Starting phenix.real_space_refine on Sat Aug 23 21:09:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8onz_17003/08_2025/8onz_17003.cif Found real_map, /net/cci-nas-00/data/ceres_data/8onz_17003/08_2025/8onz_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_2025/8onz_17003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8onz_17003/08_2025/8onz_17003.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8onz_17003/08_2025/8onz_17003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8onz_17003/08_2025/8onz_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 3.28, per 1000 atoms: 0.22 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: 0.79 Conformation dependent library (CDL) restraints added in 407.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 1.94 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: 2.85 Time building geometry restraints manager: 1.11 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=" CB GLU A 275 " pdb=" CG GLU A 275 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.96e+00 bond pdb=" N1 C 11958 " pdb=" C2 C 11958 " ideal model delta sigma weight residual 1.397 1.370 0.027 2.00e-02 2.50e+03 1.87e+00 bond pdb=" C3' G 12030 " pdb=" O3' G 12030 " ideal model delta sigma weight residual 1.417 1.437 -0.020 1.50e-02 4.44e+03 1.86e+00 bond pdb=" N1 C 11957 " pdb=" C2 C 11957 " ideal model delta sigma weight residual 1.397 1.424 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" CA GLU A 392 " pdb=" CB GLU A 392 " ideal model delta sigma weight residual 1.523 1.549 -0.026 1.94e-02 2.66e+03 1.75e+00 ... (remaining 15942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 22819 2.74 - 5.48: 236 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 120.20 129.74 -9.54 1.50e+00 4.44e-01 4.05e+01 angle pdb=" C3' C 12028 " pdb=" O3' C 12028 " pdb=" P A 12029 " ideal model delta sigma weight residual 120.20 128.89 -8.69 1.50e+00 4.44e-01 3.36e+01 angle pdb=" O3' U 12024 " pdb=" P U 12025 " pdb=" O5' U 12025 " ideal model delta sigma weight residual 104.00 112.02 -8.02 1.50e+00 4.44e-01 2.86e+01 angle pdb=" C4' A 12029 " pdb=" C3' A 12029 " pdb=" O3' A 12029 " ideal model delta sigma weight residual 113.00 120.76 -7.76 1.50e+00 4.44e-01 2.67e+01 angle pdb=" C4' C 12028 " pdb=" C3' C 12028 " pdb=" O3' C 12028 " ideal model delta sigma weight residual 109.40 116.85 -7.45 1.50e+00 4.44e-01 2.46e+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: 2762 0.104 - 0.209: 80 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: 34.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 14.320 Find NCS groups from input model: 0.040 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:7.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0316 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= 0.189 Angle : 0.743 13.703 23084 Z= 0.413 Chirality : 0.045 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 aren 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 covalent geometry : bond 0.00377 (15947) covalent geometry : angle 0.74287 (23084) hydrogen bonds : bond 0.17864 ( 600) hydrogen bonds : angle 6.27643 ( 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 : 0.401 Fit side-chains revert: symmetry clash 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: 0.2125 (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: 0.0070 (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: 0.5635 time to fit residues: 48.8098 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 : 0.360 ------------------------------------------------------------------------------- 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: 9.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.2980 chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 overall best weight: 3.