0.5288 target = 0.286811 restraints weight = 51662.058| |-----------------------------------------------------------------------------| r_work (start): 0.5279 rms_B_bonded: 1.14 r_work: 0.5219 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.5219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1618 moved from start: 0.6530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 15947 Z= 0.262 Angle : 0.944 11.589 23084 Z= 0.509 Chirality : 0.058 0.327 2851 Planarity : 0.011 0.169 1715 Dihedral : 23.545 153.327 6221 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.93 % Allowed : 13.06 % Favored : 83.01 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.75 (0.24), residues: 979 helix: -0.76 (0.23), residues: 420 sheet: -1.08 (0.58), residues: 72 loop : -1.49 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARGLY 27 TYR 0.044 0.004 TYRLY 73 PHE 0.036 0.004 PHELY 19 TRP 0.019 0.003 TRPLR 95 HIS 0.016 0.003 HISLR 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.26 (15947) covalent geometry : angle 0.94413 / 0.51 (23084) hydrogen bonds : bond 0.12377 / 8.65 ( 600) hydrogen bonds : angle 5.49351 / 4.03 ( 1462) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 45 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: LR 89 MET cc_start: 0.3153 (tpp) cc_final: 0.2835 (tpp) REVERT: LY 11 ARG cc_start: 0.5206 (ttt90) cc_final: 0.2520 (ptt-90) REVERT: Lh 83 LEU cc_start: 0.3216 (OUTLIER) cc_final: 0.2285 (tp) REVERT: Lh 113 LEU cc_start: 0.0834 (OUTLIER) cc_final: -0.0827 (tp) REVERT: Lk 12 ILE cc_start: 0.1914 (OUTLIER) cc_final: 0.1631 (mp) REVERT: Lk 18 LYS cc_start: 0.0932 (OUTLIER) cc_final: 0.0459 (tptt) REVERT: Lk 31 THR cc_start: 0.0669 (OUTLIER) cc_final: -0.1585 (t) REVERT: A 316 HIS cc_start: 0.3781 (OUTLIER) cc_final: 0.3368 (t-90) REVERT: A 342 GLU cc_start: 0.1484 (pm20) cc_final: -0.0293 (mt-10) outliers start: 34 outliers final: 13 residues processed: 75 average time/residue: 0.4635 time to fit residues: 39.0063 Evaluate side-chains 55 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 36 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LX residue 77 ILE Chi-restraints excluded: chain LX residue 146 LEU Chi-restraints excluded: chain LY residue 19 PHE Chi-restraints excluded: chain LY residue 76 LYS Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain LY residue 85 THR Chi-restraints excluded: chain Lh residue 18 GLU Chi-restraints excluded: chain Lh residue 83 LEU Chi-restraints excluded: chain Lh residue 90 THR Chi-restraints excluded: chain Lh residue 113 LEU Chi-restraints excluded: chain Lk residue 12 ILE Chi-restraints excluded: chain Lk residue 18 LYS Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 369 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 13 optimal weight: 5.9990 chunk 51 optimal weight: 0.0060 chunk 98 optimal weight: 9.9990 chunk 3 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 8 optimal weight: 0.0060 chunk 12 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 overall best weight: 0.5412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... LR 39 GLN ** Lk 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5365 r_free = 0.5365 target = 0.295266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.5301 r_free = 0.5301 target = 0.288620 restraints weight = 51792.265| |-----------------------------------------------------------------------------| r_work (start): 0.5294 rms_B_bonded: 1.06 r_work: 0.5234 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.5234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1291 moved from start: 0.6379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 15947 Z= 0.130 Angle : 0.572 10.381 23084 Z= 0.325 Chirality : 0.039 0.266 2851 Planarity : 0.006 0.080 1715 Dihedral : 22.994 149.550 6221 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.08 % Allowed : 15.72 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.87 (0.26), residues: 979 helix: 0.08 (0.24), residues: 430 sheet: -1.00 (0.50), residues: 98 loop : -1.05 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 431 TYR 0.011 0.001 TYR A 394 PHE 0.026 0.002 PHE A 327 