Starting phenix.real_space_refine on Fri Jul 3 05:36:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gfm_51313/07_2026/9gfm_51313.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gfm_51313/07_2026/9gfm_51313.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gfm_51313/07_2026/9gfm_51313.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gfm_51313/07_2026/9gfm_51313.map" model { file = "/net/cci-nas-00/data/ceres_data/9gfm_51313/07_2026/9gfm_51313.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gfm_51313/07_2026/9gfm_51313.cif" } resolution = 3.8 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= 0.046 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 278 5.49 5 S 14 5.16 5 C 6736 2.51 5 N 2277 2.21 5 O 2820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 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: 12125 Number of models: 1 Model: "" Number of chains: 11 Chain: "H" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 404 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'TRANS': 49} Chain: "K" Number of atoms: 2868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2868 Classifications: {'DNA': 139} Link IDs: {'rna3p': 138} Chain: "L" Number of atoms: 2831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2831 Classifications: {'DNA': 139} Link IDs: {'rna3p': 138} Chain: "M" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 756 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "N" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "O" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "P" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 755 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "Q" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 825 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "R" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "S" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 854 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "T" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 732 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Time building chain proxies: 2.45, per 1000 atoms: 0.20 Number of scatterers: 12125 At special positions: 0 Unit cell: (116.439, 134.272, 112.243, 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 14 16.00 P 278 15.00 O 2820 8.00 N 2277 7.00 C 6736 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: 0.78 Conformation dependent library (CDL) restraints added in 314.5 milliseconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 10 sheets defined 72.3% alpha, 3.0% beta 135 base pairs and 223 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'H' and resid 141 through 159 removed outlier: 4.038A pdb=" N GLU H 145 " --> pdb=" O LEU H 141 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU H 148 " --> pdb=" O GLN H 144 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU H 149 " --> pdb=" O GLU H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 176 Processing helix chain 'H' and resid 177 through 188 Processing helix chain 'M' and resid 44 through 57 removed outlier: 4.257A pdb=" N LEU M 48 " --> pdb=" O GLY M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 76 Processing helix chain 'M' and resid 85 through 114 removed outlier: 3.554A pdb=" N VAL M 89 " --> pdb=" O GLN M 85 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET M 90 " --> pdb=" O SER M 86 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP M 106 " --> pdb=" O GLY M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 132 Processing helix chain 'N' and resid 24 through 29 removed outlier: 3.884A pdb=" N GLN N 27 " --> pdb=" O ASP N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 41 Processing helix chain 'N' and resid 49 through 76 removed outlier: 3.722A pdb=" N GLU N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY N 56 " --> pdb=" O GLU N 52 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP N 68 " --> pdb=" O ASN N 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 93 removed outlier: 3.593A pdb=" N VAL N 86 " --> pdb=" O THR N 82 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA N 89 " --> pdb=" O ASP N 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 22 Processing helix chain 'O' and resid 26 through 37 Processing helix chain 'O' and resid 45 through 73 removed outlier: 4.489A pdb=" N VAL O 49 " --> pdb=" O ALA O 45 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 90 removed outlier: 3.638A pdb=" N LEU O 83 " --> pdb=" O ILE O 79 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP O 90 " --> pdb=" O ALA O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 97 Processing helix chain 'O' and resid 112 through 116 Processing helix chain 'P' and resid 37 through 46 Processing helix chain 'P' and resid 55 through 84 removed outlier: 3.703A pdb=" N ARG P 79 " --> pdb=" O GLY P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 102 removed outlier: 4.720A pdb=" N THR P 96 " --> pdb=" O ARG P 92 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG P 99 " --> pdb=" O GLN P 95 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU P 102 " --> pdb=" O VAL P 98 " (cutoff:3.500A) Processing helix chain 'P' and resid 103 through 125 removed outlier: 3.509A pdb=" N LYS P 108 " --> pdb=" O GLY P 104 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 57 Processing helix chain 'Q' and resid 63 through 76 Processing helix chain 'Q' and resid 87 through 114 Processing helix chain 'Q' and resid 120 through 131 removed outlier: 3.564A pdb=" N ILE Q 124 " --> pdb=" O MET Q 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 29 Processing helix chain 'R' and resid 30 through 41 Processing helix chain 'R' and resid 49 through 76 removed outlier: 3.573A pdb=" N GLU R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY R 56 " --> pdb=" O GLU R 52 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP R 68 " --> pdb=" O ASN R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 93 Processing helix chain 'S' and resid 16 through 22 Processing helix chain 'S' and resid 26 through 37 