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** LR 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 73 HIS ** LX 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LY 109 HIS Lk 28 ASN Lk 33 GLN ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN A 400 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5366 r_free = 0.5366 target = 0.295776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5304 r_free = 0.5304 target = 0.289401 restraints weight = 51658.295| |-----------------------------------------------------------------------------| r_work (start): 0.5300 rms_B_bonded: 0.99 r_work: 0.5220 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.5220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0871 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15947 Z= 0.171 Angle : 0.719 7.586 23084 Z= 0.371 Chirality : 0.040 0.218 2851 Planarity : 0.007 0.061 1715 Dihedral : 22.858 154.915 6221 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.62 % Allowed : 6.59 % Favored : 91.79 % 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 aren not related in a simple way. whole: 0.39 (0.26), residues: 979 helix: 0.59 (0.24), residues: 424 sheet: 0.80 (0.48), residues: 112 loop : -0.06 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGLX 138 TYR 0.025 0.002 TYRLR 124 PHE 0.029 0.003 PHELY 19 TRP 0.014 0.001 TRP A 235 HIS 0.009 0.002 HISLR 118 Details of bonding type rmsd covalent geometry : bond 0.00342 (15947) covalent geometry : angle 0.71912 (23084) hydrogen bonds : bond 0.08654 ( 600) hydrogen bonds : angle 4.66238 ( 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 57 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: LY 11 ARG cc_start: 0.4808 (ttt90) cc_final: 0.2470 (pmm-80) REVERT: A 233 MET cc_start: 0.1750 (ptm) cc_final: 0.0910 (tpp) outliers start: 14 outliers final: 4 residues processed: 53 average time/residue: 0.4760 time to fit residues: 28.8736 Evaluate side-chains 32 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 17 CYS Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LR residue 146 LYS Chi-restraints excluded: chain Lk residue 51 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 32 optimal weight: 9.9990 chunk 106 optimal weight: 20.0000 chunk 33 optimal weight: 0.0060 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 30.0000 chunk 66 optimal weight: 9.9990 chunk 123 optimal weight: 8.9990 chunk 51 optimal weight: 0.4980 chunk 29 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LR 7 GLN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5364 r_free = 0.5364 target = 0.295521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5302 r_free = 0.5302 target = 0.288906 restraints weight = 52140.939| |-----------------------------------------------------------------------------| r_work (start): 0.5286 rms_B_bonded: 0.98 r_work: 0.5223 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.5172 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.5172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1074 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15947 Z= 0.143 Angle : 0.618 10.014 23084 Z= 0.315 Chirality : 0.037 0.243 2851 Planarity : 0.006 0.054 1715 Dihedral : 22.674 152.582 6221 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.31 % Allowed : 10.17 % Favored : 87.51 % 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 aren not related in a simple way. whole: 0.47 (0.26), residues: 979 helix: 0.91 (0.25), residues: 425 sheet: 0.59 (0.49), residues: 112 loop : -0.26 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGLR 144 TYR 0.025 0.002 TYRLY 73 PHE 0.012 0.002 PHELh 116 TRP 0.010 0.002 TRP A 235 HIS 0.008 0.002 HISLR 141 Details of bonding type rmsd covalent geometry : bond 0.00291 (15947) covalent geometry : angle 0.61780 (23084) hydrogen bonds : bond 0.07101 ( 600) hydrogen bonds : angle 4.20333 ( 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 48 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 28 time to evaluate : 0.392 Fit side-chains REVERT: LR 7 GLN cc_start: 0.2495 (OUTLIER) cc_final: 0.2266 (OUTLIER) REVERT: LR 89 MET cc_start: 0.0893 (tpp) cc_final: -0.0026 (ppp) REVERT: LY 11 ARG cc_start: 0.4992 (ttt90) cc_final: 0.2358 (tpp80) REVERT: LY 74 ARG cc_start: 0.1068 (mtt180) cc_final: 0.0735 (tmm160) REVERT: Lh 83 LEU cc_start: 0.1779 (OUTLIER) cc_final: 0.0946 (tp) REVERT: A 233 MET cc_start: 0.1995 (ptm) cc_final: 0.1317 (tpp) REVERT: A 316 HIS cc_start: 0.4045 (OUTLIER) cc_final: 0.3792 (t-90) outliers start: 20 outliers final: 9 residues processed: 45 average time/residue: 0.5420 time to fit residues: 27.7976 Evaluate side-chains 35 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 7 GLN Chi-restraints excluded: chain LR residue 17 CYS Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LY residue 19 PHE Chi-restraints excluded: chain Lh residue 83 LEU Chi-restraints excluded: chain Lh residue 90 THR Chi-restraints excluded: chain Lk residue 51 ASP Chi-restraints excluded: chain A residue 75 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 