Starting phenix.real_space_refine on Thu Jul 2 05:03:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vz6_43682/07_2026/8vz6_43682.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vz6_43682/07_2026/8vz6_43682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vz6_43682/07_2026/8vz6_43682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vz6_43682/07_2026/8vz6_43682.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vz6_43682/07_2026/8vz6_43682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vz6_43682/07_2026/8vz6_43682.map" } resolution = 3.56 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= 0.000 sd= 0.004 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 98 5.49 5 S 28 5.16 5 C 4098 2.51 5 N 1194 2.21 5 O 1536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 6954 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2442 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 18, 'TRANS': 278} Chain: "R" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1035 Classifications: {'RNA': 49} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 15, 'rna3p_pyr': 20} Link IDs: {'rna2p': 14, 'rna3p': 34} Chain: "B" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2442 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 18, 'TRANS': 278} Chain: "S" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1035 Classifications: {'RNA': 49} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 15, 'rna3p_pyr': 20} Link IDs: {'rna2p': 14, 'rna3p': 34} Time building chain proxies: 1.83, per 1000 atoms: 0.26 Number of scatterers: 6954 At special positions: 0 Unit cell: (92.4885, 138.235, 64.6425, 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 28 16.00 P 98 15.00 O 1536 8.00 N 1194 7.00 C 4098 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: 0.59 Conformation dependent library (CDL) restraints added in 364.5 milliseconds 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1144 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 0 sheets defined 71.0% alpha, 0.0% beta 26 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 13 through 24 removed outlier: 3.713A pdb=" N VAL A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 41 removed outlier: 3.538A pdb=" N THR A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 51 removed outlier: 4.027A pdb=" N ALA A 48 " --> pdb=" O TYR A 44 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYR A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 68 through 110 removed outlier: 4.003A pdb=" N VAL A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 84 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ARG A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 121 removed outlier: 3.739A pdb=" N ASP A 117 " --> pdb=" O TRP A 114 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLY A 118 " --> pdb=" O MET A 115 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N SER A 119 " --> pdb=" O THR A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 139 removed outlier: 4.299A pdb=" N HIS A 129 " --> pdb=" O ARG A 125 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 133 " --> pdb=" O HIS A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 153 Processing helix chain 'A' and resid 159 through 164 Processing helix chain 'A' and resid 168 through 177 removed outlier: 3.535A pdb=" N ASN A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 192 removed outlier: 3.690A pdb=" N LYS A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 215 removed outlier: 3.570A pdb=" N HIS A 215 " --> pdb=" O ASN A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 263 removed outlier: 3.527A pdb=" N LEU A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 279 Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 292 through 300 removed outlier: 3.817A pdb=" N GLU A 296 " --> pdb=" O TRP A 293 " (cutoff:3.500A) Proline residue: A 297 - end of helix removed outlier: 3.680A pdb=" N GLN A 300 " --> pdb=" O PRO A 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 24 removed outlier: 3.758A pdb=" N SER B 19 " --> pdb=" O HIS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 removed outlier: 3.580A pdb=" N THR B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 removed outlier: 4.063A pdb=" N ALA B 48 " --> pdb=" O TYR B 44 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N TYR B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 54 No H-bonds generated for 'chain 'B' and resid 52 through 54' Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 68 through 110 removed outlier: 3.985A pdb=" N VAL