Processing helix chain 'S' and resid 45 through 73 removed outlier: 4.309A pdb=" N VAL S 49 " --> pdb=" O ALA S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 90 Processing helix chain 'S' and resid 90 through 97 removed outlier: 3.795A pdb=" N LYS S 95 " --> pdb=" O GLU S 91 " (cutoff:3.500A) Processing helix chain 'S' and resid 112 through 116 Processing helix chain 'T' and resid 37 through 49 Processing helix chain 'T' and resid 55 through 83 removed outlier: 4.035A pdb=" N ASN T 67 " --> pdb=" O ASN T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 90 through 102 Processing helix chain 'T' and resid 104 through 123 removed outlier: 3.929A pdb=" N LYS T 108 " --> pdb=" O GLY T 104 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER T 123 " --> pdb=" O THR T 119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 83 through 84 removed outlier: 6.895A pdb=" N ARG M 83 " --> pdb=" O VAL N 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'M' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'N' and resid 96 through 98 removed outlier: 6.712A pdb=" N THR N 96 " --> pdb=" O THR S 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'O' and resid 42 through 43 removed outlier: 7.071A pdb=" N ARG O 42 " --> pdb=" O ILE P 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'O' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'O' and resid 100 through 102 removed outlier: 6.743A pdb=" N THR O 101 " --> pdb=" O TYR R 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'Q' and resid 83 through 84 removed outlier: 7.065A pdb=" N ARG Q 83 " --> pdb=" O VAL R 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'Q' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'S' and resid 42 through 43 removed outlier: 6.996A pdb=" N ARG S 42 " --> pdb=" O ILE T 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'S' and resid 77 through 78 409 hydrogen bonds defined for protein. 1197 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 344 hydrogen bonds 684 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 223 stacking parallelities Total time for adding SS restraints: 2.16 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3039 1.34 - 1.46: 3607 1.46 - 1.58: 5671 1.58 - 1.70: 555 1.70 - 1.82: 24 Bond restraints: 12896 Sorted by residual: bond pdb=" CA ARG P 92 " pdb=" C ARG P 92 " ideal model delta sigma weight residual 1.522 1.644 -0.122 1.45e-02 4.76e+03 7.09e+01 bond pdb=" C4 DC K 46 " pdb=" N4 DC K 46 " ideal model delta sigma weight residual 1.335 1.294 0.041 9.00e-03 1.23e+04 2.07e+01 bond pdb=" C5' DT L -58 " pdb=" C4' DT L -58 " ideal model delta sigma weight residual 1.512 1.543 -0.031 7.00e-03 2.04e+04 2.01e+01 bond pdb=" C4 DC L 14 " pdb=" N4 DC L 14 " ideal model delta sigma weight residual 1.335 1.295 0.040 9.00e-03 1.23e+04 1.98e+01 bond pdb=" C4 DC L -40 " pdb=" N4 DC L -40 " ideal model delta sigma weight residual 1.335 1.295 0.040 9.00e-03 1.23e+04 1.95e+01 ... (remaining 12891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.53: 17444 3.53 - 7.06: 1117 7.06 - 10.58: 29 10.58 - 14.11: 3 14.11 - 17.64: 1 Bond angle restraints: 18594 Sorted by residual: angle pdb=" N6 DA L -47 " pdb=" C6 DA L -47 " pdb=" N1 DA L -47 " ideal model delta sigma weight residual 118.60 111.07 7.53 6.00e-01 2.78e+00 1.58e+02 angle pdb=" N6 DA L 28 " pdb=" C6 DA L 28 " pdb=" N1 DA L 28 " ideal model delta sigma weight residual 118.60 111.90 6.70 6.00e-01 2.78e+00 1.25e+02 angle pdb=" O5' DG L -33 " pdb=" C5' DG L -33 " pdb=" C4' DG L -33 " ideal model delta sigma weight residual 109.40 118.02 -8.62 8.00e-01 1.56e+00 1.16e+02 angle pdb=" N6 DA K 48 " pdb=" C6 DA K 48 " pdb=" N1 DA K 48 " ideal model delta sigma weight residual 118.60 112.30 6.30 6.00e-01 2.78e+00 1.10e+02 angle pdb=" N GLU P 93 " pdb=" CA GLU P 93 " pdb=" CB GLU P 93 " ideal model delta sigma weight residual 110.49 92.85 17.64 1.69e+00 3.50e-01 1.09e+02 ... (remaining 18589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.43: 5896 34.43 - 68.86: 1146 68.86 - 103.29: 28 103.29 - 137.72: 0 137.72 - 172.15: 1 Dihedral angle restraints: 7071 sinusoidal: 4737 harmonic: 2334 Sorted by residual: dihedral pdb=" C ARG P 92 " pdb=" N ARG P 92 " pdb=" CA ARG P 92 " pdb=" CB ARG P 92 " ideal model delta harmonic sigma weight residual -122.60 -137.36 14.76 0 2.50e+00 1.60e-01 3.49e+01 dihedral pdb=" CA THR T 88 " pdb=" C THR T 88 " pdb=" N ILE T 89 " pdb=" CA ILE T 89 " ideal model delta harmonic sigma weight residual 180.00 150.73 29.27 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA LEU T 100 " pdb=" C LEU T 100 " pdb=" N LEU T 101 " pdb=" CA LEU T 101 " ideal model delta harmonic sigma weight residual -180.00 -150.93 -29.07 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 7068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1601 0.098 - 0.195: 451 0.195 - 0.293: 46 0.293 - 0.390: 8 0.390 - 0.488: 3 Chirality restraints: 2109 Sorted by residual: chirality pdb=" C3' DC L 20 " pdb=" C4' DC L 20 " pdb=" O3' DC L 20 " pdb=" C2' DC L 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.24 -0.49 2.00e-01 2.50e+01 5.96e+00 chirality pdb=" CA ARG P 92 " pdb=" N ARG P 92 " pdb=" C ARG P 92 " pdb=" CB ARG P 92 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.45e+00 chirality pdb=" CA LYS R 79 " pdb=" N LYS R 79 " pdb=" C LYS R 79 " pdb=" CB LYS R 79 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.44 2.00e-01 2.50e+01 4.74e+00 ... (remaining 2106 not shown) Planarity restraints: 1401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT K 6 " 0.372 2.00e-02 2.50e+03 2.08e-01 1.08e+03 pdb=" N1 DT K 6 " 0.035 2.00e-02 2.50e+03 pdb=" C2 DT K 6 " -0.064 2.00e-02 2.50e+03 pdb=" O2 DT K 6 " -0.351 2.00e-02 2.50e+03 pdb=" N3 DT K 6 " 0.019 2.00e-02 2.50e+03 pdb=" C4 DT K 6 " 0.091 2.00e-02 2.50e+03 pdb=" O4 DT K 6 " 0.301 2.00e-02 2.50e+03 pdb=" C5 DT K 6 " -0.089 2.00e-02 2.50e+03 pdb=" C7 DT K 6 " -0.227 2.00e-02 2.50e+03 pdb=" C6 DT K 6 " -0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG K 26 " 0.439 2.00e-02 2.50e+03 1.76e-01 9.26e+02 pdb=" N9 