Starting phenix.real_space_refine on Sat May 10 05:36:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cq7_45810/05_2025/9cq7_45810.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cq7_45810/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cq7_45810/05_2025/9cq7_45810.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cq7_45810/05_2025/9cq7_45810.map" model { file = "/net/cci-nas-00/data/ceres_data/9cq7_45810/05_2025/9cq7_45810.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cq7_45810/05_2025/9cq7_45810.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.94, per 1000 atoms: 0.95 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: 1.38 Conformation dependent library (CDL) restraints added in 668.5 milliseconds 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: 0.81 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: 1.46 Time building geometry restraints manager: 1.61 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: 3.140 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.920 Find NCS groups from input model: 0.060 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.250 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP G 196 HIS 0.003 0.001 HIS I 33 PHE 0.028 0.002 PHE I 96 TYR 0.011 0.001 TYR D 90 ARG 0.002 0.000 ARG I 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 2) link_NAG-ASN : angle 1.80363 ( 6) link_BETA1-4 : bond 0.00536 ( 1) link_BETA1-4 : angle 1.02146 ( 3) hydrogen bonds : bond 0.25741 ( 151) hydrogen bonds : angle 10.39689 ( 408) SS BOND : bond 0.00321 ( 6) SS BOND : angle 1.05494 ( 12) covalent geometry : bond 0.00342 ( 5343) covalent geometry : angle 0.62151 ( 7246) *********************** 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 : 0.640 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: 0.2012 time to fit residues: 25.1233 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 : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 chunk 26 optimal weight: 0.0370 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.0020 chunk 37 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.4266 ------------------------------------------------------------------------------- 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 = 0.4252 r_free = 0.4252 target = 0.194647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.158496 restraints weight = 6426.391| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.99 r_work: 0.3740 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5352 Z= 0.144 Angle : 0.648 6.171 7267 Z= 0.345 Chirality : 0.048 0.197 816 Planarity : 0.005 0.047 910 Dihedral : 5.634 33.360 793 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.32), residues: 652 helix: None (None), residues: 0 sheet: 0.43 (0.34), residues: 260 loop : -1.06 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 196 HIS 0.005 0.001 HIS G 167 PHE 0.018 0.002 PHE I 96 TYR 0.018 0.001 TYR D 90 ARG 0.010 0.001 ARG G 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 2) link_NAG-ASN : angle 1.74371 ( 6) link_BETA1-4 : bond 0.00177 ( 1) link_BETA1-4 : angle 1.19728 ( 3) hydrogen bonds : bond 0.04220 ( 151) hydrogen bonds : angle 7.23080 ( 408) SS BOND : bond 0.00513 ( 6) SS BOND : angle 1.49406 ( 12) covalent geometry : bond 0.00327 ( 5343) covalent geometry : angle 0.64388 ( 7246) *********************** 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 97 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: D 33 TYR cc_start: 0.7810 (m-80) cc_final: 0.6953 (m-80) REVERT: D 80 LEU cc_start: 0.7381 (mm) cc_final: 0.7014 (mm) REVERT: D 105 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7740 (p0) REVERT: G 5 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7856 (tp30) REVERT: G 133 LYS cc_start: 0.7879 (mmmt) cc_final: 0.7528 (mmtt) REVERT: H 23 LYS cc_start: 0.7915 (ttmm) cc_final: 0.7633 (tptm) outliers start: 17 outliers final: 12 residues processed: 86 average time/residue: 0.1541 time to fit residues: 17.8358 Evaluate side-chains 85 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 5 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 47 GLN G 167 HIS H 39 GLN I 