B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 84 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LYS B 92 " --> pdb=" O ASN B 88 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE B 93 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG B 98 " --> pdb=" O GLU B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 121 removed outlier: 3.737A pdb=" N ASP B 117 " --> pdb=" O TRP B 114 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLY B 118 " --> pdb=" O MET B 115 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N SER B 119 " --> pdb=" O THR B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 139 removed outlier: 4.301A pdb=" N HIS B 129 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU B 133 " --> pdb=" O HIS B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 153 Processing helix chain 'B' and resid 159 through 164 Processing helix chain 'B' and resid 168 through 177 removed outlier: 3.536A pdb=" N ASN B 174 " --> pdb=" O GLY B 170 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER B 177 " --> pdb=" O THR B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 192 removed outlier: 3.691A pdb=" N LYS B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE B 192 " --> pdb=" O ILE B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 215 removed outlier: 3.573A pdb=" N HIS B 215 " --> pdb=" O ASN B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 263 removed outlier: 3.528A pdb=" N LEU B 252 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE B 261 " --> pdb=" O TYR B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 279 removed outlier: 3.628A pdb=" N ALA B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 292 through 300 removed outlier: 3.809A pdb=" N GLU B 296 " --> pdb=" O TRP B 293 " (cutoff:3.500A) Proline residue: B 297 - end of helix removed outlier: 3.715A pdb=" N GLN B 300 " --> pdb=" O PRO B 297 " (cutoff:3.500A) 239 hydrogen bonds defined for protein. 669 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 0.79 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: 1331 1.33 - 1.45: 2242 1.45 - 1.57: 3506 1.57 - 1.69: 197 1.69 - 1.81: 50 Bond restraints: 7326 Sorted by residual: bond pdb=" N9 A S 33 " pdb=" C4 A S 33 " ideal model delta sigma weight residual 1.374 1.389 -0.015 6.00e-03 2.78e+04 6.38e+00 bond pdb=" N9 A R 33 " pdb=" C4 A R 33 " ideal model delta sigma weight residual 1.374 1.389 -0.015 6.00e-03 2.78e+04 5.89e+00 bond pdb=" N1 C R 9 " pdb=" C2 C R 9 " ideal model delta sigma weight residual 1.397 1.419 -0.022 1.00e-02 1.00e+04 4.95e+00 bond pdb=" N1 C S 12 " pdb=" C2 C S 12 " ideal model delta sigma weight residual 1.397 1.419 -0.022 1.00e-02 1.00e+04 4.89e+00 bond pdb=" N1 C R 12 " pdb=" C2 C R 12 " ideal model delta sigma weight residual 1.397 1.419 -0.022 1.00e-02 1.00e+04 4.75e+00 ... (remaining 7321 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 10037 2.85 - 5.71: 307 5.71 - 8.56: 40 8.56 - 11.42: 2 11.42 - 14.27: 4 Bond angle restraints: 10390 Sorted by residual: angle pdb=" C2 C S 25 " pdb=" N1 C S 25 " pdb=" C6 C S 25 " ideal model delta sigma weight residual 120.30 116.51 3.79 4.00e-01 6.25e+00 8.98e+01 angle pdb=" C2 C R 25 " pdb=" N1 C R 25 " pdb=" C6 C R 25 " ideal model delta sigma weight residual 120.30 116.57 3.73 4.00e-01 6.25e+00 8.71e+01 angle pdb=" N1 C R 20 " pdb=" C2 C R 20 " pdb=" O2 C R 20 " ideal model delta sigma weight residual 118.90 123.49 -4.59 6.00e-01 2.78e+00 5.86e+01 angle pdb=" N1 C S 20 " pdb=" C2 C S 20 " pdb=" O2 C S 20 " ideal model delta sigma weight residual 118.90 123.45 -4.55 6.00e-01 2.78e+00 5.75e+01 angle pdb=" O2 C S 25 " pdb=" C2 C S 25 " pdb=" N3 C S 25 " ideal model delta sigma weight residual 121.90 116.84 5.06 7.00e-01 2.04e+00 5.22e+01 ... (remaining 10385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.63: 4155 31.63 - 63.26: 302 63.26 - 94.89: 81 94.89 - 126.51: 0 126.51 - 158.14: 4 Dihedral angle restraints: 4542 sinusoidal: 2780 harmonic: 1762 Sorted by residual: dihedral pdb=" CA PRO A 159 " pdb=" C PRO A 159 " pdb=" N ALA A 160 " pdb=" CA ALA A 160 " ideal model delta harmonic sigma weight residual -180.00 -154.21 -25.79 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA PRO B 159 " pdb=" C PRO B 159 " pdb=" N ALA B 160 " pdb=" CA ALA B 160 " ideal model delta harmonic sigma weight residual 180.00 -154.25 -25.75 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" O4' C R 25 " pdb=" C1' C R 25 " pdb=" N1 C R 25 " pdb=" C2 C R 25 " ideal model delta sinusoidal sigma weight residual -128.00 -50.37 -77.63 1 1.70e+01 