DG K 26 " -0.070 2.00e-02 2.50e+03 pdb=" C8 DG K 26 " -0.224 2.00e-02 2.50e+03 pdb=" N7 DG K 26 " -0.140 2.00e-02 2.50e+03 pdb=" C5 DG K 26 " -0.040 2.00e-02 2.50e+03 pdb=" C6 DG K 26 " 0.098 2.00e-02 2.50e+03 pdb=" O6 DG K 26 " 0.213 2.00e-02 2.50e+03 pdb=" N1 DG K 26 " 0.094 2.00e-02 2.50e+03 pdb=" C2 DG K 26 " -0.043 2.00e-02 2.50e+03 pdb=" N2 DG K 26 " -0.113 2.00e-02 2.50e+03 pdb=" N3 DG K 26 " -0.115 2.00e-02 2.50e+03 pdb=" C4 DG K 26 " -0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT K 47 " -0.365 2.00e-02 2.50e+03 1.88e-01 8.81e+02 pdb=" N1 DT K 47 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DT K 47 " 0.094 2.00e-02 2.50e+03 pdb=" O2 DT K 47 " 0.282 2.00e-02 2.50e+03 pdb=" N3 DT K 47 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DT K 47 " -0.100 2.00e-02 2.50e+03 pdb=" O4 DT K 47 " -0.267 2.00e-02 2.50e+03 pdb=" C5 DT K 47 " 0.081 2.00e-02 2.50e+03 pdb=" C7 DT K 47 " 0.177 2.00e-02 2.50e+03 pdb=" C6 DT K 47 " 0.108 2.00e-02 2.50e+03 ... (remaining 1398 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 5825 3.01 - 3.49: 13500 3.49 - 3.96: 23156 3.96 - 4.43: 26209 4.43 - 4.90: 34712 Nonbonded interactions: 103402 Sorted by model distance: nonbonded pdb=" OP2 DC L -54 " pdb=" OG SER T 56 " model vdw 2.543 3.040 nonbonded pdb=" OG1 THR T 90 " pdb=" OE1 GLU T 93 " model vdw 2.550 3.040 nonbonded pdb=" OH TYR Q 99 " pdb=" OE1 GLU Q 133 " model vdw 2.551 3.040 nonbonded pdb=" OP1 DG K -34 " pdb=" OG1 THR P 88 " model vdw 2.574 3.040 nonbonded pdb=" OP1 DC L 48 " pdb=" OH TYR P 40 " model vdw 2.575 3.040 ... (remaining 103397 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 Found NCS groups: ncs_group { reference = chain 'M' selection = (chain 'Q' and resid 43 through 135) } ncs_group { reference = (chain 'N' and resid 24 through 102) selection = chain 'R' } ncs_group { reference = chain 'O' selection = (chain 'S' and resid 13 through 118) } ncs_group { reference = (chain 'P' and resid 31 through 123) selection = (chain 'T' and (resid 31 through 122 or (resid 123 and (name N or name CA or nam \ e C or name O or name CB or name OG )))) } 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: 4.240 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.210 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 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 : 0.013 0.122 12896 Z= 1.224 Angle : 1.882 17.640 18594 Z= 1.878 Chirality : 0.088 0.488 2109 Planarity : 0.036 0.208 1401 Dihedral : 26.362 172.148 5567 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.79 % Favored : 95.71 % Rotamer: Outliers : 1.19 % Allowed : 3.58 % Favored : 95.23 % Cbeta Deviations : 0.53 % 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: -0.89 (0.28), residues: 792 helix: -0.52 (0.20), residues: 558 sheet: None (None), residues: 0 loop : -0.31 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG M 129 TYR 0.136 0.021 TYR Q 54 PHE 0.044 0.010 PHE M 84 TRP 0.054 0.026 TRP H 152 HIS 0.010 0.003 HIS P 82 Details of bonding type rmsd/Z covalent geometry : bond 0.01281 / 1.22 (12896) covalent geometry : angle 1.88245 / 1.88 (18594) hydrogen bonds : bond 0.11870 / 12.23 ( 753) hydrogen bonds : angle 6.45087 / 7.52 ( 1881) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 374 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 161 LEU cc_start: 0.8872 (mt) cc_final: 0.8307 (mp) REVERT: H 164 ASN cc_start: 0.9081 (m110) cc_final: 0.8694 (p0) REVERT: H 180 GLN cc_start: 0.9495 (mt0) cc_final: 0.9089 (mt0) REVERT: M 58 THR cc_start: 0.9315 (p) cc_final: 0.9081 (t) REVERT: M 81 ASP cc_start: 0.9106 (m-30) cc_final: 0.8808 (p0) REVERT: M 97 GLU cc_start: 0.9265 (mt-10) cc_final: 0.9055 (mt-10) REVERT: M 101 VAL cc_start: 0.9496 (t) cc_final: 0.9290 (m) REVERT: M 118 THR cc_start: 0.9196 (m) cc_final: 0.8905 (p) REVERT: N 84 MET cc_start: 0.9055 (mmm) cc_final: 0.8553 (mmm) REVERT: N 98 TYR cc_start: 0.9649 (m-10) cc_final: 0.9424 (m-80) REVERT: O 35 ARG cc_start: 0.8857 (mtm-85) cc_final: 0.8528 (mtm-85) REVERT: O 50 TYR cc_start: 0.9215 (t80) cc_final: 0.8964 (t80) REVERT: O 90 ASP cc_start: 0.8104 (t70) cc_final: 0.7401 (t0) REVERT: O 91 GLU cc_start: 0.9218 (pm20) cc_final: 0.8718 (tm-30) REVERT: O 111 ILE cc_start: 0.9673 (mm) cc_final: 0.9455 (mp) REVERT: O 118 LYS cc_start: 0.8741 (mmmt) cc_final: 0.8382 (mtmm) REVERT: P 68 ASP cc_start: 0.9457 (t70) cc_final: 0.9251 (t0) REVERT: P 86 ARG cc_start: 0.9005 (mmt-90) cc_final: 0.8766 (ttm-80) REVERT: P 125 LYS cc_start: 0.8710 (mttt) cc_final: 0.8373 (tppt) REVERT: Q 70 LEU cc_start: 0.9245 (tp) cc_final: 0.8994 (tt) REVERT: Q 77 ASP cc_start: 0.9469 (m-30) cc_final: 0.8993 (m-30) REVERT: Q 93 GLN cc_start: 0.9235 (tt0) cc_final: 0.9014 (tt0) REVERT: R 39 ARG cc_start: 0.9091 (mmt90) cc_final: 0.8829 (tpp-160) REVERT: R 93 GLN cc_start: 0.8544 (mt0) cc_final: 0.7992 (mt0) REVERT: R 100 PHE cc_start: 0.9302 (m-80) cc_final: 0.9037 (m-10) REVERT: S 39 TYR cc_start: 0.9446 (m-80) cc_final: 0.9205 (m-80) REVERT: S 90 ASP cc_start: 0.9174 (t0) cc_final: 0.8951 (t0) REVERT: T 51 ASP cc_start: 0.9333 (p0) cc_final: 0.9129 (t0) REVERT: T 54 ILE cc_start: 0.9296 (mm) cc_final: 0.8943 (tt) REVERT: T 57 LYS cc_start: 0.9365 (mppt) cc_final: 0.9156 (tppt) REVERT: T 68 ASP cc_start: 0.9483 (t0) cc_final: 0.9004 (t0) REVERT: T 93 GLU cc_start: 0.9225 (mp0) cc_final: 0.8997 (mm-30) REVERT: T 106 LEU cc_start: 0.9284 (mt) cc_final: 0.8943 (mp) outliers start: 8 outliers final: 2 residues processed: 377 average time/residue: 0.1330 time to fit residues: 67.5867 Evaluate side-chains 281 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 279 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 96 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 164 ASN P 47 GLN ** P 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.072851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.051982 restraints weight = 45871.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.053650 restraints weight = 22673.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.054771 restraints weight = 15150.