Starting phenix.real_space_refine on Fri Jul 3 15:07:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8onz_17003/07_2026/8onz_17003.cif Found real_map, /net/cci-nas-00/data/ceres_data/8onz_17003/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8onz_17003/07_2026/8onz_17003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8onz_17003/07_2026/8onz_17003.map" model { file = "/net/cci-nas-00/data/ceres_data/8onz_17003/07_2026/8onz_17003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8onz_17003/07_2026/8onz_17003.cif" } 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-dev-6108/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: 3.05, per 1000 atoms: 0.20 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: 0.89 Conformation dependent library (CDL) restraints added in 341.8 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: 1.66 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: 3.24 Time building geometry restraints manager: 1.16 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: 22818 2.74 - 5.48: 237 5.48 - 8.22: 23 8.22 - 10.96: 5 10.96 - 13.70: 1 Bond angle restraints: 23084 Sorted by residual: 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=" 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 angle pdb=" C2 C 11957 " pdb=" N1 C 11957 " pdb=" C6 C 11957 " ideal model delta sigma weight residual 120.30 117.53 2.77 4.00e-01 6.25e+00 4.81e+01 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 ... (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: 35.130 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: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.180 Find NCS groups from input model: 0.060 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:7.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.970 ------------------------------------------------------------------------------- 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= 0.283 Angle : 0.743 13.703 23084 Z= 0.583 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 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 0.00377 / 0.28 (15947) covalent geometry : angle 0.74309 / 0.58 (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 : 0.236 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: 0.4871 time to fit residues: 42.2595 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 : 0.354 ------------------------------------------------------------------------------- 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: 20.0000 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: 4.9990 chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** LR 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5362 r_free = 0.5362 target = 0.295983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5296 r_free = 0.5296 target = 0.288976 restraints weight = 51633.316| |-----------------------------------------------------------------------------| r_work (start): 0.5290 rms_B_bonded: 1.00 r_work: 0.5215 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.5215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0631 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 15947 Z= 0.201 Angle : 0.701 9.862 23084 Z= 0.397 Chirality : 0.044 0.356 2851 Planarity : 0.007 0.068 1715 Dihedral : 23.084 139.337 6221 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.62 % Allowed : 7.17 % Favored : 91.21 % 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: 0.32 (0.24), residues: 430 sheet: 0.67 (0.46), residues: 119 loop : -0.02 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 130 TYR 0.019 0.003 TYR A 394 PHE 0.032 0.004 PHE A 327 TRP 0.013 0.002 TRP A 235 HIS 0.009 0.002 HIS A 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.20 (15947) covalent geometry : angle 0.70076 / 0.40 (23084) hydrogen bonds : bond 0.09470 / 6.50 ( 600) hydrogen bonds : angle 4.81365 / 3.58 ( 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 53 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: LR 89 MET cc_start: 0.2127 (tpp) cc_final: 0.0913 (ppp) REVERT: LY 11 ARG cc_start: 0.4361 (ttt90) cc_final: 0.1431 (ttp-170) REVERT: A 62 LYS cc_start: 0.1644 (mttt) cc_final: 0.0935 (ptmm) REVERT: A 302 TYR cc_start: 0.1313 (m-80) cc_final: 0.1003 (m-80) outliers start: 14 outliers final: 3 residues processed: 50 average time/residue: 0.4743 time to fit residues: 26.4938 Evaluate side-chains 33 