44 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 83 optimal weight: 30.0000 chunk 24 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 31 optimal weight: 0.0370 chunk 64 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LR 7 GLN LY 80 HIS ** A 197 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 = 0.5369 r_free = 0.5369 target = 0.295827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.5309 r_free = 0.5309 target = 0.289710 restraints weight = 51783.263| |-----------------------------------------------------------------------------| r_work (start): 0.5304 rms_B_bonded: 0.95 r_work: 0.5238 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.5238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0997 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15947 Z= 0.105 Angle : 0.524 10.291 23084 Z= 0.266 Chirality : 0.033 0.208 2851 Planarity : 0.004 0.040 1715 Dihedral : 22.484 155.446 6221 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.31 % Allowed : 11.45 % 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 aren not related in a simple way. whole: 0.74 (0.27), residues: 979 helix: 1.22 (0.25), residues: 430 sheet: 0.57 (0.50), residues: 112 loop : -0.18 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 361 TYR 0.013 0.001 TYRLY 73 PHE 0.026 0.002 PHE A 424 TRP 0.008 0.001 TRP A 235 HIS 0.007 0.001 HISLh 50 Details of bonding type rmsd covalent geometry : bond 0.00204 (15947) covalent geometry : angle 0.52362 (23084) hydrogen bonds : bond 0.06332 ( 600) hydrogen bonds : angle 3.83276 ( 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 49 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 29 time to evaluate : 0.247 Fit side-chains REVERT: LR 7 GLN cc_start: 0.2406 (OUTLIER) cc_final: 0.1942 (tm-30) REVERT: LR 89 MET cc_start: 0.1817 (tpp) cc_final: 0.0715 (ppp) REVERT: LY 11 ARG cc_start: 0.4812 (ttt90) cc_final: 0.2590 (mtt90) REVERT: Lh 83 LEU cc_start: 0.1499 (OUTLIER) cc_final: 0.0741 (tp) REVERT: A 316 HIS cc_start: 0.3550 (OUTLIER) cc_final: 0.3221 (t-90) outliers start: 20 outliers final: 9 residues processed: 46 average time/residue: 0.3853 time to fit residues: 20.6595 Evaluate side-chains 38 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 26 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 7 GLN Chi-restraints excluded: chain LR residue 17 CYS Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LR residue 146 LYS Chi-restraints excluded: chain LX residue 74 LYS Chi-restraints excluded: chain LY residue 8 SER 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 A residue 75 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 316 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 47 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5368 r_free = 0.5368 target = 0.295677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.5304 r_free = 0.5304 target = 0.289160 restraints weight = 51979.558| |-----------------------------------------------------------------------------| r_work (start): 0.5297 rms_B_bonded: 1.07 r_work: 0.5223 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.5223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1137 moved from start: 0.5761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 15947 Z= 0.112 Angle : 0.543 9.765 23084 Z= 0.275 Chirality : 0.034 0.245 2851 Planarity : 0.004 0.038 1715 Dihedral : 22.423 157.905 6221 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.54 % Allowed : 12.14 % Favored : 85.32 % 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 aren not related in a simple way. whole: 0.80 (0.27), residues: 979 helix: 1.25 (0.25), residues: 432 sheet: 0.55 (0.52), residues: 108 loop : -0.11 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 247 TYR 0.016 0.001 TYR A 198 PHE 0.010 0.001 PHE A 185 TRP 0.006 0.001 TRPLR 95 HIS 0.008 0.001 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.00224 (15947) covalent geometry : angle 0.54345 (23084) hydrogen bonds : bond 0.06379 ( 600) hydrogen bonds : angle 3.82186 ( 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 53 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 31 time to evaluate : 0.446 Fit side-chains REVERT: LR 7 GLN cc_start: 0.2145 (OUTLIER) cc_final: 0.1674 (tm-30) REVERT: LR 89 MET cc_start: 0.1738 (tpp) cc_final: 0.0693 (ppp) REVERT: LY 11 ARG cc_start: 0.4841 (ttt90) cc_final: 0.2381 (pmm-80) REVERT: Lh 83 LEU cc_start: 