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.055451 restraints weight = 11906.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.055872 restraints weight = 10388.916| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12896 Z= 0.221 Angle : 0.931 8.910 18594 Z= 0.528 Chirality : 0.061 0.269 2109 Planarity : 0.006 0.043 1401 Dihedral : 30.364 175.846 3952 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.53 % Favored : 97.22 % Rotamer: Outliers : 3.28 % Allowed : 19.97 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.29), residues: 792 helix: 0.48 (0.21), residues: 561 sheet: None (None), residues: 0 loop : -0.57 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 36 TYR 0.028 0.003 TYR T 83 PHE 0.011 0.002 PHE N 100 TRP 0.017 0.004 TRP H 152 HIS 0.006 0.002 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.22 (12896) covalent geometry : angle 0.93080 / 0.53 (18594) hydrogen bonds : bond 0.06656 / 5.51 ( 753) hydrogen bonds : angle 3.73389 / 4.19 ( 1881) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 300 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 147 GLU cc_start: 0.8952 (pp20) cc_final: 0.8684 (pp20) REVERT: H 151 ARG cc_start: 0.9172 (mtt-85) cc_final: 0.8704 (ptt180) REVERT: H 180 GLN cc_start: 0.9491 (mt0) cc_final: 0.9091 (mt0) REVERT: M 54 TYR cc_start: 0.9260 (m-10) cc_final: 0.9009 (m-10) REVERT: M 93 GLN cc_start: 0.8957 (tt0) cc_final: 0.8573 (tp40) REVERT: M 108 ASN cc_start: 0.9378 (t0) cc_final: 0.8896 (m-40) REVERT: M 122 LYS cc_start: 0.8991 (ttpt) cc_final: 0.8610 (ttpp) REVERT: N 44 LYS cc_start: 0.9456 (ttpt) cc_final: 0.8918 (ttmm) REVERT: N 84 MET cc_start: 0.8938 (mmm) cc_final: 0.8219 (mmm) REVERT: N 98 TYR cc_start: 0.9395 (m-10) cc_final: 0.8835 (m-80) REVERT: O 84 GLN cc_start: 0.9328 (tp40) cc_final: 0.9111 (tp40) REVERT: O 90 ASP cc_start: 0.7758 (t70) cc_final: 0.7229 (t0) REVERT: O 91 GLU cc_start: 0.8716 (pm20) cc_final: 0.8305 (tm-30) REVERT: O 95 LYS cc_start: 0.9420 (OUTLIER) cc_final: 0.9000 (ttmm) REVERT: O 116 LEU cc_start: 0.9448 (mt) cc_final: 0.9049 (pp) REVERT: P 68 ASP cc_start: 0.9246 (t70) cc_final: 0.8795 (t0) REVERT: P 71 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8775 (tm-30) REVERT: P 93 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8397 (pt0) REVERT: P 125 LYS cc_start: 0.8463 (mttt) cc_final: 0.7998 (tppt) REVERT: Q 77 ASP cc_start: 0.8015 (m-30) cc_final: 0.7789 (m-30) REVERT: Q 107 THR cc_start: 0.9422 (m) cc_final: 0.9089 (p) REVERT: Q 123 ASP cc_start: 0.8978 (m-30) cc_final: 0.7916 (m-30) REVERT: R 84 MET cc_start: 0.8847 (mmm) cc_final: 0.8392 (mmp) REVERT: R 92 ARG cc_start: 0.8993 (tmm-80) cc_final: 0.8681 (tmm-80) REVERT: S 39 TYR cc_start: 0.8799 (m-80) cc_final: 0.8287 (m-80) REVERT: S 56 GLU cc_start: 0.8753 (tt0) cc_final: 0.8353 (tt0) REVERT: S 59 THR cc_start: 0.9195 (m) cc_final: 0.8864 (p) REVERT: S 89 ASN cc_start: 0.9458 (m-40) cc_final: 0.8944 (m-40) REVERT: S 90 ASP cc_start: 0.8762 (t0) cc_final: 0.8155 (t0) REVERT: S 104 GLN cc_start: 0.9087 (mt0) cc_final: 0.8858 (mt0) REVERT: S 108 LEU cc_start: 0.9218 (tp) cc_final: 0.8960 (pt) REVERT: T 34 LYS cc_start: 0.9095 (mmtm) cc_final: 0.8759 (mmmm) REVERT: T 51 ASP cc_start: 0.8278 (p0) cc_final: 0.7796 (t0) REVERT: T 57 LYS cc_start: 0.9212 (mppt) cc_final: 0.8924 (mmmt) REVERT: T 64 SER cc_start: 0.9191 (m) cc_final: 0.8407 (p) REVERT: T 68 ASP cc_start: 0.8845 (t0) cc_final: 0.8298 (t0) REVERT: T 105 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8741 (mm-30) REVERT: T 108 LYS cc_start: 0.8982 (ptmt) cc_final: 0.8622 (ptpp) outliers start: 22 outliers final: 11 residues processed: 309 average time/residue: 0.1274 time to fit residues: 53.6247 Evaluate side-chains 273 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 260 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 95 LYS Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain P residue 93 GLU Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain T residue 111 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 45 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 30 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.072981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.052453 restraints weight = 46909.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.054117 restraints weight = 22382.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.055241 restraints weight = 14696.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.055950 restraints weight = 11499.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.056372 restraints weight = 9984.726| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 12896 Z= 0.198 Angle : 0.803 8.792 18594 Z= 0.466 Chirality : 0.053 0.255 2109 Planarity : 0.006 0.073 1401 Dihedral : 30.538 171.688 3951 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.54 % Favored : 96.21 % Rotamer: Outliers : 4.62 % Allowed : 22.95 % Favored : 72.43 % 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: 0.36 (0.29), residues: 792 helix: 0.67 (0.21), residues: 568 sheet: None (None), residues: 0 loop : -0.66 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 99 TYR 0.027 0.003 TYR T 83 PHE 0.016 0.002 PHE Q 78 TRP 0.016 0.004 TRP H 152 HIS 0.007 0.001 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.20 (12896) covalent geometry : angle 0.80290 / 0.47 (18594) hydrogen bonds : bond 0.05877 / 4.69 ( 753) hydrogen bonds : angle 3.49158 / 3.93 ( 1881) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 280 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 147 GLU cc_start: 0.8977 (pp20) cc_final: 0.8581 (pp20) REVERT: H 148 GLU cc_start: 0.9125 (tt0) cc_final: 0.8797 (tm-30) REVERT: H 151 ARG cc_start: 0.9186 (mtt-85) cc_final: 0.8739 (ptt90) REVERT: M 105 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8444 (mt-10) REVERT: M 108 ASN cc_start: 0.9471 (t0) cc_final: 0.9073 (m-40) REVERT: M 122 LYS cc_start: 0.9150 (ttpt) cc_final: 0.8754 (ttpp) REVERT: N 44 LYS cc_start: 0.9421 (ttpt) cc_final: 0.8960 (ttmt) REVERT: N 84 MET