Starting phenix.real_space_refine on Fri Aug 22 15:44:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cq7_45810/08_2025/9cq7_45810.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cq7_45810/08_2025/9cq7_45810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cq7_45810/08_2025/9cq7_45810.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cq7_45810/08_2025/9cq7_45810.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cq7_45810/08_2025/9cq7_45810.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cq7_45810/08_2025/9cq7_45810.map" } resolution = 3.21 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= 0.020 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: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 3319 2.51 5 N 859 2.21 5 O 1021 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5222 Number of models: 1 Model: "" Number of chains: 7 Chain: "D" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1611 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "G" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1837 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 12, 'TRANS': 218} Chain: "H" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 930 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "I" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 99} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.61, per 1000 atoms: 0.31 Number of scatterers: 5222 At special positions: 0 Unit cell: (72.154, 88.934, 101.519, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 1021 8.00 N 859 7.00 C 3319 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 191 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 154 " - pdb=" SG CYS G 210 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 87 " distance=2.04 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG D 301 " - " ASN D 197 " " NAG G 301 " - " ASN G 188 " Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 252.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1222 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 20 sheets defined 3.3% alpha, 42.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'G' and resid 143 through 148 Processing helix chain 'G' and resid 200 through 205 removed outlier: 4.024A pdb=" N ASP G 205 " --> pdb=" O GLU G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 221 removed outlier: 3.505A pdb=" N GLY G 220 " --> pdb=" O ASN G 217 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 82 removed outlier: 3.640A pdb=" N ALA I 82 " --> pdb=" O ALA I 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.899A pdb=" N GLU D 3 " --> pdb=" O LYS D 26 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP D 69 " --> pdb=" O LEU D 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 13 through 14 removed outlier: 6.813A pdb=" N VAL D 13 " --> pdb=" O GLU D 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 47 through 48 removed outlier: 3.539A pdb=" N ALA D 93 " --> pdb=" O ASN D 36 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER D 89 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 47 through 48 removed outlier: 3.539A pdb=" N ALA D 93 " --> pdb=" O ASN D 36 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER D 89 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 50 through 51 removed outlier: 4.280A pdb=" N ILE D 55 " --> pdb=" O ARG D 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 133 through 134 removed outlier: 3.850A pdb=" N ASN D 137 " --> pdb=" O ASN D 134 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS D 179 " --> pdb=" O CYS D 140 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL D 142 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU D 144 " --> pdb=" O TYR D 175 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N TYR D 175 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL D 178 " --> pdb=" O ALA D 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 151 through 154 removed outlier: 3.871A pdb=" N ASN D 153 " --> pdb=" O SER D 192 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER D 192 " --> pdb=" O ASN D 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AA9, first strand: chain 'G' and resid 11 through 14 removed outlier: 5.629A pdb=" N SER G 11 " --> pdb=" O ILE G 120 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N THR G 122 " --> pdb=" O SER G 11 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LYS G 13 " --> pdb=" O THR G 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 