3.46e-03 2.61e+01 ... (remaining 4539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1063 0.082 - 0.164: 143 0.164 - 0.246: 19 0.246 - 0.328: 2 0.328 - 0.410: 3 Chirality restraints: 1230 Sorted by residual: chirality pdb=" CG LEU B 17 " pdb=" CB LEU B 17 " pdb=" CD1 LEU B 17 " pdb=" CD2 LEU B 17 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" C3' C R 40 " pdb=" C4' C R 40 " pdb=" O3' C R 40 " pdb=" C2' C R 40 " both_signs ideal model delta sigma weight residual False -2.48 -2.10 -0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" C3' C S 40 " pdb=" C4' C S 40 " pdb=" O3' C S 40 " pdb=" C2' C S 40 " both_signs ideal model delta sigma weight residual False -2.48 -2.10 -0.37 2.00e-01 2.50e+01 3.50e+00 ... (remaining 1227 not shown) Planarity restraints: 954 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 44 " -0.012 2.00e-02 2.50e+03 2.34e-02 1.09e+01 pdb=" CG TYR B 44 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR B 44 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR B 44 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR B 44 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 44 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 44 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 44 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 44 " -0.013 2.00e-02 2.50e+03 2.27e-02 1.03e+01 pdb=" CG TYR A 44 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR A 44 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 44 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR A 44 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 44 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 44 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 44 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 289 " 0.007 2.00e-02 2.50e+03 1.99e-02 6.91e+00 pdb=" CG PHE B 289 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE B 289 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE B 289 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE B 289 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 289 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 289 " -0.008 2.00e-02 2.50e+03 ... (remaining 951 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1376 2.78 - 3.31: 5950 3.31 - 3.84: 12336 3.84 - 4.37: 14365 4.37 - 4.90: 22246 Nonbonded interactions: 56273 Sorted by model distance: nonbonded pdb=" O ASP A 273 " pdb=" OG SER A 277 " model vdw 2.255 3.040 nonbonded pdb=" O ARG B 227 " pdb=" O2' A S 7 " model vdw 2.316 3.040 nonbonded pdb=" O ARG A 227 " pdb=" O2' A R 7 " model vdw 2.325 3.040 nonbonded pdb=" O ASP B 273 " pdb=" OG SER B 277 " model vdw 2.337 3.040 nonbonded pdb=" OG1 THR B 204 " pdb=" N4 C S 2 " model vdw 2.424 3.120 ... (remaining 56268 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'R' selection = chain 'S' } 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 group one per residue 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: 1.210 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: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 8.610 Find NCS groups from input model: 0.140 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: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 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 : 0.006 0.067 7326 Z= 0.357 Angle : 1.160 14.274 10390 Z= 0.887 Chirality : 0.060 0.410 1230 Planarity : 0.008 0.046 954 Dihedral : 21.093 158.143 3398 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.37 % Allowed : 9.18 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.30), residues: 590 helix: -1.38 (0.22), residues: 340 sheet: None (None), residues: 0 loop : -0.14 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 36 TYR 0.054 0.004 TYR B 44 PHE 0.042 0.004 PHE B 289 TRP 0.039 0.004 TRP A 220 HIS 0.006 0.002 HIS B 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.36 ( 7326) covalent geometry : angle 1.15979 / 0.89 (10390) hydrogen bonds : bond 0.15620 / 10.05 ( 311) hydrogen bonds : angle 5.55665 / 3.83 ( 805) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.220 Fit side-chains REVERT: A 120 ASN cc_start: 0.7184 (OUTLIER) cc_final: 0.6641 (t0) REVERT: B 120 ASN cc_start: 0.7188 (OUTLIER) cc_final: 0.6673 (t0) outliers start: 2 outliers final: 0 residues processed: 99 average time/residue: 0.0919 time to fit residues: 12.0997 Evaluate side-chains 67 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain B residue 120 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN B 151 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.166483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.138875 restraints weight = 10239.