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 316 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 32 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 chunk 77 optimal weight: 50.0000 chunk 66 optimal weight: 30.0000 chunk 123 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** LX 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 33 GLN Lk 28 ASN A 197 HIS ** A 221 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 = 0.5361 r_free = 0.5361 target = 0.295619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.5296 r_free = 0.5296 target = 0.289010 restraints weight = 52253.491| |-----------------------------------------------------------------------------| r_work (start): 0.5292 rms_B_bonded: 0.95 r_work: 0.5213 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.5213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0809 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 15947 Z= 0.167 Angle : 0.593 10.760 23084 Z= 0.341 Chirality : 0.039 0.284 2851 Planarity : 0.006 0.069 1715 Dihedral : 22.893 151.598 6221 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.20 % Allowed : 9.36 % Favored : 88.44 % 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: 0.18 (0.26), residues: 979 helix: 0.54 (0.24), residues: 427 sheet: 0.20 (0.46), residues: 115 loop : -0.17 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGLY 86 TYR 0.043 0.003 TYR A 444 PHE 0.028 0.003 PHE A 231 TRP 0.008 0.001 TRP A 235 HIS 0.012 0.002 HISLX 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 (15947) covalent geometry : angle 0.59316 / 0.34 (23084) hydrogen bonds : bond 0.08541 / 5.93 ( 600) hydrogen bonds : angle 4.50939 / 3.34 ( 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 57 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 38 time to evaluate : 0.412 Fit side-chains REVERT: LR 89 MET cc_start: 0.2196 (tpp) cc_final: 0.0705 (ppp) REVERT: LX 124 ASN cc_start: 0.4732 (p0) cc_final: 0.4091 (p0) REVERT: LY 11 ARG cc_start: 0.4688 (ttt90) cc_final: 0.2474 (pmm150) REVERT: LY 74 ARG cc_start: 0.0920 (mtt180) cc_final: 0.0345 (ptt90) REVERT: LY 96 ILE cc_start: 0.2957 (OUTLIER) cc_final: 0.1600 (mt) REVERT: Lk 12 ILE cc_start: 0.1691 (OUTLIER) cc_final: 0.1379 (mp) REVERT: A 62 LYS cc_start: 0.1853 (mttt) cc_final: 0.1140 (ptmm) REVERT: A 302 TYR cc_start: 0.1430 (m-80) cc_final: 0.1046 (m-80) outliers start: 19 outliers final: 7 residues processed: 55 average time/residue: 0.3958 time to fit residues: 25.1116 Evaluate side-chains 42 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 19 PHE Chi-restraints excluded: chain LY residue 96 ILE 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 299 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 44 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 83 optimal weight: 50.0000 chunk 24 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 31 optimal weight: 0.0070 chunk 64 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** LX 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 33 GLN A 170 HIS A 221 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5365 r_free = 0.5365 target = 0.295734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5303 r_free = 0.5303 target = 0.289097 restraints weight = 51856.808| |-----------------------------------------------------------------------------| r_work (start): 0.5295 rms_B_bonded: 0.94 r_work: 0.5223 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.5223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0861 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15947 Z= 0.127 Angle : 0.521 11.192 23084 Z= 0.303 Chirality : 0.037 0.232 2851 Planarity : 0.005 0.046 1715 Dihedral : 22.738 147.522 6221 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.89 % Allowed : 11.10 % Favored : 86.01 % 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: 0.76 (0.25), residues: 432 sheet: -0.12 (0.45), residues: 120 loop : -0.21 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGLY 86 TYR 0.019 0.001 TYRLY 73 PHE 0.018 0.002 PHE A 332 TRP 0.007 0.001 TRP A 142 HIS 0.010 0.002 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.13 (15947) covalent geometry : angle 0.52132 / 0.30 (23084) hydrogen bonds : bond 0.07685 / 5.32 ( 600) hydrogen bonds : angle 4.19194 / 3.14 ( 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 54 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 