TRP 0.014 0.002 TRPLR 95 HIS 0.013 0.002 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.13 (15947) covalent geometry : angle 0.57234 / 0.33 (23084) hydrogen bonds : bond 0.08137 / 5.73 ( 600) hydrogen bonds : angle 4.56708 / 3.43 ( 1462) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 34 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: LY 11 ARG cc_start: 0.4487 (ttt90) cc_final: 0.2266 (ptt180) REVERT: Lh 83 LEU cc_start: 0.2392 (OUTLIER) cc_final: 0.1298 (tp) REVERT: Lk 31 THR cc_start: 0.0880 (OUTLIER) cc_final: -0.1716 (t) REVERT: A 312 ILE cc_start: -0.1213 (OUTLIER) cc_final: -0.1641 (tt) REVERT: A 316 HIS cc_start: 0.3620 (OUTLIER) cc_final: 0.3324 (t-90) outliers start: 18 outliers final: 9 residues processed: 52 average time/residue: 0.4146 time to fit residues: 24.4708 Evaluate side-chains 42 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 29 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 146 LYS Chi-restraints excluded: chain LY residue 19 PHE Chi-restraints excluded: chain LY residue 77 TYR Chi-restraints excluded: chain Lh residue 18 GLU Chi-restraints excluded: chain Lh residue 83 LEU Chi-restraints excluded: chain Lh residue 113 LEU Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 51 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 323 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 30.0000 chunk 88 optimal weight: 50.0000 chunk 74 optimal weight: 50.0000 chunk 100 optimal weight: 8.9990 chunk 114 optimal weight: 20.0000 chunk 82 optimal weight: 50.0000 chunk 64 optimal weight: 30.0000 chunk 1 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 69 optimal weight: 30.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Lk 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5344 r_free = 0.5344 target = 0.292581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.5282 r_free = 0.5282 target = 0.285979 restraints weight = 52066.461| |-----------------------------------------------------------------------------| r_work (start): 0.5274 rms_B_bonded: 1.02 r_work: 0.5237 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.5192 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.5192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1857 moved from start: 0.7747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 15947 Z= 0.286 Angle : 0.987 13.609 23084 Z= 0.526 Chirality : 0.061 0.361 2851 Planarity : 0.011 0.174 1715 Dihedral : 23.604 154.999 6221 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 22.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.01 % Allowed : 15.03 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -1.99 (0.25), residues: 979 helix: -0.90 (0.23), residues: 420 sheet: -1.61 (0.50), residues: 90 loop : -1.57 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARGLY 11 TYR 0.038 0.004 TYRLY 77 PHE 0.037 0.004 PHELY 19 TRP 0.015 0.003 TRPLR 95 HIS 0.021 0.003 HISLR 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.29 (15947) covalent geometry : angle 0.98655 / 0.53 (23084) hydrogen bonds : bond 0.12509 / 8.83 ( 600) hydrogen bonds : angle 5.61187 / 4.11 ( 1462) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 36 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: LR 89 MET cc_start: 0.3454 (tpp) cc_final: 0.1861 (tmm) REVERT: LY 11 ARG cc_start: 0.5219 (ttt90) cc_final: 0.2496 (pmm150) REVERT: Lh 74 PHE cc_start: 0.3604 (t80) cc_final: 0.3348 (t80) REVERT: Lh 83 LEU cc_start: 0.3424 (OUTLIER) cc_final: 0.2907 (tp) REVERT: Lk 12 ILE cc_start: 0.2081 (OUTLIER) cc_final: 0.1878 (mp) REVERT: Lk 31 THR cc_start: 0.1056 (OUTLIER) cc_final: -0.1490 (t) REVERT: A 274 MET cc_start: -0.0525 (mtt) cc_final: -0.0852 (ttm) REVERT: A 316 HIS cc_start: 0.4230 (OUTLIER) cc_final: 0.3897 (t-90) outliers start: 26 outliers final: 12 residues processed: 58 average time/residue: 0.3814 time to fit residues: 25.2874 Evaluate side-chains 46 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 30 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 17 CYS Chi-restraints excluded: chain LY residue 19 PHE Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain LY residue 