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.141546 restraints weight = 6286.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.143349 restraints weight = 4676.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.144406 restraints weight = 3895.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.144935 restraints weight = 3491.027| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7326 Z= 0.178 Angle : 0.636 7.098 10390 Z= 0.357 Chirality : 0.042 0.207 1230 Planarity : 0.006 0.051 954 Dihedral : 22.994 169.381 2182 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.62 % Allowed : 11.61 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.34), residues: 590 helix: 0.02 (0.27), residues: 350 sheet: None (None), residues: 0 loop : 0.40 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 125 TYR 0.012 0.002 TYR A 44 PHE 0.016 0.002 PHE B 289 TRP 0.013 0.002 TRP B 220 HIS 0.002 0.001 HIS B 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 ( 7326) covalent geometry : angle 0.63620 / 0.36 (10390) hydrogen bonds : bond 0.06856 / 4.54 ( 311) hydrogen bonds : angle 3.91768 / 2.70 ( 805) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ASN cc_start: 0.7770 (OUTLIER) cc_final: 0.7043 (t0) outliers start: 14 outliers final: 10 residues processed: 90 average time/residue: 0.0759 time to fit residues: 9.2253 Evaluate side-chains 82 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 181 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 20.0000 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 chunk 11 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 32 optimal weight: 20.0000 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN A 266 ASN B 151 GLN B 266 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.167912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.140439 restraints weight = 10123.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.143205 restraints weight = 6110.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.145081 restraints weight = 4487.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.146282 restraints weight = 3692.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.146982 restraints weight = 3270.671| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7326 Z= 0.125 Angle : 0.532 7.920 10390 Z= 0.293 Chirality : 0.037 0.184 1230 Planarity : 0.005 0.049 954 Dihedral : 22.964 173.237 2180 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.87 % Allowed : 14.04 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.34), residues: 590 helix: 0.42 (0.27), residues: 350 sheet: None (None), residues: 0 loop : 0.55 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 125 TYR 0.009 0.001 TYR A 249 PHE 0.010 0.001 PHE A 289 TRP 0.005 0.001 TRP B 220 HIS 0.002 0.000 HIS A 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 7326) covalent geometry : angle 0.53249 / 0.29 (10390) hydrogen bonds : bond 0.05552 / 3.68 ( 311) hydrogen bonds : angle 3.46599 / 2.42 ( 805) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ASN cc_start: 0.7892 (OUTLIER) cc_final: 0.7527 (t0) outliers start: 10 outliers final: 6 residues processed: 92 average time/residue: 0.0759 time to fit residues: 9.8543 Evaluate side-chains 80 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 284 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 64 optimal weight: 30.0000 chunk 36 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN B 151 GLN B 266 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.164337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.136231 restraints weight = 10257.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.138959 restraints weight = 6285.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.140741 restraints weight = 4643.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.141830 restraints weight = 3848.