58 through 59 removed outlier: 6.714A pdb=" N TRP G 37 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER G 51 " --> pdb=" O VAL G 35 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL G 35 " --> pdb=" O SER G 51 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 135 through 137 removed outlier: 3.515A pdb=" N PHE G 137 " --> pdb=" O LEU G 153 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU G 153 " --> pdb=" O PHE G 137 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER G 195 " --> pdb=" O CYS G 154 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TYR G 191 " --> pdb=" O LYS G 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 135 through 137 removed outlier: 3.515A pdb=" N PHE G 137 " --> pdb=" O LEU G 153 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU G 153 " --> pdb=" O PHE G 137 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER G 195 " --> pdb=" O CYS G 154 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TYR G 191 " --> pdb=" O LYS G 158 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N MET G 192 " --> pdb=" O MET G 185 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET G 185 " --> pdb=" O MET G 192 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 150 through 151 Processing sheet with id=AB5, first strand: chain 'G' and resid 165 through 170 removed outlier: 4.306A pdb=" N GLN G 169 " --> pdb=" O ARG G 209 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG G 209 " --> pdb=" O GLN G 169 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE G 225 " --> pdb=" O CYS G 210 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL G 212 " --> pdb=" O GLN G 223 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.516A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 9 through 11 removed outlier: 3.510A pdb=" N THR H 118 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASN H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 9 through 11 removed outlier: 3.510A pdb=" N THR H 118 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 4 through 5 removed outlier: 3.545A pdb=" N ILE I 19 " --> pdb=" O ILE I 74 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE I 69 " --> pdb=" O SER I 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.606A pdb=" N MET I 11 " --> pdb=" O LYS I 101 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU I 103 " --> pdb=" O MET I 11 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N MET I 32 " --> pdb=" O TYR I 48 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N TYR I 48 " --> pdb=" O MET I 32 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N TRP I 34 " --> pdb=" O LEU I 46 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.606A pdb=" N MET I 11 " --> pdb=" O LYS I 101 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU I 103 " --> pdb=" O MET I 11 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN I 89 " --> pdb=" O THR I 95 " (cutoff:3.500A) 174 hydrogen bonds defined for protein. 408 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.80 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1640 1.34 - 1.46: 1279 1.46 - 1.58: 2391 1.58 - 1.70: 0 1.70 - 1.82: 33 Bond restraints: 5343 Sorted by residual: bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.40e+00 bond pdb=" C1 NAG G 301 " pdb=" O5 NAG G 301 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.10e+00 bond pdb=" C1 NAG D 301 " pdb=" O5 NAG D 301 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.63e+00 bond pdb=" C5 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.25e+00 bond pdb=" C5 NAG G 301 " pdb=" O5 NAG G 301 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.22e+00 ... (remaining 5338 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 6948 1.37 - 2.74: 236 2.74 - 4.11: 47 4.11 - 5.48: 13 5.48 - 6.85: 2 Bond angle restraints: 7246 Sorted by residual: angle pdb=" C ALA G 128 " pdb=" N ASP G 129 " pdb=" CA ASP G 129 " ideal model delta sigma weight residual 122.82 127.10 -4.28 1.42e+00 4.96e-01 9.07e+00 angle pdb=" N GLY H 44 " pdb=" CA GLY H 44 " pdb=" C GLY H 44 " ideal model delta sigma weight residual 113.18 107.66 5.52 2.37e+00 1.78e-01 5.42e+00 angle pdb=" C LYS D 143 " pdb=" N GLU D 144 " pdb=" CA GLU D 144 " ideal model delta sigma weight residual 123.34 119.18 4.16 1.80e+00 3.09e-01 5.34e+00 angle pdb=" CA THR I 50 " pdb=" CB THR I 50 " pdb=" CG2 THR I 50 " ideal model delta sigma weight residual 110.50 114.10 -3.60 1.70e+00 3.46e-01 4.49e+00 angle pdb=" C LYS G 68 " pdb=" N PHE G 69 " pdb=" CA PHE G 69 " ideal model delta sigma weight residual 121.54 125.53 -3.99 1.91e+00 2.74e-01 4.36e+00 ... (remaining 7241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 2922 16.90 - 33.79: 263 33.79 - 50.69: 46 50.69 - 67.59: 13 67.59 - 84.49: 12 Dihedral angle restraints: 3256 sinusoidal: 1343 harmonic: 1913 Sorted by residual: dihedral pdb=" CB CYS D 140 " pdb=" SG CYS D 140 " pdb=" SG CYS D 191 " pdb=" CB CYS D 191 " ideal model delta sinusoidal sigma weight residual 93.00 20.45 72.55 1 1.00e+01 1.00e-02 6.72e+01 dihedral pdb=" CB CYS D 23 " pdb=" SG CYS D 23 " pdb=" SG CYS D 92 " pdb=" CB CYS D 92 " ideal model delta sinusoidal sigma weight residual 93.00 31.59 61.41 1 1.00e+01 1.00e-02 5.01e+01 dihedral pdb=" CA VAL D 142 " pdb=" C VAL D 142 " pdb=" N LYS D 143 " pdb=" CA LYS D 143 " ideal model delta harmonic sigma weight residual -180.00 -157.16 -22.84 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 3253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 698 0.063 - 0.126: 107 0.126 - 0.189: 10 0.189 - 0.252: 0 0.252 - 0.315: 1 Chirality restraints: 816 Sorted by residual: chirality pdb=" CB ILE D 55 " pdb=" CA ILE D 55 " pdb=" CG1 ILE D 55 " pdb=" CG2 ILE D 55 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" C1 NAG D 301 " pdb=" ND2 ASN D 197 " pdb=" C2 NAG D 301 " pdb=" O5 NAG D 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.79e-01 chirality pdb=" CA THR I 50 " pdb=" N THR I 50 " pdb=" C THR I 50 " pdb=" CB THR I 50 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 6.87e-01 ... (remaining 813 not shown) Planarity restraints: 912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG H 40 " -0.035 5.00e-02 4.00e+02 5.26e-02 4.43e+00 pdb=" N PRO H 41 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO H 41 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 41 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL I 57 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO I 58 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO I 58 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO I 58 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 96 " 0.009 2.00e-02 2.50e+03 1.22e-02 2.62e+00 pdb=" CG PHE I 96 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE I 96 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE I 96 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE I 96 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE I 96 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE I 96 " -0.000 2.00e-02 2.50e+03 ... (remaining 909 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 118 2.69 - 3.24: 4907 3.24 - 3.79: 7535 3.79 - 4.35: 10310 4.35 - 4.90: 17533 Nonbonded interactions: 40403 Sorted by model distance: nonbonded pdb=" O THR I 50 " pdb=" OG SER I 51 " model vdw 2.131 3.040 nonbonded pdb=" OE1 GLN G 6 " pdb=" OG1 THR G 117 " model vdw 2.164 3.040 nonbonded pdb=" O LYS D 143 " pdb=" ND2 ASN D 176 " model vdw 2.170 3.120 nonbonded pdb=" OG1 THR G 187 " pdb=" O THR G 190 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR H 87 " pdb=" OD1 ASP H 89 " model vdw 2.277 3.040 ... (remaining 40398 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.480 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: 0.020 Set scattering table: 0.020 Process input model: 7.210 Find NCS groups from input model: 0.030 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 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 : 0.003 0.031 5352 Z= 0.155 Angle : 0.625 6.848 7267 Z= 0.322 Chirality : 0.047 0.315 816 Planarity : 0.004 0.053 910 Dihedral : 14.051 84.486 2016 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.33), residues: 652 helix: None (None), residues: 0 sheet: 0.43 (0.35), residues: 251 loop : -1.10 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 60 TYR 0.011 0.001 TYR D 90 PHE 0.028 0.002 PHE I 96 TRP 0.009 0.001 TRP G 196 HIS 0.003 0.001 HIS I 33 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 5343) covalent geometry : angle 0.62151 ( 7246) SS BOND : bond 0.00321 ( 6) SS BOND : angle 1.05494 ( 12) hydrogen bonds : bond 0.25741 ( 151) hydrogen bonds : angle 10.39689 ( 408) link_BETA1-4 : bond 0.00536 ( 1) link_BETA1-4 : angle 1.02146 ( 3) link_NAG-ASN : bond 0.00312 ( 2) link_NAG-ASN : angle 1.80363 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 5 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7427 (tp30) REVERT: G 133 LYS cc_start: 0.7467 (mmmt) cc_final: 0.7187 (mmtm) REVERT: G 185 MET cc_start: 0.6600 (mpp) cc_final: 0.5901 (pmm) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.0943 time to fit residues: 11.7438 Evaluate side-chains 71 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.0770 chunk 5 optimal weight: 0.0050 chunk 33 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.4752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 73 ASN G 169 GLN H 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.195100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.159867 restraints weight = 6523.097| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.86 r_work: 0.3752 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5352 Z= 0.150 Angle : 0.650 6.238 7267 Z= 0.346 Chirality : 0.049 0.196 816 Planarity : 0.005 0.047 910 Dihedral : 5.668 33.863 793 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.95 % Allowed : 7.28 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.32), residues: 652 helix: None (None), residues: 0 sheet: 0.42 (0.34), residues: 260 loop : -1.07 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 213 TYR 0.018 0.001 TYR D 90 PHE 0.019 0.002 PHE I 96 TRP 0.010 0.001 TRP G 196 HIS 0.005 0.001 HIS G 167 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 5343) covalent geometry : angle 0.64517 ( 7246) SS BOND : bond 0.00535 ( 6) SS BOND : angle 1.51586 ( 12) hydrogen bonds : bond 0.04514 ( 151) hydrogen bonds : angle 7.29098 ( 408) link_BETA1-4 : bond 0.00582 ( 1) link_BETA1-4 : angle 1.31720 ( 3) link_NAG-ASN : bond 0.00485 ( 2) link_NAG-ASN : angle 1.75353 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: D 33 TYR cc_start: 0.7780 (m-80) cc_final: 0.6909 (m-80) REVERT: D 80 LEU cc_start: 0.7368 (mm) cc_final: 0.6980 (mm) REVERT: D 105 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7675 (p0) REVERT: G 5 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7812 (tp30) REVERT: G 133 LYS cc_start: 0.7896 (mmmt) cc_final: 0.7503 (mmtt) REVERT: G 213 ARG cc_start: 0.7317 (tpp-160) cc_final: 0.7090 (tpp-160) outliers start: 17 outliers final: 12 residues processed: 83 average time/residue: 0.0696 time to fit residues: 7.8390 Evaluate side-chains 86 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 94 CYS Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain G residue 86 ASN Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 32 MET Chi-restraints excluded: chain I residue 41 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 56 optimal weight: 0.1980 chunk 46 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 47 GLN H 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.187884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.152911 restraints weight = 6537.786| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.87 r_work: 0.3685 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5352 Z= 0.221 Angle : 0.691 6.006 7267 Z= 0.366 Chirality : 0.050 0.211 816 Planarity : 0.005 0.048 910 Dihedral : 5.805 29.766 793 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.81 % Allowed : 11.44 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.32), residues: 652 helix: None (None), residues: 0 sheet: 0.12 (0.33), residues: 260 loop : -1.07 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG I 60 TYR 0.021 0.002 TYR D 90 PHE 0.032 0.003 PHE I 96 TRP 0.016 0.002 TRP G 168 HIS 0.007 0.001 HIS G 167 Details of bonding type rmsd covalent geometry : bond 0.00533 ( 5343) covalent geometry : angle 0.68616 ( 7246) SS BOND : bond 0.00656 ( 6) SS BOND : angle 1.56580 ( 12) hydrogen bonds : bond 0.04052 ( 151) hydrogen bonds : angle 6.82072 ( 408) link_BETA1-4 : bond 0.00277 ( 1) link_BETA1-4 : angle 1.14693 ( 3) link_NAG-ASN : bond 0.00593 ( 2) link_NAG-ASN : angle 1.99547 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: D 33 TYR cc_start: 0.7849 (m-80) cc_final: 0.6876 (m-80) REVERT: D 132 MET cc_start: 0.6747 (OUTLIER) cc_final: 0.6179 (ptt) REVERT: G 5 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7746 (tp30) outliers start: 22 outliers final: 19 residues processed: 81 average time/residue: 0.0773 time to fit residues: 8.3319 Evaluate side-chains 91 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 94 CYS Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 86 ASN Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 32 MET Chi-restraints excluded: chain I residue 41 