29 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: LR 89 MET cc_start: 0.2344 (tpp) cc_final: 0.0888 (ppp) REVERT: LY 11 ARG cc_start: 0.4705 (ttt90) cc_final: 0.2462 (tpp80) REVERT: Lh 83 LEU cc_start: 0.0846 (OUTLIER) cc_final: 0.0031 (tp) REVERT: Lk 12 ILE cc_start: 0.1462 (OUTLIER) cc_final: 0.1150 (mp) REVERT: A 233 MET cc_start: 0.2112 (OUTLIER) cc_final: 0.1027 (tpp) REVERT: A 373 LYS cc_start: -0.2331 (mtmt) cc_final: -0.2631 (tppt) outliers start: 25 outliers final: 10 residues processed: 48 average time/residue: 0.3910 time to fit residues: 21.7534 Evaluate side-chains 39 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 26 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LR residue 146 LYS 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 233 MET Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 369 LEU 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: 0.0570 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 30.0000 chunk 5 optimal weight: 0.0980 chunk 57 optimal weight: 0.4980 chunk 123 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 3 optimal weight: 0.0980 chunk 43 optimal weight: 7.9990 chunk 106 optimal weight: 0.4980 overall best weight: 0.2498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5368 r_free = 0.5368 target = 0.296064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.5307 r_free = 0.5307 target = 0.289756 restraints weight = 52004.635| |-----------------------------------------------------------------------------| r_work (start): 0.5301 rms_B_bonded: 0.91 r_work: 0.5228 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.5228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0766 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15947 Z= 0.098 Angle : 0.451 9.236 23084 Z= 0.263 Chirality : 0.035 0.233 2851 Planarity : 0.004 0.044 1715 Dihedral : 22.604 149.896 6221 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.08 % Allowed : 12.49 % Favored : 85.43 % 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: 0.74 (0.27), residues: 979 helix: 1.16 (0.25), residues: 432 sheet: 0.23 (0.47), residues: 120 loop : -0.01 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGLY 74 TYR 0.017 0.001 TYR A 302 PHE 0.013 0.001 PHE A 231 TRP 0.008 0.001 TRPLR 95 HIS 0.005 0.001 HISLh 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.10 (15947) covalent geometry : angle 0.45095 / 0.26 (23084) hydrogen bonds : bond 0.06971 / 4.86 ( 600) hydrogen bonds : angle 3.88074 / 2.92 ( 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 48 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 30 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: LR 89 MET cc_start: 0.2175 (tpp) cc_final: 0.0774 (ppp) REVERT: LY 11 ARG cc_start: 0.4704 (ttt90) cc_final: 0.2507 (pmm-80) REVERT: Lh 83 LEU cc_start: 0.0834 (OUTLIER) cc_final: 0.0069 (mt) REVERT: A 62 LYS cc_start: 0.1620 (mttt) cc_final: 0.1036 (ptmm) REVERT: A 233 MET cc_start: 0.2028 (OUTLIER) cc_final: 0.1090 (tpp) REVERT: A 373 LYS cc_start: -0.2178 (mtmt) cc_final: -0.2568 (tppt) outliers start: 18 outliers final: 6 residues processed: 46 average time/residue: 0.4254 time to fit residues: 22.5082 Evaluate side-chains 36 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 146 LYS 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 233 MET Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 378 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 56 optimal weight: 0.8980 chunk 90 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 101 optimal weight: 2.9990 chunk 75 optimal weight: 50.0000 chunk 65 optimal weight: 30.0000 chunk 97 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 35 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 74 optimal weight: 50.0000 overall best weight: 8.