0.1944 (OUTLIER) cc_final: 0.0755 (tp) REVERT: A 316 HIS cc_start: 0.3349 (OUTLIER) cc_final: 0.3044 (t-90) outliers start: 22 outliers final: 9 residues processed: 50 average time/residue: 0.4115 time to fit residues: 23.8450 Evaluate side-chains 44 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 7 GLN Chi-restraints excluded: chain LR residue 17 CYS Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LX residue 101 VAL Chi-restraints excluded: chain LY residue 19 PHE 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 A residue 75 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 369 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 56 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 91 optimal weight: 0.2980 chunk 101 optimal weight: 2.9990 chunk 75 optimal weight: 40.0000 chunk 65 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 35 optimal weight: 0.4980 chunk 61 optimal weight: 9.9990 chunk 74 optimal weight: 30.0000 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LR 7 GLN Lh 11 GLN Lh 33 GLN ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5355 r_free = 0.5355 target = 0.293530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5299 r_free = 0.5299 target = 0.287807 restraints weight = 52321.668| |-----------------------------------------------------------------------------| r_work (start): 0.5293 rms_B_bonded: 0.88 r_work: 0.5260 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.5219 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.5219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1666 moved from start: 0.7911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 15947 Z= 0.198 Angle : 0.802 9.320 23084 Z= 0.406 Chirality : 0.043 0.245 2851 Planarity : 0.007 0.089 1715 Dihedral : 23.198 160.850 6221 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.01 % Allowed : 12.83 % Favored : 84.16 % 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 aren not related in a simple way. whole: -0.31 (0.26), residues: 979 helix: 0.30 (0.24), residues: 422 sheet: 0.01 (0.53), residues: 97 loop : -0.64 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 361 TYR 0.038 0.003 TYRLY 73 PHE 0.025 0.003 PHELY 19 TRP 0.011 0.002 TRPLR 23 HIS 0.008 0.002 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00408 (15947) covalent geometry : angle 0.80211 (23084) hydrogen bonds : bond 0.08503 ( 600) hydrogen bonds : angle 4.68212 ( 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 69 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 43 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: LR 7 GLN cc_start: 0.2561 (OUTLIER) cc_final: 0.1882 (tt0) REVERT: LX 90 GLU cc_start: 0.2380 (OUTLIER) cc_final: 0.2052 (tm-30) REVERT: LY 11 ARG cc_start: 0.4969 (ttt90) cc_final: 0.2816 (mmt90) REVERT: Lk 31 THR cc_start: 0.1308 (OUTLIER) cc_final: -0.1474 (t) REVERT: A 114 GLU cc_start: -0.0562 (OUTLIER) cc_final: -0.1149 (mm-30) REVERT: A 121 MET cc_start: 0.4242 (ppp) cc_final: 0.3830 (ptm) REVERT: A 316 HIS cc_start: 0.4318 (OUTLIER) cc_final: 0.3922 (t-90) outliers start: 26 outliers final: 11 residues processed: 65 average time/residue: 0.4664 time to fit residues: 34.2239 Evaluate side-chains 50 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 34 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 7 GLN Chi-restraints excluded: chain LR residue 17 CYS Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LR residue 146 LYS Chi-restraints excluded: chain LX residue 90 GLU Chi-restraints excluded: chain LY residue 1 MET Chi-restraints excluded: chain LY residue 19 PHE Chi-restraints excluded: chain Lh residue 90 THR Chi-restraints excluded: chain Lh residue 113 LEU Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 323 GLU 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: 1.9990 chunk 98 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 95 optimal weight: 0.0010 overall best weight: 2.