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 34 optimal weight: 0.1980 chunk 2 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 167 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.187815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.153417 restraints weight = 6502.656| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.84 r_work: 0.3692 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5352 Z= 0.169 Angle : 0.630 5.562 7267 Z= 0.335 Chirality : 0.048 0.198 816 Planarity : 0.004 0.047 910 Dihedral : 5.554 22.875 793 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.99 % Allowed : 13.69 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.32), residues: 652 helix: None (None), residues: 0 sheet: 0.02 (0.33), residues: 260 loop : -1.04 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 60 TYR 0.015 0.002 TYR D 50 PHE 0.019 0.002 PHE I 96 TRP 0.012 0.002 TRP G 168 HIS 0.003 0.001 HIS G 208 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 5343) covalent geometry : angle 0.62521 ( 7246) SS BOND : bond 0.00523 ( 6) SS BOND : angle 1.31114 ( 12) hydrogen bonds : bond 0.03604 ( 151) hydrogen bonds : angle 6.43917 ( 408) link_BETA1-4 : bond 0.00290 ( 1) link_BETA1-4 : angle 1.54183 ( 3) link_NAG-ASN : bond 0.00570 ( 2) link_NAG-ASN : angle 1.84856 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.136 Fit side-chains REVERT: D 33 TYR cc_start: 0.7861 (m-80) cc_final: 0.6922 (m-80) REVERT: D 132 MET cc_start: 0.6754 (OUTLIER) cc_final: 0.6151 (ptt) REVERT: G 101 GLU cc_start: 0.7147 (pt0) cc_final: 0.6835 (pp20) REVERT: G 225 ILE cc_start: 0.7093 (OUTLIER) cc_final: 0.6787 (tp) REVERT: H 23 LYS cc_start: 0.8056 (ttmm) cc_final: 0.7743 (tptm) REVERT: H 46 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7375 (mp0) outliers start: 23 outliers final: 18 residues processed: 82 average time/residue: 0.0713 time to fit residues: 7.5679 Evaluate side-chains 91 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 94 CYS Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain G residue 86 ASN Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 32 MET Chi-restraints excluded: chain I residue 41 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 0.0070 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 25 optimal weight: 0.0970 chunk 47 optimal weight: 0.0470 chunk 59 optimal weight: 1.9990 overall best weight: 0.6096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 125 GLN G 167 HIS ** I 6 GLN ** 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 = 0.4187 r_free = 0.4187 target = 0.188988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.155667 restraints weight = 6634.293| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.74 r_work: 0.3701 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5352 Z= 0.150 Angle : 0.605 5.688 7267 Z= 0.322 Chirality : 0.048 0.208 816 Planarity : 0.004 0.049 910 Dihedral : 5.382 21.957 793 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 4.85 % Allowed : 15.25 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.32), residues: 652 helix: None (None), residues: 0 sheet: -0.05 (0.33), residues: 262 loop : -1.06 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 60 TYR 0.009 0.001 TYR H 95 PHE 0.015 0.002 PHE G 69 TRP 0.011 0.001 TRP G 196 HIS 0.003 0.001 HIS G 208 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 5343) covalent geometry : angle 0.60162 ( 7246) SS BOND : bond 0.00473 ( 6) SS BOND : angle 1.14644 ( 12) hydrogen bonds : bond 0.03396 ( 151) hydrogen bonds : angle 6.22615 ( 408) link_BETA1-4 : bond 0.00266 ( 1) link_BETA1-4 : angle 1.53513 ( 3) link_NAG-ASN : bond 0.00540 ( 2) link_NAG-ASN : angle 1.76886 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 67 time to evaluate : 0.128 Fit side-chains REVERT: D 33 TYR cc_start: 0.7805 (m-80) cc_final: 0.6895 (m-80) REVERT: G 225 ILE cc_start: 0.7072 (OUTLIER) cc_final: 0.6787 (tp) REVERT: H 23 LYS cc_start: 0.8032 (ttmm) cc_final: 0.7694 (tptm) REVERT: H 46 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7274 (mp0) outliers start: 28 outliers final: 20 residues processed: 82 average time/residue: 0.0499 time to fit residues: 5.5552 Evaluate side-chains 86 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 94 CYS Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 32 MET Chi-restraints excluded: chain I residue 41 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 63 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 