85 THR Chi-restraints excluded: chain Lh residue 18 GLU Chi-restraints excluded: chain Lh residue 83 LEU Chi-restraints excluded: chain Lh residue 90 THR Chi-restraints excluded: chain Lh residue 113 LEU Chi-restraints excluded: chain Lk residue 12 ILE Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 369 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 105 optimal weight: 8.9990 chunk 123 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 43 optimal weight: 0.0980 chunk 51 optimal weight: 0.0060 chunk 42 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 108 optimal weight: 30.0000 chunk 85 optimal weight: 30.0000 chunk 17 optimal weight: 5.9990 overall best weight: 3.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... LR 39 GLN ** Lk 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5355 r_free = 0.5355 target = 0.293527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.5299 r_free = 0.5299 target = 0.287600 restraints weight = 52281.675| |-----------------------------------------------------------------------------| r_work (start): 0.5292 rms_B_bonded: 0.90 r_work: 0.5254 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.5208 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.5208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1661 moved from start: 0.7775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15947 Z= 0.148 Angle : 0.645 9.647 23084 Z= 0.366 Chirality : 0.043 0.256 2851 Planarity : 0.006 0.052 1715 Dihedral : 23.206 152.150 6221 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.54 % Allowed : 16.07 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -1.54 (0.25), residues: 979 helix: -0.47 (0.24), residues: 428 sheet: -1.49 (0.51), residues: 91 loop : -1.38 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGLR 38 TYR 0.022 0.002 TYRLY 73 PHE 0.020 0.003 PHELY 19 TRP 0.011 0.001 TRPLR 95 HIS 0.009 0.002 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.15 (15947) covalent geometry : angle 0.64548 / 0.37 (23084) hydrogen bonds : bond 0.09079 / 6.41 ( 600) hydrogen bonds : angle 5.01840 / 3.73 ( 1462) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 33 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: LY 11 ARG cc_start: 0.4722 (ttt90) cc_final: 0.2588 (mmt90) REVERT: Lh 83 LEU cc_start: 0.3167 (OUTLIER) cc_final: 0.2276 (tp) REVERT: Lk 12 ILE cc_start: 0.1927 (OUTLIER) cc_final: 0.1684 (mp) REVERT: Lk 31 THR cc_start: 0.1183 (OUTLIER) cc_final: -0.1420 (t) REVERT: A 316 HIS cc_start: 0.4014 (OUTLIER) cc_final: 0.3589 (t-90) outliers start: 22 outliers final: 16 residues processed: 53 average time/residue: 0.4071 time to fit residues: 24.7504 Evaluate side-chains 50 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 30 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 17 CYS Chi-restraints excluded: chain LX residue 90 GLU Chi-restraints excluded: chain LY residue 19 PHE Chi-restraints excluded: chain LY residue 77 TYR Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain LY residue 85 THR Chi-restraints excluded: chain Lh residue 18 GLU Chi-restraints excluded: chain Lh residue 83 LEU Chi-restraints excluded: chain Lh residue 90 THR Chi-restraints excluded: chain Lh residue 113 LEU Chi-restraints excluded: chain Lk residue 12 ILE Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 51 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 369 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 125 optimal weight: 5.9990 chunk 43 optimal weight: 0.0770 chunk 52 optimal weight: 0.0980 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 88 optimal weight: 50.0000 chunk 75 optimal weight: 50.0000 chunk 64 optimal weight: 30.0000 chunk 10 optimal weight: 0.8980 chunk 104 optimal weight: 30.0000 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Lk 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 HIS ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 HIS ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5367 r_free = 0.5367 target = 0.294790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5304 r_free = 0.5304 target = 0.288589 restraints weight = 