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.142511 restraints weight = 3441.186| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7326 Z= 0.185 Angle : 0.578 8.919 10390 Z= 0.313 Chirality : 0.039 0.195 1230 Planarity : 0.006 0.055 954 Dihedral : 23.019 173.256 2180 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.62 % Allowed : 15.17 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.34), residues: 590 helix: 0.47 (0.27), residues: 350 sheet: None (None), residues: 0 loop : 0.39 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 24 TYR 0.011 0.001 TYR B 11 PHE 0.023 0.002 PHE A 289 TRP 0.009 0.001 TRP A 220 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 ( 7326) covalent geometry : angle 0.57824 / 0.31 (10390) hydrogen bonds : bond 0.06143 / 4.05 ( 311) hydrogen bonds : angle 3.58234 / 2.50 ( 805) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 82 average time/residue: 0.0620 time to fit residues: 7.6271 Evaluate side-chains 75 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 284 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 45 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 48 optimal weight: 0.0040 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 30.0000 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN B 151 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.168093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.140518 restraints weight = 10220.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.143308 restraints weight = 6184.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.145112 restraints weight = 4532.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.146180 restraints weight = 3741.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.147035 restraints weight = 3334.895| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7326 Z= 0.109 Angle : 0.496 7.710 10390 Z= 0.270 Chirality : 0.035 0.184 1230 Planarity : 0.005 0.056 954 Dihedral : 23.005 174.939 2178 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.87 % Allowed : 15.73 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.34), residues: 590 helix: 0.79 (0.28), residues: 344 sheet: None (None), residues: 0 loop : 0.35 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 36 TYR 0.007 0.001 TYR B 249 PHE 0.010 0.001 PHE A 78 TRP 0.007 0.001 TRP A 220 HIS 0.002 0.000 HIS A 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 7326) covalent geometry : angle 0.49643 / 0.27 (10390) hydrogen bonds : bond 0.04991 / 3.31 ( 311) hydrogen bonds : angle 3.29193 / 2.33 ( 805) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 86 average time/residue: 0.0605 time to fit residues: 7.6894 Evaluate side-chains 76 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 284 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- 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: 67.5331 > 50: distance: 36 - 43: 13.061 distance: 43 - 44: 26.561 distance: 44 - 45: 20.243 distance: 45 - 46: 17.264 distance: 45 - 47: 7.450 distance: 47 - 48: 25.386 distance: 48 - 49: 24.451 distance: 48 - 51: 14.336 distance: 49 - 55: 47.030 distance: 51 - 52: 22.408 distance: 52 - 53: 34.428 distance: 52 - 54: 27.365 distance: 55 - 56: 11.368 distance: 56 - 57: 10.360 distance: 56 - 59: 46.953 distance: 57 - 64: 25.869 distance: 58 - 83: 4.537 distance: 59 - 60: 19.359 distance: 60 - 61: 19.910 distance: 61 - 62: 49.974 distance: 64 - 65: 23.836 distance: 65 - 66: 34.990 distance: 65 - 68: 27.841 distance: 66 - 67: 3.239 distance: 66 - 71: 26.078 distance: 67 - 94: 43.398 distance: 68 - 70: 39.662 distance: 71 - 72: 44.829 distance: 72 - 73: 32.165 distance: 73 - 74: 32.917 distance: 73 - 76: 8.297 distance: 74 - 103: 39.257 distance: 76 - 77: 22.982 distance: 76 - 82: 34.202 distance: 77 - 78: 8.480 distance: 77 - 80: 35.341 distance: 78 - 79: 11.825 distance: 78 - 83: 41.482 distance: 79 - 109: 8.716 distance: 80 - 81: 30.245 distance: 81 - 82: 15.426 distance: 83 - 84: 10.499 distance: 84 - 85: 17.659 distance: 84 - 87: 14.417 distance: 85 - 86: 22.260 distance: 85 - 94: 8.266 distance: 86 - 123: 25.567 distance: 87 - 88: 31.480 distance: 88 - 89: 40.633 distance: 88 - 90: 4.700 distance: 89 - 91: 6.301 distance: 90 - 92: 15.774 distance: 91 - 93: 11.742 distance: 92 - 93: 28.055 distance: 94 - 95: 20.166 distance: 95 - 96: 15.453 distance: 95 - 98: 28.342 distance: 96 - 97: 39.339 distance: 96 - 103: 31.165 distance: 97 - 131: 36.308 distance: 98 - 99: 41.557 distance: 99 - 100: 25.382 distance: 100 - 101: 44.106 distance: 100 - 102: 11.240 distance: 103 - 104: 16.901 distance: 104 - 105: 42.071 distance: 104 - 107: 26.894 distance: 105 - 109: 11.301 distance: 106 - 137: 33.374 distance: 107 - 108: 53.240 distance: 109 - 110: 14.948 distance: 110 - 111: 23.567 distance: 110 - 113: 30.693 distance: 111 - 112: 19.676 distance: 111 - 123: 11.884 distance: 112 - 145: 24.401 distance: 113 - 114: 22.368 distance: 114 - 115: 14.319 distance: 114 - 116: 14.922 distance: 115 - 117: 12.693 distance: 116 - 118: 20.670 distance: 116 - 119: 19.911 distance: 118 - 120: 3.084 distance: 119 - 121: 13.980 distance: 120 - 122: 5.682 distance: 121 - 122: 23.162