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.191039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.156002 restraints weight = 6519.498| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.87 r_work: 0.3716 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5352 Z= 0.167 Angle : 0.636 6.076 7267 Z= 0.337 Chirality : 0.049 0.200 816 Planarity : 0.004 0.048 910 Dihedral : 5.553 30.616 793 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.29 % Allowed : 10.92 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.32), residues: 652 helix: None (None), residues: 0 sheet: 0.20 (0.33), residues: 267 loop : -0.99 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 168 HIS 0.005 0.001 HIS G 167 PHE 0.021 0.002 PHE I 96 TYR 0.017 0.002 TYR D 90 ARG 0.009 0.001 ARG G 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00525 ( 2) link_NAG-ASN : angle 1.85359 ( 6) link_BETA1-4 : bond 0.00277 ( 1) link_BETA1-4 : angle 1.15010 ( 3) hydrogen bonds : bond 0.03913 ( 151) hydrogen bonds : angle 6.63522 ( 408) SS BOND : bond 0.00568 ( 6) SS BOND : angle 1.47702 ( 12) covalent geometry : bond 0.00394 ( 5343) covalent geometry : angle 0.63099 ( 7246) *********************** 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 88 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: D 33 TYR cc_start: 0.7809 (m-80) cc_final: 0.6885 (m-80) REVERT: D 105 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7728 (p0) REVERT: G 5 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7746 (tp30) REVERT: G 133 LYS cc_start: 0.8079 (mmmt) cc_final: 0.7526 (mmtm) REVERT: G 213 ARG cc_start: 0.7745 (tpp-160) cc_final: 0.7415 (mpt180) REVERT: H 81 MET cc_start: 0.7838 (ttt) cc_final: 0.7293 (ttt) outliers start: 19 outliers final: 16 residues processed: 75 average time/residue: 0.1605 time to fit residues: 16.1337 Evaluate side-chains 84 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 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 7 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.189025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.154432 restraints weight = 6615.647| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.86 r_work: 0.3704 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5352 Z= 0.166 Angle : 0.618 5.567 7267 Z= 0.328 Chirality : 0.048 0.197 816 Planarity : 0.004 0.048 910 Dihedral : 5.424 23.984 793 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 4.16 % Allowed : 14.04 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.32), residues: 652 helix: None (None), residues: 0 sheet: 0.10 (0.33), residues: 260 loop : -1.02 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 168 HIS 0.004 0.001 HIS G 167 PHE 0.023 0.002 PHE I 96 TYR 0.018 0.002 TYR D 50 ARG 0.003 0.000 ARG I 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 2) link_NAG-ASN : angle 1.81157 ( 6) link_BETA1-4 : bond 0.00208 ( 1) link_BETA1-4 : angle 1.42134 ( 3) hydrogen bonds : bond 0.03441 ( 151) hydrogen bonds : angle 6.30996 ( 408) SS BOND : bond 0.00521 ( 6) SS BOND : angle 1.32743 ( 12) covalent geometry : bond 0.00396 ( 5343) covalent geometry : angle 0.61329 ( 7246) *********************** 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 99 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.552 Fit side-chains REVERT: D 33 TYR cc_start: 0.7840 (m-80) cc_final: 0.6940 (m-80) REVERT: D 132 MET cc_start: 0.6620 (OUTLIER) cc_final: 0.6102 (ptt) REVERT: G 101 GLU cc_start: 0.7120 (pt0) cc_final: 0.6789 (pp20) REVERT: G 213 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7412 (tpp80) REVERT: G 225 ILE cc_start: 0.7041 (OUTLIER) cc_final: 0.6764 (tp) REVERT: H 23 LYS cc_start: 0.8006 (ttmm) cc_final: 0.7679 (tptm) REVERT: H 46 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: H 81 MET cc_start: 0.7998 (ttt) cc_final: 0.7548 (ttt) outliers start: 24 outliers final: 17 residues processed: 84 average time/residue: 0.1624 time to fit residues: 18.0053 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 : 0.631 ------------------------------------------------------------------------------- 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 G residue 80 SER Chi-restraints