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Lk 28 ASN ** A 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 GLN ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5361 r_free = 0.5361 target = 0.294123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.5306 r_free = 0.5306 target = 0.288271 restraints weight = 51989.632| |-----------------------------------------------------------------------------| r_work (start): 0.5298 rms_B_bonded: 0.95 r_work: 0.5267 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.5228 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.5228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1548 moved from start: 0.8254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15947 Z= 0.126 Angle : 0.611 9.811 23084 Z= 0.308 Chirality : 0.036 0.257 2851 Planarity : 0.005 0.042 1715 Dihedral : 22.735 157.138 6221 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.77 % Allowed : 14.45 % Favored : 82.77 % 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 aren not related in a simple way. whole: 0.03 (0.27), residues: 979 helix: 0.58 (0.25), residues: 429 sheet: 0.11 (0.54), residues: 98 loop : -0.45 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGLY 74 TYR 0.019 0.002 TYRLY 77 PHE 0.019 0.002 PHE A 327 TRP 0.006 0.001 TRPLR 95 HIS 0.009 0.001 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.00249 (15947) covalent geometry : angle 0.61136 (23084) hydrogen bonds : bond 0.06614 ( 600) hydrogen bonds : angle 4.17272 ( 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 61 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 37 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: LR 7 GLN cc_start: 0.2547 (OUTLIER) cc_final: 0.1806 (tm-30) REVERT: LX 90 GLU cc_start: 0.2385 (OUTLIER) cc_final: 0.1865 (tm-30) REVERT: LX 128 ARG cc_start: 0.3015 (mtm180) cc_final: 0.2793 (mtm110) REVERT: LY 11 ARG cc_start: 0.4452 (ttt90) cc_final: 0.2310 (mtt90) REVERT: Lk 31 THR cc_start: 0.0587 (OUTLIER) cc_final: 0.0152 (p) REVERT: A 75 THR cc_start: 0.2573 (OUTLIER) cc_final: 0.2281 (m) REVERT: A 114 GLU cc_start: -0.0644 (OUTLIER) cc_final: -0.1107 (mm-30) REVERT: A 121 MET cc_start: 0.4040 (ppp) cc_final: 0.3665 (ptm) REVERT: A 316 HIS cc_start: 0.4012 (OUTLIER) cc_final: 0.3616 (t-90) outliers start: 24 outliers final: 13 residues processed: 56 average time/residue: 0.4264 time to fit residues: 27.1780 Evaluate side-chains 49 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 30 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 7 GLN Chi-restraints excluded: chain LR residue 17 CYS Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LR residue 146 LYS Chi-restraints excluded: chain LX residue 90 GLU Chi-restraints excluded: chain LX residue 146 LEU 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 Lh residue 90 THR 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 114 GLU Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 369 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 74 optimal weight: 40.0000 chunk 100 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LR 75 HIS LR 99 GLN LX 93 ASN ** LY 62 HIS ** 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 236 ASN A 305 HIS ** A 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5333 r_free = 0.5333 target = 0.290516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.5286 r_free = 0.5286 target = 0.285134 restraints weight = 52437.634| |-----------------------------------------------------------------------------| r_work (start): 0.5279 rms_B_bonded: 0.99 r_work: 0.5241 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.5198 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.5198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2186 moved from start: 1.0740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 15947 Z= 0.287 Angle : 1.094 11.024 23084 Z= 0.549 Chirality : 0.055 0.390 2851 Planarity : 0.009 0.126 1715 Dihedral : 24.129 162.083 6221 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 21.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.80 % Favored : 95.10 % Rotamer: Outliers : 3.35 % Allowed : 14.80 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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 aren not related in a simple way. whole: -1.52 (0.25), residues: 979 helix: -0.64 (0.24), residues: 415 sheet: -0.77 (0.47), residues: 103 loop : -1.32 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARGLR 76 TYR 0.033 0.003 TYRLY 77 PHE 0.040 0.004 PHELY 19 TRP 0.014 0.003 TRP A 142 HIS 0.021 0.004 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00557 (15947) covalent geometry : angle 1.09399 (23084) hydrogen bonds : bond 0.11475 ( 600) hydrogen bonds : angle 5.76125 ( 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 71 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 42 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: LR 23 TRP cc_start: 