51845.325| |-----------------------------------------------------------------------------| r_work (start): 0.5299 rms_B_bonded: 1.01 r_work: 0.5257 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.5213 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.5213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1442 moved from start: 0.7657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 15947 Z= 0.115 Angle : 0.537 10.325 23084 Z= 0.303 Chirality : 0.037 0.262 2851 Planarity : 0.005 0.046 1715 Dihedral : 22.867 149.212 6221 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.97 % Allowed : 16.99 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.75 (0.27), residues: 979 helix: 0.21 (0.25), residues: 433 sheet: -1.13 (0.51), residues: 98 loop : -0.96 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 431 TYR 0.013 0.001 TYRLY 73 PHE 0.030 0.003 PHELh 74 TRP 0.020 0.002 TRPLR 95 HIS 0.007 0.001 HIS A 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.12 (15947) covalent geometry : angle 0.53692 / 0.30 (23084) hydrogen bonds : bond 0.07490 / 5.32 ( 600) hydrogen bonds : angle 4.43519 / 3.34 ( 1462) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 33 time to evaluate : 0.408 Fit side-chains REVERT: LR 144 ARG cc_start: 0.2266 (ptm160) cc_final: 0.2005 (ptm-80) REVERT: LX 90 GLU cc_start: 0.2295 (OUTLIER) cc_final: 0.1865 (tm-30) REVERT: LY 11 ARG cc_start: 0.4420 (ttt90) cc_final: 0.2193 (pmt170) REVERT: Lk 12 ILE cc_start: 0.2029 (OUTLIER) cc_final: 0.1552 (mp) REVERT: A 316 HIS cc_start: 0.4137 (OUTLIER) cc_final: 0.3769 (t-90) outliers start: 17 outliers final: 12 residues processed: 47 average time/residue: 0.4493 time to fit residues: 24.0647 Evaluate side-chains 46 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 31 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LX residue 90 GLU Chi-restraints excluded: chain LY residue 77 TYR Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain LY residue 85 THR Chi-restraints excluded: chain Lh residue 90 THR Chi-restraints excluded: chain Lh residue 113 LEU Chi-restraints excluded: chain Lk residue 12 ILE Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 51 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 339 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 127 optimal weight: 7.9990 chunk 8 optimal weight: 0.5980 chunk 61 optimal weight: 30.0000 chunk 123 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 58 optimal weight: 0.0270 chunk 43 optimal weight: 8.9990 chunk 49 optimal weight: 0.6980 chunk 83 optimal weight: 50.0000 overall best weight: 2.8642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Lh 11 GLN ** Lk 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5357 r_free = 0.5357 target = 0.293778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.5300 r_free = 0.5300 target = 0.287885 restraints weight = 51867.666| |-----------------------------------------------------------------------------| r_work (start): 0.5294 rms_B_bonded: 0.95 r_work: 0.5254 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.5215 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.5215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1606 moved from start: 0.7996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15947 Z= 0.137 Angle : 0.592 9.227 23084 Z= 0.330 Chirality : 0.040 0.353 2851 Planarity : 0.006 0.073 1715 Dihedral : 22.949 153.223 6221 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.20 % Allowed : 16.53 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.81 (0.27), residues: 979 helix: 0.12 (0.25), residues: 433 sheet: -1.15 (0.51), residues: 98 loop : -0.96 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGLk 42 TYR 0.016 0.002 TYRLR 120 PHE 0.030 0.003 PHE A 332 TRP 0.007 0.001 TRPLR 95 HIS 0.009 0.002 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.14 (15947) covalent geometry : angle 0.59196 / 0.33 (23084) hydrogen bonds : bond 0.08085 / 5.72 ( 600) hydrogen bonds : angle 4.58172 / 3.41 ( 1462) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4272.51 seconds wall clock time: 73 minutes 44.40 seconds (4424.40 seconds total)