excluded: chain G residue 86 ASN Chi-restraints excluded: chain G residue 169 GLN Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 213 ARG Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 18 VAL 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 24 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 0.0070 chunk 14 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 0.0870 chunk 48 optimal weight: 0.0980 chunk 35 optimal weight: 0.6980 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.192698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.159519 restraints weight = 6485.380| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.74 r_work: 0.3742 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5352 Z= 0.112 Angle : 0.569 5.568 7267 Z= 0.303 Chirality : 0.046 0.202 816 Planarity : 0.004 0.049 910 Dihedral : 5.183 22.100 793 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.51 % Allowed : 14.73 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.33), residues: 652 helix: None (None), residues: 0 sheet: 0.05 (0.33), residues: 269 loop : -0.95 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 196 HIS 0.002 0.001 HIS G 167 PHE 0.014 0.001 PHE G 69 TYR 0.008 0.001 TYR I 93 ARG 0.003 0.000 ARG I 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00493 ( 2) link_NAG-ASN : angle 1.68699 ( 6) link_BETA1-4 : bond 0.00302 ( 1) link_BETA1-4 : angle 1.55375 ( 3) hydrogen bonds : bond 0.03155 ( 151) hydrogen bonds : angle 5.94987 ( 408) SS BOND : bond 0.00417 ( 6) SS BOND : angle 1.04565 ( 12) covalent geometry : bond 0.00255 ( 5343) covalent geometry : angle 0.56486 ( 7246) *********************** 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 98 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.623 Fit side-chains REVERT: D 33 TYR cc_start: 0.7718 (m-80) cc_final: 0.7066 (m-80) REVERT: D 132 MET cc_start: 0.6663 (OUTLIER) cc_final: 0.6143 (ptt) REVERT: G 213 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7355 (tpp80) REVERT: H 23 LYS cc_start: 0.7939 (ttmm) cc_final: 0.7495 (tptm) REVERT: H 46 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: H 81 MET cc_start: 0.7925 (ttt) cc_final: 0.7462 (ttt) outliers start: 26 outliers final: 17 residues processed: 84 average time/residue: 0.1353 time to fit residues: 15.8065 Evaluate side-chains 86 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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 97 LEU Chi-restraints excluded: chain D residue 105 ASP 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 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 213 ARG 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 17 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 167 HIS G 216 ASN ** 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 = 0.4181 r_free = 0.4181 target = 0.188431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.154968 restraints weight = 6474.799| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.70 r_work: 0.3695 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5352 Z= 0.178 Angle : 0.632 5.828 7267 Z= 0.336 Chirality : 0.048 0.186 816 Planarity : 0.004 0.047 910 Dihedral : 5.352 23.012 793 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 4.85 % Allowed : 16.29 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.32), residues: 652 helix: None (None), residues: 0 sheet: -0.07 (0.32), residues: 262 loop : -1.03 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 168 HIS 0.003 0.001 HIS G 208 PHE 0.019 0.002 PHE I 96 TYR 0.017 0.002 TYR D 50 ARG 0.003 0.000 ARG I 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00553 ( 2) link_NAG-ASN : angle 1.74976 ( 6) link_BETA1-4 : bond 0.00220 ( 1) link_BETA1-4 : angle 1.31208 ( 3) hydrogen bonds : bond 0.03335 ( 151) hydrogen bonds : angle 6.17040 ( 408) SS BOND : bond 0.00531 ( 6) SS BOND : angle 1.27891 ( 12) covalent geometry : bond 0.00428 ( 5343) covalent geometry : angle 0.62769 ( 7246) *********************** 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 99 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 0.573 Fit side-chains REVERT: D 25 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.6619 (tpt) REVERT: D 33 TYR cc_start: 0.7973 (m-80) cc_final: 0.7057 (m-80) REVERT: D 132 MET cc_start: 0.6531 (OUTLIER) cc_final: 0.6044 (ptt) REVERT: G 84 ILE cc_start: 0.6225 (mm) cc_final: 0.5987 (mm) REVERT: G 213 ARG cc_start: 0.7824 (tpp-160) cc_final: 0.7386 (tpp80) REVERT: G 225 ILE cc_start: 0.7033 (OUTLIER) cc_final: 0.6775 (tp) REVERT: H 23 LYS cc_start: 0.8051 (ttmm) cc_final: 0.7685 (tptm) REVERT: H 46 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: H 81 MET cc_start: 0.8093 (ttt) cc_final: 0.7606 (ttt) outliers start: 28 outliers final: 21 residues processed: 85 average time/residue: 0.1537 time to fit residues: 17.7299 Evaluate side-chains 94 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 25 MET 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 86 ASN Chi-restraints excluded: chain G residue 153 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 ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 48 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4179 r_free = 0.4179 target = 0.188125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.154682 restraints weight = 6454.139| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.70 r_work: 0.3700 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5352 Z= 0.164 Angle : 0.618 5.764 7267 Z= 0.328 Chirality : 0.048 0.227 816 Planarity : 0.004 0.049 910 Dihedral : 5.314 23.047 793 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 5.03 % Allowed : 17.33 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.32), residues: 652 helix: None (None), residues: 0 sheet: -0.02 (0.33), residues: 257 loop : -1.05 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 196 HIS 0.003 0.001 HIS G 208 PHE 0.017 0.002 PHE G 69 TYR 0.009 0.001 TYR H 95 ARG 0.006 0.001 ARG I 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00513 ( 2) link_NAG-ASN : angle 1.68504 ( 6) link_BETA1-4 : bond 0.00306 ( 1) link_BETA1-4 : angle 1.47924 ( 3) hydrogen bonds : bond 0.03255 ( 151) hydrogen bonds : angle 6.09903 ( 408) SS BOND : bond 0.00487 ( 6) SS BOND : angle 1.21418 ( 12) covalent geometry : bond 0.00396 ( 5343) covalent geometry : angle 0.61392 ( 7246) *********************** REFINEMENT MACRO_CYCLE 7 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 98 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 0.585 Fit side-chains REVERT: D 3 GLU cc_start: 0.8034 (tt0) cc_final: 0.7580 (tt0) REVERT: D 25 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.6601 (tpt) REVERT: D 33 TYR cc_start: 0.8023 (m-80) cc_final: 0.7127 (m-80) REVERT: D 132 MET cc_start: 0.6556 (OUTLIER) cc_final: 0.6080 (ptt) REVERT: G 84 ILE cc_start: 0.6314 (mm) cc_final: 0.6056 (mm) REVERT: G 213 ARG cc_start: 0.7799 (tpp-160) cc_final: 0.7418 (tpp80) REVERT: G 225 ILE cc_start: 0.7089 (OUTLIER) cc_final: 0.6832 (tp) REVERT: H 23 LYS cc_start: 0.8067 (ttmm) cc_final: 0.7853 (tppt) REVERT: H 46 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7324 (mp0) REVERT: H 81 MET cc_start: 0.8062 (ttt) cc_final: 0.7535 (ttt) outliers start: 29 outliers final: 22 residues processed: 85 average time/residue: 0.1579 time to fit residues: 18.2128 Evaluate side-chains 92 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 25 MET 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 86 ASN Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 153 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 29 optimal weight: 0.3980 chunk 28 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 0.0040 overall best weight: 0.4592 ------------------------------------------------------------------------------- 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 = 0.4194 r_free = 0.4194 target = 0.189682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.156434 restraints weight = 6416.121| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.69 r_work: 0.3716 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5352 Z= 0.130 Angle : 0.599 5.866 7267 Z= 0.319 Chirality : 0.047 0.206 816 Planarity : 0.004 0.049 910 Dihedral : 5.179 21.712 793 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.33 % Allowed : 19.06 