cc_start: 0.8847 (mmm) cc_final: 0.8072 (mmm) REVERT: N 98 TYR cc_start: 0.9384 (m-10) cc_final: 0.8924 (m-80) REVERT: O 75 LYS cc_start: 0.9384 (mttm) cc_final: 0.9111 (mmmm) REVERT: O 84 GLN cc_start: 0.9290 (tp40) cc_final: 0.9087 (tp-100) REVERT: O 90 ASP cc_start: 0.7730 (t70) cc_final: 0.7308 (t0) REVERT: O 91 GLU cc_start: 0.8717 (pm20) cc_final: 0.8338 (tm-30) REVERT: O 95 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.8988 (ttmm) REVERT: O 104 GLN cc_start: 0.8514 (pm20) cc_final: 0.8202 (pm20) REVERT: P 68 ASP cc_start: 0.9264 (t70) cc_final: 0.8760 (t0) REVERT: P 71 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8415 (tm-30) REVERT: P 106 LEU cc_start: 0.9677 (tp) cc_final: 0.9280 (tp) REVERT: P 125 LYS cc_start: 0.8404 (mttt) cc_final: 0.7974 (tppt) REVERT: Q 50 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8849 (mm-30) REVERT: Q 64 LYS cc_start: 0.9545 (mmmm) cc_final: 0.9252 (mmmm) REVERT: Q 68 GLN cc_start: 0.8714 (tt0) cc_final: 0.8113 (tm-30) REVERT: Q 123 ASP cc_start: 0.8989 (m-30) cc_final: 0.8006 (m-30) REVERT: R 36 ARG cc_start: 0.8503 (mtm-85) cc_final: 0.8073 (mtm-85) REVERT: R 37 LEU cc_start: 0.8709 (mt) cc_final: 0.8467 (tt) REVERT: R 39 ARG cc_start: 0.8892 (mmt90) cc_final: 0.8508 (tpp-160) REVERT: R 63 GLU cc_start: 0.9172 (tt0) cc_final: 0.8819 (mt-10) REVERT: R 84 MET cc_start: 0.8773 (mmm) cc_final: 0.8374 (mmp) REVERT: S 59 THR cc_start: 0.9111 (m) cc_final: 0.8858 (p) REVERT: S 61 GLU cc_start: 0.8959 (tp30) cc_final: 0.8697 (tp30) REVERT: S 90 ASP cc_start: 0.8722 (t0) cc_final: 0.7644 (t0) REVERT: S 91 GLU cc_start: 0.8643 (pm20) cc_final: 0.8119 (tm-30) REVERT: S 108 LEU cc_start: 0.9249 (tp) cc_final: 0.8991 (pt) REVERT: S 110 ASN cc_start: 0.9118 (t0) cc_final: 0.8777 (t0) REVERT: T 34 LYS cc_start: 0.9011 (mmtm) cc_final: 0.8687 (mmmm) REVERT: T 35 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7776 (tp30) REVERT: T 38 SER cc_start: 0.9516 (t) cc_final: 0.9272 (m) REVERT: T 47 GLN cc_start: 0.9012 (tp40) cc_final: 0.8688 (tm-30) REVERT: T 51 ASP cc_start: 0.8276 (p0) cc_final: 0.7812 (t0) REVERT: T 57 LYS cc_start: 0.9233 (mppt) cc_final: 0.8931 (mmmt) REVERT: T 64 SER cc_start: 0.9258 (m) cc_final: 0.8485 (p) REVERT: T 68 ASP cc_start: 0.8748 (t0) cc_final: 0.8267 (t0) REVERT: T 71 GLU cc_start: 0.8834 (tp30) cc_final: 0.8559 (tp30) REVERT: T 93 GLU cc_start: 0.7876 (mp0) cc_final: 0.7663 (mp0) REVERT: T 105 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8624 (mm-30) outliers start: 31 outliers final: 20 residues processed: 288 average time/residue: 0.1109 time to fit residues: 44.1252 Evaluate side-chains 276 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 255 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 158 LYS Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 112 ILE Chi-restraints excluded: chain N residue 93 GLN Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 95 LYS Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain S residue 40 SER Chi-restraints excluded: chain S residue 62 ILE Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 61 ILE Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 91 SER Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 111 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 78 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.073771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.053488 restraints weight = 46989.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.055160 restraints weight = 22541.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.056303 restraints weight = 14838.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.057010 restraints weight = 11593.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.057422 restraints weight = 10057.115| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12896 Z= 0.188 Angle : 0.748 8.828 18594 Z= 0.436 Chirality : 0.049 0.270 2109 Planarity : 0.005 0.047 1401 Dihedral : 30.475 171.269 3950 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.03 % Favored : 96.72 % Rotamer: Outliers : 4.62 % Allowed : 24.29 % Favored : 71.09 % 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: 0.54 (0.28), residues: 792 helix: 0.83 (0.21), residues: 570 sheet: None (None), residues: 0 loop : -0.67 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 53 TYR 0.024 0.003 TYR O 50 PHE 0.013 0.002 PHE M 67 TRP 0.009 0.002 TRP H 152 HIS 0.008 0.002 HIS N 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.19 (12896) covalent geometry : angle 0.74805 / 0.44 (18594) hydrogen bonds : bond 0.05466 / 4.35 ( 753) hydrogen bonds : angle 3.32960 / 3.67 ( 1881) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 268 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 147 GLU cc_start: 0.8991 (pp20) cc_final: 0.8751 (pp20) REVERT: H 148 GLU cc_start: 0.9101 (tt0) cc_final: 0.8832 (tm-30) REVERT: H 151 ARG cc_start: 0.9162 (mtt-85) cc_final: 0.8731 (ptt90) REVERT: H 153 LEU cc_start: 0.8364 (mt) cc_final: 0.8153 (mp) REVERT: H 166 ASP cc_start: 0.8897 (t0) cc_final: 0.8532 (t0) REVERT: H 167 LEU cc_start: 0.8148 (mp) cc_final: 0.7510 (mp) REVERT: M 48 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8938 (tt) REVERT: M 81 ASP cc_start: 0.8633 (m-30) cc_final: 0.8408 (m-30) REVERT: M 105 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8449 (mt-10) REVERT: M 108 ASN cc_start: 0.9460 (t0) cc_final: 0.9137 (m-40) REVERT: M 122 LYS cc_start: 0.9190 (ttpt) cc_final: 0.8816 (ttpp) REVERT: N 44 LYS cc_start: 0.9407 (ttpt) cc_final: 0.9101 (mttm) REVERT: N 54 THR cc_start: 0.9532 (m) cc_final: 0.9306 (p) REVERT: N 84 MET cc_start: 0.8877 (mmm) cc_final: 0.8123 (mmm) REVERT: N 98 TYR cc_start: 0.9388 (m-10) cc_final: 0.8815 (m-80) REVERT: O 75 LYS cc_start: 0.9375 (mttm) cc_final: 0.9102 (mmmm) REVERT: O 90 ASP cc_start: 0.7777 (t70) cc_final: 0.7428 (t0) REVERT: O 91 GLU cc_start: 0.8728 (pm20) cc_final: 0.8452 (tm-30) REVERT: O 104 GLN cc_start: 0.8695 (pm20) cc_final: 0.8382 (pm20) REVERT: P 48 VAL cc_start: 0.9613 (t) cc_final: 0.9278 (p) REVERT: P 59 MET