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... LY 109 HIS ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 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 = 0.5351 r_free = 0.5351 target = 0.293716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.5282 r_free = 0.5282 target = 0.286486 restraints weight = 51588.631| |-----------------------------------------------------------------------------| r_work (start): 0.5273 rms_B_bonded: 1.23 r_work: 0.5218 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.5218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1494 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 15947 Z= 0.313 Angle : 0.965 12.178 23084 Z= 0.539 Chirality : 0.057 0.345 2851 Planarity : 0.012 0.203 1715 Dihedral : 23.525 156.103 6221 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.35 % Allowed : 12.60 % Favored : 84.05 % 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: -1.42 (0.24), residues: 979 helix: -0.58 (0.23), residues: 412 sheet: -0.99 (0.46), residues: 100 loop : -1.18 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARGLR 88 TYR 0.058 0.005 TYRLY 73 PHE 0.034 0.005 PHELY 19 TRP 0.023 0.004 TRPLR 95 HIS 0.015 0.003 HISLh 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.31 (15947) covalent geometry : angle 0.96452 / 0.54 (23084) hydrogen bonds : bond 0.12921 / 9.08 ( 600) hydrogen bonds : angle 5.34705 / 3.89 ( 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 75 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 46 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: LX 126 LEU cc_start: 0.3701 (OUTLIER) cc_final: 0.3325 (tt) REVERT: LY 11 ARG cc_start: 0.5337 (ttt90) cc_final: 0.2321 (ptm160) REVERT: LY 74 ARG cc_start: 0.1495 (mtt180) cc_final: 0.1246 (mmt90) REVERT: Lh 83 LEU cc_start: 0.2870 (OUTLIER) cc_final: 0.1817 (tp) REVERT: Lh 113 LEU cc_start: 0.0385 (OUTLIER) cc_final: -0.1420 (tp) REVERT: A 114 GLU cc_start: 0.0231 (OUTLIER) cc_final: -0.0328 (tt0) REVERT: A 122 GLN cc_start: 0.5751 (OUTLIER) cc_final: 0.3993 (pp30) REVERT: A 233 MET cc_start: 0.2240 (OUTLIER) cc_final: 0.1182 (tpp) REVERT: A 316 HIS cc_start: 0.3211 (OUTLIER) cc_final: 0.2956 (t-90) REVERT: A 342 GLU cc_start: 0.1001 (pm20) cc_final: -0.0357 (mt-10) outliers start: 29 outliers final: 11 residues processed: 73 average time/residue: 0.5529 time to fit residues: 44.5821 Evaluate side-chains 56 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 38 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LX residue 126 LEU Chi-restraints excluded: chain LX residue 146 LEU Chi-restraints excluded: chain LY residue 19 PHE Chi-restraints excluded: chain LY residue 69 VAL 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 6 SER Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain A residue 233 MET 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 346 VAL Chi-restraints excluded: chain A residue 369 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.9761 > 50: distance: 7 - 29: 20.892 distance: 24 - 29: 22.412 distance: 29 - 30: 20.615 distance: 30 - 31: 36.945 distance: 30 - 33: 16.265 distance: 31 - 32: 38.592 distance: 31 - 40: 22.166 distance: 33 - 34: 22.762 distance: 34 - 35: 21.093 distance: 34 - 36: 28.784 distance: 35 - 37: 34.255 distance: 36 - 38: 36.826 distance: 37 - 39: 39.920 distance: 38 - 39: 8.603 distance: 40 - 41: 17.849 distance: 41 - 42: 43.189 distance: 41 - 44: 16.549 distance: 42 - 43: 37.466 distance: 42 - 47: 26.861 distance: 44 - 45: 11.971 distance: 45 - 46: 14.220 distance: 47 - 48: 33.062 distance: 48 - 49: 14.214 distance: 48 - 51: 49.665 distance: 49 - 50: 48.792 distance: 49 - 55: 35.002 distance: 51 - 52: 52.383 distance: 52 - 53: 35.521 distance: 52 - 54: 41.310 distance: 55 - 56: 43.694 distance: 56 - 57: 37.167 distance: 57 - 58: 18.523 distance: 57 - 59: 14.665 distance: 59 - 60: 8.035 distance: 60 - 61: 31.013 distance: 60 - 63: 36.366 distance: 61 - 62: 11.235 distance: 61 - 68: 28.686 distance: 63 - 64: 30.631 distance: 64 - 65: 16.935 distance: 65 - 66: 35.524 distance: 66 - 67: 13.472 distance: 69 - 70: 24.471 distance: 69 - 72: 41.331 distance: 70 - 71: 30.292 distance: 70 - 80: 24.296 distance: 73 - 75: 41.118 distance: 74 - 76: 4.849 distance: 75 - 77: 45.890 distance: 76 - 78: 46.412 distance: 77 - 78: 40.249 distance: 78 - 79: 37.226 distance: 80 - 81: 42.273 distance: 80 - 86: 8.450 distance: 81 - 82: 15.254 distance: 81 - 84: 41.936 distance: 82 - 83: 41.203 distance: 84 - 85: 50.346 distance: 85 - 86: 43.004 distance: 87 - 88: 53.914 distance: 88 - 89: 41.064 distance: 88 - 91: 24.386 distance: 89 - 90: 40.852 distance: 89 - 92: 54.895 distance: 92 - 93: 45.816 distance: 93 - 94: 33.263 distance: 94 - 95: 28.381 distance: 94 - 96: 31.085 distance: 96 - 97: 33.845 distance: 96 - 155: 21.499 distance: 97 - 98: 39.635 distance: 97 - 100: 41.087 distance: 98 - 99: 6.397 distance: 98 - 105: 22.134 distance: 99 - 152: 26.363 distance: 102 - 103: 34.124 distance: 119 - 128: 3.123