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.32), residues: 652 helix: None (None), residues: 0 sheet: -0.01 (0.33), residues: 252 loop : -1.04 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 196 HIS 0.002 0.001 HIS G 208 PHE 0.015 0.001 PHE G 69 TYR 0.019 0.001 TYR D 50 ARG 0.005 0.000 ARG I 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00497 ( 2) link_NAG-ASN : angle 1.62985 ( 6) link_BETA1-4 : bond 0.00361 ( 1) link_BETA1-4 : angle 1.49900 ( 3) hydrogen bonds : bond 0.03071 ( 151) hydrogen bonds : angle 5.93599 ( 408) SS BOND : bond 0.00414 ( 6) SS BOND : angle 1.05633 ( 12) covalent geometry : bond 0.00308 ( 5343) covalent geometry : angle 0.59525 ( 7246) *********************** REFINEMENT MACRO_CYCLE 8 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: 25 poor density : 70 time to evaluate : 0.575 Fit side-chains REVERT: D 3 GLU cc_start: 0.8028 (tt0) cc_final: 0.7575 (tt0) REVERT: D 25 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.6700 (tpt) REVERT: D 33 TYR cc_start: 0.8040 (m-80) cc_final: 0.7167 (m-80) REVERT: D 132 MET cc_start: 0.6530 (OUTLIER) cc_final: 0.6146 (ptt) REVERT: G 84 ILE cc_start: 0.6270 (mm) cc_final: 0.6032 (mm) REVERT: G 213 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7428 (tpp80) REVERT: H 23 LYS cc_start: 0.8011 (ttmm) cc_final: 0.7800 (tppt) REVERT: H 46 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: H 81 MET cc_start: 0.8042 (ttt) cc_final: 0.7526 (ttt) REVERT: I 11 MET cc_start: 0.6005 (ppp) cc_final: 0.5292 (ppp) outliers start: 25 outliers final: 19 residues processed: 83 average time/residue: 0.1675 time to fit residues: 18.2922 Evaluate side-chains 90 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 25 MET 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 45 VAL Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 213 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 27 optimal weight: 0.0070 chunk 37 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 167 HIS H 39 GLN ** 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 = 0.4180 r_free = 0.4180 target = 0.188128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.154893 restraints weight = 6496.673| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.70 r_work: 0.3698 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5352 Z= 0.155 Angle : 0.616 5.811 7267 Z= 0.328 Chirality : 0.047 0.198 816 Planarity : 0.004 0.049 910 Dihedral : 5.184 22.779 793 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.33 % Allowed : 19.58 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.32), residues: 652 helix: None (None), residues: 0 sheet: -0.05 (0.33), residues: 257 loop : -1.04 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 168 HIS 0.002 0.001 HIS G 214 PHE 0.017 0.002 PHE G 69 TYR 0.011 0.001 TYR H 95 ARG 0.005 0.000 ARG I 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00514 ( 2) link_NAG-ASN : angle 1.63743 ( 6) link_BETA1-4 : bond 0.00264 ( 1) link_BETA1-4 : angle 1.26528 ( 3) hydrogen bonds : bond 0.03169 ( 151) hydrogen bonds : angle 6.02706 ( 408) SS BOND : bond 0.00473 ( 6) SS BOND : angle 1.17067 ( 12) covalent geometry : bond 0.00370 ( 5343) covalent geometry : angle 0.61228 ( 7246) *********************** REFINEMENT MACRO_CYCLE 9 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 92 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.540 Fit side-chains REVERT: D 3 GLU cc_start: 0.8066 (tt0) cc_final: 0.7609 (tt0) REVERT: D 25 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.6746 (tpt) REVERT: D 132 MET cc_start: 0.6561 (OUTLIER) cc_final: 0.6115 (ptt) REVERT: G 84 ILE cc_start: 0.6352 (mm) cc_final: 0.6128 (mm) REVERT: G 213 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7381 (tpp80) REVERT: H 23 LYS cc_start: 0.8041 (ttmm) cc_final: 0.7819 (tppt) REVERT: H 46 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7435 (mp0) REVERT: H 81 MET cc_start: 0.8088 (ttt) cc_final: 0.7601 (ttt) REVERT: I 11 MET cc_start: 0.6057 (ppp) cc_final: 0.5472 (ppp) outliers start: 25 outliers final: 20 residues processed: 79 average time/residue: 0.1756 time to fit residues: 18.0711 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 : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 25 MET 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 45 VAL Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 213 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 0.0870 chunk 52 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.4187 r_free = 0.4187 target = 0.188984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.155775 restraints weight = 6513.490| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.70 r_work: 0.3708 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3424 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= 0.144 Angle : 0.603 5.693 7267 Z= 0.322 Chirality : 0.047 0.193 816 Planarity : 0.004 0.048 910 Dihedral : 5.152 22.585 793 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.33 % Allowed : 19.76 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.32), residues: 652 helix: None (None), residues: 0 sheet: -0.09 (0.33), residues: 253 loop : -1.04 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 196 HIS 0.002 0.001 HIS G 208 PHE 0.016 0.002 PHE G 69 TYR 0.020 0.001 TYR D 50 ARG 0.005 0.000 ARG I 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 2) link_NAG-ASN : angle 1.56272 ( 6) link_BETA1-4 : bond 0.00285 ( 1) link_BETA1-4 : angle 1.32130 ( 3) hydrogen bonds : bond 0.03064 ( 151) hydrogen bonds : angle 5.94561 ( 408) SS BOND : bond 0.00435 ( 6) SS BOND : angle 1.10444 ( 12) covalent geometry : bond 0.00342 ( 5343) covalent geometry : angle 0.60039 ( 7246) ********************** REFINEMENT MACRO_CYCLE 10 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 93 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: D 3 GLU cc_start: 0.8082 (tt0) cc_final: 0.7595 (tt0) REVERT: D 25 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.6704 (tpt) REVERT: D 132 MET cc_start: 0.6584 (OUTLIER) cc_final: 0.6145 (ptt) REVERT: G 84 ILE cc_start: 0.6365 (mm) cc_final: 0.6109 (mm) REVERT: G 213 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7389 (tpp80) REVERT: H 23 LYS cc_start: 0.8054 (ttmm) cc_final: 0.7832 (tppt) REVERT: H 46 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7298 (mp0) REVERT: H 81 MET cc_start: 0.8068 (ttt) cc_final: 0.7589 (ttt) outliers start: 25 outliers final: 21 residues processed: 81 average time/residue: 0.1834 time to fit residues: 19.2937 Evaluate side-chains 91 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 25 MET 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 45 VAL Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 213 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 55 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 4 optimal weight: 0.0470 chunk 63 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.0670 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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** I 37 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 = 0.188733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.155540 restraints weight = 6510.285| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.69 r_work: 0.3713 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5352 Z= 0.146 Angle : 0.605 5.704 7267 Z= 0.322 Chirality : 0.047 0.199 816 Planarity : 0.004 0.049 910 Dihedral : 5.155 22.807 793 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 4.33 % Allowed : 19.58 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.32), residues: 652 helix: None (None), residues: 0 sheet: -0.01 (0.34), residues: 247 loop : -1.10 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 196 HIS 0.002 0.001 HIS G 208 PHE 0.016 0.002 PHE G 69 TYR 0.009 0.001 TYR H 95 ARG 0.005 0.000 ARG I 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00493 ( 2) link_NAG-ASN : angle 1.52291 ( 6) link_BETA1-4 : bond 0.00198 ( 1) link_BETA1-4 : angle 1.20075 ( 3) hydrogen bonds : bond 0.03077 ( 151) hydrogen bonds : angle 5.93552 ( 408) SS BOND : bond 0.00450 ( 6) SS BOND : angle 1.14829 ( 12) covalent geometry : bond 0.00349 ( 5343) covalent geometry : angle 0.60173 ( 7246) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2727.34 seconds wall clock time: 48 minutes 22.82 seconds (2902.82 seconds total)