0.0770 chunk 15 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 47 optimal weight: 0.0980 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 167 HIS ** I 6 GLN ** 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 = 0.4196 r_free = 0.4196 target = 0.189906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.156086 restraints weight = 6610.366| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.76 r_work: 0.3707 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5352 Z= 0.154 Angle : 0.610 5.818 7267 Z= 0.324 Chirality : 0.048 0.183 816 Planarity : 0.004 0.045 910 Dihedral : 5.328 22.290 793 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 4.51 % Allowed : 16.98 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.32), residues: 652 helix: None (None), residues: 0 sheet: 0.01 (0.33), residues: 257 loop : -1.10 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 60 TYR 0.018 0.001 TYR D 50 PHE 0.015 0.002 PHE G 69 TRP 0.011 0.001 TRP G 196 HIS 0.003 0.001 HIS G 208 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 5343) covalent geometry : angle 0.60609 ( 7246) SS BOND : bond 0.00472 ( 6) SS BOND : angle 1.13079 ( 12) hydrogen bonds : bond 0.03305 ( 151) hydrogen bonds : angle 6.15673 ( 408) link_BETA1-4 : bond 0.00261 ( 1) link_BETA1-4 : angle 1.50412 ( 3) link_NAG-ASN : bond 0.00544 ( 2) link_NAG-ASN : angle 1.72092 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 0.208 Fit side-chains REVERT: D 33 TYR cc_start: 0.7850 (m-80) cc_final: 0.6873 (m-80) REVERT: D 132 MET cc_start: 0.6633 (OUTLIER) cc_final: 0.6106 (ptt) REVERT: G 225 ILE cc_start: 0.7066 (OUTLIER) cc_final: 0.6777 (tp) REVERT: H 23 LYS cc_start: 0.8023 (ttmm) cc_final: 0.7684 (tptm) REVERT: H 46 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7217 (mp0) outliers start: 26 outliers final: 21 residues processed: 83 average time/residue: 0.0585 time to fit residues: 6.6193 Evaluate side-chains 91 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 94 CYS Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 32 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.4195 > 50: distance: 46 - 51: 19.253 distance: 51 - 52: 31.481 distance: 52 - 53: 13.404 distance: 52 - 55: 36.952 distance: 53 - 54: 35.828 distance: 53 - 65: 11.766 distance: 55 - 56: 13.506 distance: 56 - 57: 21.183 distance: 56 - 58: 17.026 distance: 57 - 59: 17.579 distance: 58 - 60: 22.165 distance: 58 - 61: 12.550 distance: 60 - 62: 8.066 distance: 61 - 63: 12.121 distance: 62 - 64: 8.198 distance: 63 - 64: 16.835 distance: 65 - 66: 7.352 distance: 65 - 139: 29.057 distance: 66 - 67: 30.774 distance: 66 - 69: 23.452 distance: 67 - 68: 21.778 distance: 67 - 74: 34.574 distance: 68 - 136: 26.724 distance: 69 - 70: 13.284 distance: 70 - 71: 24.267 distance: 71 - 72: 17.005 distance: 71 - 73: 34.100 distance: 74 - 75: 5.101 distance: 75 - 76: 21.141 distance: 75 - 78: 35.523 distance: 76 - 77: 14.364 distance: 76 - 79: 22.985 distance: 79 - 80: 11.530 distance: 80 - 81: 4.304 distance: 80 - 83: 14.443 distance: 81 - 82: 15.136 distance: 81 - 88: 16.879 distance: 83 - 84: 13.368 distance: 84 - 85: 9.215 distance: 85 - 86: 10.900 distance: 85 - 87: 6.902 distance: 88 - 89: 3.213 distance: 89 - 90: 6.235 distance: 89 - 92: 11.562 distance: 90 - 91: 20.617 distance: 90 - 97: 14.389 distance: 93 - 94: 20.181 distance: 94 - 95: 22.048 distance: 94 - 96: 31.257 distance: 97 - 98: 15.092 distance: 98 - 99: 15.624 distance: 98 - 101: 16.638 distance: 99 - 100: 12.244 distance: 99 - 106: 10.160 distance: 101 - 102: 9.277 distance: 102 - 103: 16.717 distance: 103 - 105: 36.632 distance: 106 - 107: 20.158 distance: 107 - 108: 16.945 distance: 107 - 110: 18.657 distance: 108 - 109: 21.900 distance: 108 - 114: 24.204 distance: 110 - 111: 13.099 distance: 111 - 112: 18.283 distance: 111 - 113: 5.533 distance: 114 - 115: 16.528 distance: 115 - 116: 14.101 distance: 116 - 117: 8.999 distance: 116 - 118: 6.534 distance: 118 - 119: 9.147 distance: 119 - 120: 13.419 distance: 119 - 122: 14.307 distance: 120 - 121: 7.218 distance: 120 - 127: 17.454 distance: 122 - 123: 7.444 distance: 123 - 124: 5.561 distance: 124 - 125: 10.173 distance: 125 - 126: 25.072 distance: 127 - 128: 10.869 distance: 128 - 129: 9.481 distance: 128 - 131: 8.317 distance: 129 - 130: 13.746 distance: 129 - 136: 8.710 distance: 131 - 132: 7.287 distance: 132 - 133: 16.940 distance: 133 - 134: 18.751 distance: 134 - 135: 29.983