cc_start: 0.9165 (tpp) cc_final: 0.8869 (tpp) REVERT: P 68 ASP cc_start: 0.9206 (t70) cc_final: 0.8737 (t0) REVERT: P 71 GLU cc_start: 0.9067 (tm-30) cc_final: 0.8717 (tm-30) REVERT: P 84 ASN cc_start: 0.9501 (m-40) cc_final: 0.9118 (m110) REVERT: P 125 LYS cc_start: 0.8369 (mttt) cc_final: 0.7946 (tppt) REVERT: Q 50 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8832 (mm-30) REVERT: Q 68 GLN cc_start: 0.8710 (tt0) cc_final: 0.8112 (tm-30) REVERT: Q 110 CYS cc_start: 0.8843 (m) cc_final: 0.8261 (m) REVERT: Q 123 ASP cc_start: 0.8975 (m-30) cc_final: 0.7996 (m-30) REVERT: R 31 LYS cc_start: 0.9280 (tttt) cc_final: 0.8782 (tptt) REVERT: R 39 ARG cc_start: 0.8947 (mmt90) cc_final: 0.8520 (tpp-160) REVERT: R 92 ARG cc_start: 0.9013 (tmm-80) cc_final: 0.8435 (tmm-80) REVERT: S 38 ASN cc_start: 0.8933 (p0) cc_final: 0.8718 (p0) REVERT: S 56 GLU cc_start: 0.8668 (tt0) cc_final: 0.8450 (tt0) REVERT: S 90 ASP cc_start: 0.8684 (t0) cc_final: 0.8058 (t0) REVERT: S 108 LEU cc_start: 0.9261 (tp) cc_final: 0.8974 (pp) REVERT: S 110 ASN cc_start: 0.9151 (t0) cc_final: 0.8932 (t0) REVERT: T 38 SER cc_start: 0.9492 (t) cc_final: 0.9240 (m) REVERT: T 51 ASP cc_start: 0.8240 (p0) cc_final: 0.7755 (t0) REVERT: T 57 LYS cc_start: 0.9180 (mppt) cc_final: 0.8946 (mmmt) REVERT: T 64 SER cc_start: 0.9298 (m) cc_final: 0.8486 (p) REVERT: T 68 ASP cc_start: 0.8663 (t0) cc_final: 0.8275 (t0) REVERT: T 71 GLU cc_start: 0.8879 (tp30) cc_final: 0.8623 (tm-30) REVERT: T 93 GLU cc_start: 0.7795 (mp0) cc_final: 0.7583 (mp0) outliers start: 31 outliers final: 22 residues processed: 277 average time/residue: 0.1106 time to fit residues: 42.4462 Evaluate side-chains 276 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 253 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 158 LYS Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 112 ILE Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 93 GLN Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 61 ILE Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain T residue 91 SER Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 111 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 66 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 82 optimal weight: 0.0470 chunk 34 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.074544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.054270 restraints weight = 46619.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.055981 restraints weight = 22127.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.057154 restraints weight = 14468.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.057864 restraints weight = 11261.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.058274 restraints weight = 9777.704| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12896 Z= 0.167 Angle : 0.729 12.187 18594 Z= 0.425 Chirality : 0.048 0.270 2109 Planarity : 0.004 0.035 1401 Dihedral : 30.373 171.810 3950 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.41 % Favored : 96.34 % Rotamer: Outliers : 3.73 % Allowed : 25.04 % Favored : 71.24 % 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: 0.65 (0.28), residues: 792 helix: 0.94 (0.21), residues: 567 sheet: None (None), residues: 0 loop : -0.70 (0.38), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 67 TYR 0.033 0.003 TYR P 40 PHE 0.013 0.001 PHE M 67 TRP 0.003 0.001 TRP H 152 HIS 0.008 0.002 HIS N 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.17 (12896) covalent geometry : angle 0.72881 / 0.43 (18594) hydrogen bonds : bond 0.04946 / 3.98 ( 753) hydrogen bonds : angle 3.23350 / 3.50 ( 1881) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 278 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 147 GLU cc_start: 0.8989 (pp20) cc_final: 0.8547 (pp20) REVERT: H 148 GLU cc_start: 0.9086 (tt0) cc_final: 0.8864 (tm-30) REVERT: H 151 ARG cc_start: 0.9177 (mtt-85) cc_final: 0.8724 (ptt90) REVERT: M 105 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8447 (mt-10) REVERT: M 122 LYS cc_start: 0.9229 (ttpt) cc_final: 0.8864 (ttpp) REVERT: N 44 LYS cc_start: 0.9409 (ttpt) cc_final: 0.8980 (ttmm) REVERT: N 54 THR cc_start: 0.9529 (m) cc_final: 0.9309 (p) REVERT: N 84 MET cc_start: 0.8873 (mmm) cc_final: 0.7954 (mmm) REVERT: N 88 TYR cc_start: 0.8520 (m-80) cc_final: 0.8264 (m-80) REVERT: N 98 TYR cc_start: 0.9369 (m-10) cc_final: 0.8836 (m-80) REVERT: O 19 SER cc_start: 0.9616 (t) cc_final: 0.9332 (p) REVERT: O 75 LYS cc_start: 0.9349 (mttm) cc_final: 0.9092 (mmmm) REVERT: O 90 ASP cc_start: 0.7749 (t70) cc_final: 0.7404 (t0) REVERT: O 91 GLU cc_start: 0.8680 (pm20) cc_final: 0.8427 (tm-30) REVERT: O 92 GLU cc_start: 0.9014 (tp30) cc_final: 0.8695 (tp30) REVERT: O 104 GLN cc_start: 0.8673 (pm20) cc_final: 0.8352 (pm20) REVERT: P 48 VAL cc_start: 0.9571 (t) cc_final: 0.9227 (p) REVERT: P 68 ASP cc_start: 0.9199 (t70) cc_final: 0.8809 (t0) REVERT: P 71 GLU cc_start: 0.9087 (tm-30) cc_final: 0.8738 (tm-30) REVERT: P 84 ASN cc_start: 0.9487 (m-40) cc_final: 0.9077 (m110) REVERT: P 125 LYS cc_start: 0.8377 (mttt) cc_final: 0.7945 (tppt) REVERT: Q 68 GLN cc_start: 0.8655 (tt0) cc_final: 0.7876 (tm-30) REVERT: Q 79 LYS cc_start: 0.8478 (tttp) cc_final: 0.8186 (tptp) REVERT: Q 110 CYS cc_start: 0.8893 (m) cc_final: 0.8445 (m) REVERT: Q 123 ASP cc_start: 0.8992 (m-30) cc_final: 0.8140 (m-30) REVERT: R 31 LYS cc_start: 0.9257 (tttt) cc_final: 0.8736 (tptt) REVERT: R 37 LEU cc_start: 0.8822 (mt) cc_final: 0.8609 (tt) REVERT: R 39 ARG cc_start: 0.8940 (mmt90) cc_final: 0.8527 (tpp-160) REVERT: S 19 SER cc_start: 0.9519 (t) cc_final: 0.9073 (p) REVERT: S 38 ASN cc_start: 0.8949 (p0) cc_final: 0.8733 (p0) REVERT: S 90 ASP cc_start: 0.8659 (t0) cc_final: 0.7856 (t0) REVERT: S 108 LEU cc_start: 0.9222 (tp) cc_final: 0.8969 (pp) REVERT: S 110 ASN cc_start: 0.9160 (t0) cc_final: 0.8936 (t0) REVERT: T 38 SER cc_start: 0.9517 (t) cc_final: 0.9294 (m) REVERT: T 51 ASP cc_start: 0.8171 (p0) cc_final: 0.7697 (t0) REVERT: T 57 LYS cc_start: 0.9140 (mppt) cc_final: 0.8917 (mmmt) REVERT: T 64 SER cc_start: 0.9280 (m) cc_final: 0.8440 (p) REVERT: T 68 ASP cc_start: 0.8646 (t0) cc_final: 0.8304 (t0) REVERT: T 80 LEU cc_start: 0.9165 (tt) cc_final: 0.8821 (tt) REVERT: T 105 GLU cc_start: 0.8938 (mm-30) cc_final: 0.7974 (mm-30) REVERT: T 108 LYS cc_start: 0.8911 (ptmt) cc_final: 0.8573 (ptpp) outliers start: 25 outliers final: 15 residues processed: 286 average time/residue: 0.1057 time to fit residues: 42.1484 Evaluate side-chains 276 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 261 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 112 ILE Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 61 ILE Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 91 SER Chi-restraints excluded: chain T residue 111 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 102 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 6 optimal weight: 20.0000 chunk 80 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 18 optimal weight: 20.0000 chunk 85 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 108 ASN R 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.073214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.051894 restraints weight = 47228.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.053581 restraints weight = 22367.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.054694 restraints weight = 14700.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.055408 restraints weight = 11573.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.055821 restraints weight = 10074.893| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12896 Z= 0.172 Angle : 0.716 12.580 18594 Z= 0.417 Chirality : 0.047 0.268 2109 Planarity : 0.004 0.060 1401 Dihedral : 30.348 171.804 3950 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.78 % Favored : 96.97 % Rotamer: Outliers : 4.32 % Allowed : 26.53 % Favored : 69.15 % 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: 0.64 (0.29), residues: 792 helix: 0.91 (0.21), residues: 570 sheet: None (None), residues: 0 loop : -0.68 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 92 TYR 0.032 0.002 TYR P 40 PHE 0.014 0.001 PHE M 67 TRP 0.004 0.001 TRP H 152 HIS 0.010 0.001 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.17 (12896) covalent geometry : angle 0.71616 / 0.42 (18594) hydrogen bonds : bond 0.04909 / 3.98 ( 753) hydrogen bonds : angle 3.23410 / 3.55 ( 1881) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 265 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 105 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8492 (mt-10) REVERT: M 108 ASN cc_start: 0.9189 (OUTLIER) cc_final: 0.8719 (m-40) REVERT: M 122 LYS cc_start: 0.9222 (ttpt) cc_final: 0.8847 (ttpp) REVERT: N 84 MET cc_start: 0.8951 (mmm) cc_final: 0.7944 (mmm) REVERT: N 88 TYR cc_start: 0.8568 (m-80) cc_final: 0.8269 (m-80) REVERT: N 98 TYR cc_start: 0.9366 (m-10) cc_final: 0.8838 (m-80) REVERT: O 39 TYR cc_start: 0.8915 (m-80) cc_final: 0.8292 (m-80) REVERT: O 41 GLU cc_start: 0.8819 (pt0) cc_final: 0.8589 (pm20) REVERT: O 75 LYS cc_start: 0.9335 (mttm) cc_final: 0.9100 (mmmm) REVERT: O 90 ASP cc_start: 0.7646 (t70) cc_final: 0.7117 (t70) REVERT: O 91 GLU cc_start: 0.8740 (pm20) cc_final: 0.8336 (tm-30) REVERT: O 92 GLU cc_start: 0.9094 (tp30) cc_final: 0.8764 (tp30) REVERT: O 104 GLN cc_start: 0.8703 (pm20) cc_final: 0.8311 (pm20) REVERT: P 48 VAL cc_start: 0.9533 (t) cc_final: 0.9193 (p) REVERT: P 59 MET cc_start: 0.9138 (tpp) cc_final: 0.8770 (tpp) REVERT: P 68 ASP cc_start: 0.9226 (t70) cc_final: 0.8823 (t0) REVERT: P 71 GLU cc_start: 0.9113 (tm-30) cc_final: 0.8753 (tm-30) REVERT: P 84 ASN cc_start: 0.9501 (m-40) cc_final: 0.9047 (m110) REVERT: P 125 LYS cc_start: 0.8385 (mttt) cc_final: 0.7951 (tppt) REVERT: Q 68 GLN cc_start: 0.8699 (tt0) cc_final: 0.8239 (tp40) REVERT: Q 123 ASP cc_start: 0.9098 (m-30) cc_final: 0.8558 (m-30) REVERT: R 37 LEU cc_start: 0.8808 (mt) cc_final: 0.8499 (tt) REVERT: R 39 ARG cc_start: 0.8655 (mmt90) cc_final: 0.8435 (tpp-160) REVERT: S 19 SER cc_start: 0.9537 (t) cc_final: 0.9080 (p) REVERT: S 41 GLU cc_start: 0.8735 (pm20) cc_final: 0.8521 (pm20) REVERT: S 90 ASP cc_start: 0.8700 (t0) cc_final: 0.8082 (t0) REVERT: S 92 GLU cc_start: 0.8600 (mp0) cc_final: 0.7702 (pm20) REVERT: T 35 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7679 (tp30) REVERT: T 51 ASP cc_start: 0.8213 (p0) cc_final: 0.7737 (t0) REVERT: T 57 LYS cc_start: 0.9113 (mppt) cc_final: 0.8865 (mmmt) REVERT: T 64 SER cc_start: 0.9211 (m) cc_final: 0.8422 (p) REVERT: T 68 ASP cc_start: 0.8758 (t0) cc_final: 0.8376 (t0) outliers start: 29 outliers final: 17 residues processed: 276 average time/residue: 0.1005 time to fit residues: 38.7110 Evaluate side-chains 270 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 252 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 158 LYS Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 108 ASN Chi-restraints excluded: chain M residue 112 ILE Chi-restraints excluded: chain N residue 93 GLN Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain S residue 40 SER Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 61 ILE Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 91 SER Chi-restraints excluded: chain T residue 111 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 28 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 108 ASN ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.073335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.052238 restraints weight = 47405.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.053931 restraints weight = 22213.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.055080 restraints weight = 14540.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.055795 restraints weight = 11335.