0.1238 (t-100) cc_final: -0.0032 (t-100) REVERT: LX 90 GLU cc_start: 0.2627 (OUTLIER) cc_final: 0.2144 (tm-30) REVERT: LY 11 ARG cc_start: 0.4816 (ttt90) cc_final: 0.2982 (mtp-110) REVERT: A 114 GLU cc_start: -0.0212 (OUTLIER) cc_final: -0.0881 (tt0) REVERT: A 275 GLU cc_start: 0.1441 (OUTLIER) cc_final: 0.0236 (mp0) REVERT: A 342 GLU cc_start: 0.2236 (pm20) cc_final: 0.1160 (mt-10) outliers start: 29 outliers final: 15 residues processed: 66 average time/residue: 0.5863 time to fit residues: 42.9757 Evaluate side-chains 55 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 37 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LR residue 120 TYR Chi-restraints excluded: chain LR residue 146 LYS Chi-restraints excluded: chain LX residue 90 GLU Chi-restraints excluded: chain LX residue 126 LEU Chi-restraints excluded: chain LY residue 1 MET Chi-restraints excluded: chain LY residue 19 PHE Chi-restraints excluded: chain LY residue 69 VAL Chi-restraints excluded: chain LY residue 77 TYR Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain Lh residue 90 THR Chi-restraints excluded: chain Lh residue 113 LEU Chi-restraints excluded: chain Lk residue 51 ASP Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 330 GLU 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: 6.9990 chunk 123 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN A 170 HIS A 236 ASN ** A 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5354 r_free = 0.5354 target = 0.292890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.5309 r_free = 0.5309 target = 0.287574 restraints weight = 52596.907| |-----------------------------------------------------------------------------| r_work (start): 0.5301 rms_B_bonded: 0.91 r_work: 0.5264 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.5223 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.5223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1830 moved from start: 1.0575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15947 Z= 0.136 Angle : 0.675 10.012 23084 Z= 0.340 Chirality : 0.039 0.274 2851 Planarity : 0.006 0.061 1715 Dihedral : 23.396 155.564 6221 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.62 % Allowed : 16.53 % Favored : 81.85 % 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 aren not related in a simple way. whole: -0.88 (0.26), residues: 979 helix: -0.09 (0.25), residues: 422 sheet: -0.39 (0.53), residues: 96 loop : -1.01 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 165 TYR 0.018 0.002 TYRLY 77 PHE 0.017 0.002 PHELY 19 TRP 0.010 0.002 TRPLR 95 HIS 0.007 0.002 HISLX 73 Details of bonding type rmsd covalent geometry : bond 0.00265 (15947) covalent geometry : angle 0.67516 (23084) hydrogen bonds : bond 0.07190 ( 600) hydrogen bonds : angle 4.65048 ( 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 50 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: LR 23 TRP cc_start: 0.1429 (t-100) cc_final: 0.1141 (t-100) REVERT: LX 90 GLU cc_start: 0.2327 (OUTLIER) cc_final: 0.1831 (tm-30) REVERT: LY 11 ARG cc_start: 0.4367 (ttt90) cc_final: 0.3067 (mtp-110) REVERT: LY 77 TYR cc_start: 0.4040 (OUTLIER) cc_final: 0.2154 (t80) REVERT: A 114 GLU cc_start: -0.0720 (OUTLIER) cc_final: -0.1268 (mm-30) REVERT: A 138 GLN cc_start: 0.2022 (OUTLIER) cc_final: -0.0566 (tt0) outliers start: 14 outliers final: 6 residues processed: 49 average time/residue: 0.5452 time to fit residues: 29.8954 Evaluate side-chains 42 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 146 LYS Chi-restraints excluded: chain LX residue 90 GLU Chi-restraints excluded: chain LY residue 1 MET Chi-restraints excluded: chain LY residue 19 PHE Chi-restraints excluded: chain LY residue 77 TYR Chi-restraints excluded: chain Lh residue 90 THR Chi-restraints excluded: chain Lk residue 51 ASP Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 323 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 125 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 88 optimal weight: 20.0000 chunk 75 optimal weight: 40.0000 chunk 64 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** LR 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS ** A 348 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 = 0.5363 r_free = 0.5363 target = 0.293733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5322 r_free = 0.5322 target = 0.288972 restraints weight = 52305.914| |-----------------------------------------------------------------------------| r_work (start): 0.5316 rms_B_bonded: 0.90 r_work: 0.5277 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.5235 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.5235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1747 moved from start: 1.0723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15947 Z= 0.119 Angle : 0.609 10.521 23084 Z= 0.304 Chirality : 0.036 0.265 2851 Planarity : 0.005 0.060 1715 Dihedral : 23.130 159.903 6221 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.62 % Allowed : 16.65 % Favored : 81.73 % 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 aren not related in a simple way. whole: -0.44 (0.27), residues: 979 helix: 0.39 (0.26), residues: 428 sheet: -0.12 (0.54), residues: 93 loop : -0.92 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 165 TYR 0.015 0.001 TYRLY 73 PHE 0.035 0.002 PHE A 332 TRP 0.010 0.001 TRPLh 13 HIS 0.012 0.002 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.00233 (15947) covalent geometry : angle 0.60863 (23084) hydrogen bonds : bond 0.06455 ( 600) hydrogen bonds : angle 4.17920 ( 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 47 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.413 Fit side-chains REVERT: LR 23 TRP cc_start: 0.1357 (t-100) cc_final: 0.1026 (t-100) REVERT: LX 136 PHE cc_start: 0.3834 (m-80) cc_final: 0.3452 (m-80) REVERT: LY 11 ARG cc_start: 0.4001 (ttt90) cc_final: 0.1914 (mtp-110) REVERT: LY 86 ARG cc_start: 0.2998 (OUTLIER) cc_final: -0.1092 (ttm-80) REVERT: A 114 GLU cc_start: -0.0946 (OUTLIER) cc_final: -0.1463 (mm-30) REVERT: A 121 MET cc_start: 0.3332 (ptm) cc_final: 0.2830 (ptm) REVERT: A 138 GLN cc_start: 0.2002 (OUTLIER) cc_final: -0.0234 (tt0) REVERT: A 339 TYR cc_start: 0.0639 (OUTLIER) cc_final: -0.1705 (p90) REVERT: A 374 ARG cc_start: 0.1775 (mtt-85) cc_final: 0.0608 (mmm-85) outliers start: 14 outliers final: 9 residues processed: 45 average time/residue: 0.6577 time to fit residues: 32.6804 Evaluate side-chains 41 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 28 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 146 LYS Chi-restraints excluded: chain LY residue 1 MET Chi-restraints excluded: chain LY residue 19 PHE Chi-restraints excluded: chain LY residue 86 ARG Chi-restraints excluded: chain Lh residue 90 THR Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 51 ASP Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 221 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 127 optimal weight: 30.0000 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 46 optimal weight: 20.0000 chunk 93 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 58 optimal weight: 0.2980 chunk 43 optimal weight: 0.0470 chunk 49 optimal weight: 0.9980 chunk 83 optimal weight: 30.0000 overall best weight: 1.2682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LR 3 ASN LX 81 ASN Lh 37 GLN ** A 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5364 r_free = 0.5364 target = 0.293864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5323 r_free = 0.5323 target = 0.289100 restraints weight = 52081.001| |-----------------------------------------------------------------------------| r_work (start): 0.5318 rms_B_bonded: 0.87 r_work: 0.5280 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.5239 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.5239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1709 moved from start: 1.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15947 Z= 0.109 Angle : 0.579 11.047 23084 Z= 0.290 Chirality : 0.034 0.216 2851 Planarity : 0.005 0.053 1715 Dihedral : 23.023 158.282 6221 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.62 % Allowed : 17.11 % 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 aren not related in a simple way. whole: -0.23 (0.27), residues: 979 helix: 0.57 (0.26), residues: 428 sheet: 0.04 (0.54), residues: 93 loop : -0.84 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 165 TYR 0.013 0.001 TYRLY 73 PHE 0.028 0.002 PHE A 332 TRP 0.009 0.001 TRPLh 13 HIS 0.008 0.001 HISLX 73 Details of bonding type rmsd covalent geometry : bond 0.00216 (15947) covalent geometry : angle 0.57937 (23084) hydrogen bonds : bond 0.06216 ( 600) hydrogen bonds : angle 4.07920 ( 1462) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4997.31 seconds wall clock time: 86 minutes 13.80 seconds (5173.80 seconds total)