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.056044 restraints weight = 9865.010| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12896 Z= 0.170 Angle : 0.715 12.749 18594 Z= 0.415 Chirality : 0.046 0.257 2109 Planarity : 0.004 0.054 1401 Dihedral : 30.337 171.844 3950 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.65 % Favored : 97.10 % Rotamer: Outliers : 4.02 % Allowed : 28.02 % Favored : 67.96 % 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: 0.72 (0.29), residues: 792 helix: 0.95 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -0.58 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 79 TYR 0.037 0.002 TYR P 40 PHE 0.013 0.001 PHE M 67 TRP 0.004 0.001 TRP H 152 HIS 0.006 0.001 HIS N 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.17 (12896) covalent geometry : angle 0.71513 / 0.42 (18594) hydrogen bonds : bond 0.04700 / 3.81 ( 753) hydrogen bonds : angle 3.18693 / 3.45 ( 1881) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 260 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 148 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8163 (tm-30) REVERT: H 151 ARG cc_start: 0.9152 (mtt-85) cc_final: 0.8802 (ptt90) REVERT: M 73 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8259 (mm-30) REVERT: M 105 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8526 (mt-10) REVERT: M 108 ASN cc_start: 0.9102 (OUTLIER) cc_final: 0.8699 (m-40) REVERT: M 122 LYS cc_start: 0.9218 (ttpt) cc_final: 0.8862 (ttpp) REVERT: N 22 LEU cc_start: 0.6571 (OUTLIER) cc_final: 0.6270 (mt) REVERT: N 44 LYS cc_start: 0.9401 (ttpt) cc_final: 0.8959 (ttmt) REVERT: N 84 MET cc_start: 0.8900 (mmm) cc_final: 0.8113 (mmm) REVERT: N 98 TYR cc_start: 0.9354 (m-10) cc_final: 0.8868 (m-80) REVERT: O 36 LYS cc_start: 0.9368 (mtmt) cc_final: 0.8845 (mtmm) REVERT: O 39 TYR cc_start: 0.8867 (m-80) cc_final: 0.8319 (m-80) REVERT: O 75 LYS cc_start: 0.9326 (mttm) cc_final: 0.9095 (mmmm) REVERT: O 90 ASP cc_start: 0.7636 (t70) cc_final: 0.7113 (t70) REVERT: O 91 GLU cc_start: 0.8769 (pm20) cc_final: 0.8359 (tm-30) REVERT: O 92 GLU cc_start: 0.9069 (tp30) cc_final: 0.8779 (tp30) REVERT: O 104 GLN cc_start: 0.8664 (pm20) cc_final: 0.8286 (pm20) REVERT: P 48 VAL cc_start: 0.9518 (t) cc_final: 0.9197 (p) REVERT: P 59 MET cc_start: 0.9129 (tpp) cc_final: 0.8881 (tpp) REVERT: P 68 ASP cc_start: 0.9209 (t70) cc_final: 0.8774 (t0) REVERT: P 71 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8764 (tm-30) REVERT: P 84 ASN cc_start: 0.9506 (m-40) cc_final: 0.9041 (m110) REVERT: P 125 LYS cc_start: 0.8393 (mttt) cc_final: 0.7870 (tppt) REVERT: Q 68 GLN cc_start: 0.8699 (tt0) cc_final: 0.8243 (tp40) REVERT: Q 123 ASP cc_start: 0.9174 (m-30) cc_final: 0.8568 (m-30) REVERT: R 37 LEU cc_start: 0.8758 (mt) cc_final: 0.8506 (tt) REVERT: R 39 ARG cc_start: 0.8643 (mmt90) cc_final: 0.8399 (tpp-160) REVERT: S 9 LYS cc_start: 0.6870 (pttp) cc_final: 0.6651 (ptpp) REVERT: S 19 SER cc_start: 0.9522 (t) cc_final: 0.9076 (p) REVERT: S 56 GLU cc_start: 0.8710 (tt0) cc_final: 0.8459 (tt0) REVERT: S 90 ASP cc_start: 0.8604 (t0) cc_final: 0.8062 (t0) REVERT: T 51 ASP cc_start: 0.8179 (p0) cc_final: 0.7727 (t0) REVERT: T 57 LYS cc_start: 0.9097 (mppt) cc_final: 0.8843 (mmmt) REVERT: T 64 SER cc_start: 0.9203 (m) cc_final: 0.8434 (p) REVERT: T 68 ASP cc_start: 0.8777 (t0) cc_final: 0.8405 (t0) REVERT: T 93 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8145 (tp30) REVERT: T 106 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9063 (mt) outliers start: 27 outliers final: 20 residues processed: 270 average time/residue: 0.0924 time to fit residues: 34.9774 Evaluate side-chains 274 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 251 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 108 ASN Chi-restraints excluded: chain M residue 112 ILE Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 93 GLN Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain S residue 40 SER Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 61 ILE Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 91 SER Chi-restraints excluded: chain T residue 102 LEU Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 111 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- 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: 51.2789 > 50: distance: 67 - 71: 3.495 distance: 71 - 72: 8.841 distance: 72 - 73: 3.676 distance: 72 - 75: 17.697 distance: 73 - 74: 9.190 distance: 73 - 79: 15.420 distance: 75 - 76: 9.883 distance: 76 - 77: 14.546 distance: 76 - 78: 19.536 distance: 79 - 80: 10.172 distance: 80 - 81: 5.635 distance: 80 - 83: 6.869 distance: 81 - 82: 25.720 distance: 81 - 90: 25.680 distance: 83 - 84: 9.851 distance: 84 - 85: 20.566 distance: 85 - 86: 6.269 distance: 86 - 87: 13.051 distance: 87 - 88: 9.227 distance: 87 - 89: 9.621 distance: 90 - 91: 19.229 distance: 91 - 92: 12.296 distance: 91 - 94: 7.068 distance: 92 - 93: 12.127 distance: 92 - 101: 6.078 distance: 94 - 95: 9.690 distance: 95 - 96: 3.085 distance: 95 - 97: 5.990 distance: 96 - 98: 7.259 distance: 97 - 99: 7.898 distance: 98 - 100: 4.421 distance: 99 - 100: 3.495 distance: 101 - 102: 5.381 distance: 102 - 103: 9.471 distance: 102 - 105: 11.845 distance: 103 - 104: 20.651 distance: 103 - 110: 16.950 distance: 105 - 106: 13.391 distance: 106 - 107: 13.805 distance: 107 - 108: 4.277 distance: 110 - 111: 3.742 distance: 111 - 112: 12.398 distance: 111 - 114: 9.899 distance: 112 - 113: 23.592 distance: 112 - 116: 6.829 distance: 114 - 115: 17.735 distance: 117 - 118: 12.122 distance: 117 - 120: 11.447 distance: 118 - 119: 17.870 distance: 118 - 122: 13.064 distance: 119 - 142: 17.217 distance: 120 - 121: 23.594 distance: 122 - 123: 6.834 distance: 123 - 124: 15.394 distance: 123 - 126: 6.652 distance: 124 - 125: 9.073 distance: 124 - 127: 5.149 distance: 125 - 147: 7.718 distance: 128 - 129: 7.033 distance: 129 - 130: 9.004 distance: 129 - 134: 3.864 distance: 130 - 155: 10.311 distance: 131 - 132: 9.214 distance: 131 - 133: 5.836 distance: 134 - 135: 6.401 distance: 135 - 136: 11.953 distance: 135 - 138: 10.502 distance: 136 - 137: 8.355 distance: 136 - 142: 8.658 distance: 137 - 163: 11.483 distance: 138 - 139: 14.039 distance: 139 - 140: 5.504 distance: 140 - 141: 14.985 distance: 142 - 143: 8.201 distance: 143 - 144: 8.418 distance: 143 - 146: 9.604 distance: 144 - 147: 8.368 distance: 145 - 172: 12.917